R 3.0.3, Windows 7: Problem installing XML package

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R 3.0.3, Windows 7: Problem installing XML package

alpeshpandya
Using install.package('XML') command produces this error:

trying URL
'
http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0/XML_3.98-1.1.zip
'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 4276224 != reported length 4288136
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
file or directory'


Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from cran
site. But this zip file is not a valid archive (cannot open using winzip).
Also trying to install using this downloaded file produces the following
error:

Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
(as 'lib' is unspecified)
Warning in install.packages :
  error 1 in extracting from zip file
Warning in install.packages :
  cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
file or directory'
Error in install.packages : cannot open the connection

I  downloaded this zip file from multiple sources and tried to install with
same result.

--
Thanks and Regards
Alpesh

        [[alternative HTML version deleted]]

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Re: R 3.0.3, Windows 7: Problem installing XML package

Uwe Ligges-3
Works for me.

Best,
Uwe Ligges



On 11.04.2014 17:10, Alpesh Pandya wrote:

> Using install.package('XML') command produces this error:
>
> trying URL
> '
> http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> '
> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> opened URL
> downloaded 4.1 Mb
>
> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>    cannot open the connection
> In addition: Warning messages:
> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>    downloaded length 4276224 != reported length 4288136
> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>    cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
> file or directory'
>
>
> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from cran
> site. But this zip file is not a valid archive (cannot open using winzip).
> Also trying to install using this downloaded file produces the following
> error:
>
> Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
> (as 'lib' is unspecified)
> Warning in install.packages :
>    error 1 in extracting from zip file
> Warning in install.packages :
>    cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
> file or directory'
> Error in install.packages : cannot open the connection
>
> I  downloaded this zip file from multiple sources and tried to install with
> same result.
>

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Re: R 3.0.3, Windows 7: Problem installing XML package

alpeshpandya
Thank you for response Uwe. I tried multiple times by downloading the zip
file from many sources but still the same error. This is a major road block
for me in using R. Appreciate any help on this.


On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <[hidden email]
> wrote:

> Works for me.
>
> Best,
> Uwe Ligges
>
>
>
>
> On 11.04.2014 17:10, Alpesh Pandya wrote:
>
>> Using install.package('XML') command produces this error:
>>
>> trying URL
>> '
>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> contrib/3.0/XML_3.98-1.1.zip
>> '
>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>> opened URL
>> downloaded 4.1 Mb
>>
>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>> "Type")) :
>>    cannot open the connection
>> In addition: Warning messages:
>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>    downloaded length 4276224 != reported length 4288136
>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>    cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
>> file or directory'
>>
>>
>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
>> cran
>> site. But this zip file is not a valid archive (cannot open using winzip).
>> Also trying to install using this downloaded file produces the following
>> error:
>>
>> Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
>> (as 'lib' is unspecified)
>> Warning in install.packages :
>>    error 1 in extracting from zip file
>> Warning in install.packages :
>>    cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
>> file or directory'
>> Error in install.packages : cannot open the connection
>>
>> I  downloaded this zip file from multiple sources and tried to install
>> with
>> same result.
>>
>>


--
Thanks and Regards
Alpesh

        [[alternative HTML version deleted]]

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Re: R 3.0.3, Windows 7: Problem installing XML package

Uwe Ligges-3


On 12.04.2014 22:39, Alpesh Pandya wrote:
> Thank you for response Uwe. I tried multiple times by downloading the zip
> file from many sources but still the same error. This is a major road block
> for me in using R. Appreciate any help on this.

Please ask your local IT staff.

I get, using the same mirror:

 > options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
 > install.packages("XML", lib="d:/temp")
trying URL
'http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

package ‘XML’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
         d:\temp\RtmpqMqL8L\downloaded_packages



Best,
Uwe Ligges





>
>
> On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <[hidden email]
>> wrote:
>
>> Works for me.
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>>
>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>
>>> Using install.package('XML') command produces this error:
>>>
>>> trying URL
>>> '
>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>> contrib/3.0/XML_3.98-1.1.zip
>>> '
>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>> opened URL
>>> downloaded 4.1 Mb
>>>
>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>> "Type")) :
>>>     cannot open the connection
>>> In addition: Warning messages:
>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>     downloaded length 4276224 != reported length 4288136
>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>>     cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
>>> file or directory'
>>>
>>>
>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
>>> cran
>>> site. But this zip file is not a valid archive (cannot open using winzip).
>>> Also trying to install using this downloaded file produces the following
>>> error:
>>>
>>> Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
>>> (as 'lib' is unspecified)
>>> Warning in install.packages :
>>>     error 1 in extracting from zip file
>>> Warning in install.packages :
>>>     cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
>>> file or directory'
>>> Error in install.packages : cannot open the connection
>>>
>>> I  downloaded this zip file from multiple sources and tried to install
>>> with
>>> same result.
>>>
>>>
>
>

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Re: R 3.0.3, Windows 7: Problem installing XML package

alpeshpandya
@Uwe I tried the same steps from office as well as home network with same
results. Are you using windows 7 with R 3.0.3?

I have seen same question being asked by others without any resolution. Is
anything special about XML package? I am OK use older version of package
but in archives there are no zip files (only gz files). Is windows platform
not recommended for R?


On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <[hidden email]
> wrote:

>
>
> On 12.04.2014 22:39, Alpesh Pandya wrote:
>
>> Thank you for response Uwe. I tried multiple times by downloading the zip
>> file from many sources but still the same error. This is a major road
>> block
>> for me in using R. Appreciate any help on this.
>>
>
> Please ask your local IT staff.
>
> I get, using the same mirror:
>
> > options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
> > install.packages("XML", lib="d:/temp")
>
> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
> contrib/3.0/XML_3.98-1.1.zip'
> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> opened URL
> downloaded 4.1 Mb
>
> package 'XML' successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
>         d:\temp\RtmpqMqL8L\downloaded_packages
>
>
>
> Best,
> Uwe Ligges
>
>
>
>
>
>
>
>>
>> On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>> [hidden email]
>>
>>> wrote:
>>>
>>
>>  Works for me.
>>>
>>> Best,
>>> Uwe Ligges
>>>
>>>
>>>
>>>
>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>
>>>  Using install.package('XML') command produces this error:
>>>>
>>>> trying URL
>>>> '
>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>> contrib/3.0/XML_3.98-1.1.zip
>>>> '
>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>> opened URL
>>>> downloaded 4.1 Mb
>>>>
>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>> "Type")) :
>>>>     cannot open the connection
>>>> In addition: Warning messages:
>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>>     downloaded length 4276224 != reported length 4288136
>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
>>>> :
>>>>     cannot open compressed file 'XML/DESCRIPTION', probable reason 'No
>>>> such
>>>> file or directory'
>>>>
>>>>
>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
>>>> cran
>>>> site. But this zip file is not a valid archive (cannot open using
>>>> winzip).
>>>> Also trying to install using this downloaded file produces the following
>>>> error:
>>>>
>>>> Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
>>>> (as 'lib' is unspecified)
>>>> Warning in install.packages :
>>>>     error 1 in extracting from zip file
>>>> Warning in install.packages :
>>>>     cannot open compressed file 'XML/DESCRIPTION', probable reason 'No
>>>> such
>>>> file or directory'
>>>> Error in install.packages : cannot open the connection
>>>>
>>>> I  downloaded this zip file from multiple sources and tried to install
>>>> with
>>>> same result.
>>>>
>>>>
>>>>
>>
>>


--
Thanks and Regards
Alpesh

        [[alternative HTML version deleted]]

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Re: R 3.0.3, Windows 7: Problem installing XML package

Uwe Ligges-3


On 13.04.2014 01:30, Alpesh Pandya wrote:
> @Uwe I tried the same steps from office as well as home network with same
> results. Are you using windows 7 with R 3.0.3?
>
> I have seen same question being asked by others without any resolution. Is
> anything special about XML package? I am OK use older version of package
> but in archives there are no zip files (only gz files). Is windows platform
> not recommended for R?

Right, and you can try to install these from sources.
But I doubt you need it. You still have not told us if you tried another
mirror to download the XML file from and what you local IT support tells
you while your downloads are incomplete.

Best,
Uwe Ligges





>
>
> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <[hidden email]
>> wrote:
>
>>
>>
>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>>
>>> Thank you for response Uwe. I tried multiple times by downloading the zip
>>> file from many sources but still the same error. This is a major road
>>> block
>>> for me in using R. Appreciate any help on this.
>>>
>>
>> Please ask your local IT staff.
>>
>> I get, using the same mirror:
>>
>>> options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>>> install.packages("XML", lib="d:/temp")
>>
>> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> contrib/3.0/XML_3.98-1.1.zip'
>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>> opened URL
>> downloaded 4.1 Mb
>>
>> package 'XML' successfully unpacked and MD5 sums checked
>>
>> The downloaded binary packages are in
>>          d:\temp\RtmpqMqL8L\downloaded_packages
>>
>>
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>>
>>
>>
>>
>>>
>>> On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>>> [hidden email]
>>>
>>>> wrote:
>>>>
>>>
>>>   Works for me.
>>>>
>>>> Best,
>>>> Uwe Ligges
>>>>
>>>>
>>>>
>>>>
>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>>
>>>>   Using install.package('XML') command produces this error:
>>>>>
>>>>> trying URL
>>>>> '
>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>> '
>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>> opened URL
>>>>> downloaded 4.1 Mb
>>>>>
>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>> "Type")) :
>>>>>      cannot open the connection
>>>>> In addition: Warning messages:
>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>>>      downloaded length 4276224 != reported length 4288136
>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
>>>>> :
>>>>>      cannot open compressed file 'XML/DESCRIPTION', probable reason 'No
>>>>> such
>>>>> file or directory'
>>>>>
>>>>>
>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
>>>>> cran
>>>>> site. But this zip file is not a valid archive (cannot open using
>>>>> winzip).
>>>>> Also trying to install using this downloaded file produces the following
>>>>> error:
>>>>>
>>>>> Installing package into 'C:/Users/APandya/Documents/R/win-library/3.0'
>>>>> (as 'lib' is unspecified)
>>>>> Warning in install.packages :
>>>>>      error 1 in extracting from zip file
>>>>> Warning in install.packages :
>>>>>      cannot open compressed file 'XML/DESCRIPTION', probable reason 'No
>>>>> such
>>>>> file or directory'
>>>>> Error in install.packages : cannot open the connection
>>>>>
>>>>> I  downloaded this zip file from multiple sources and tried to install
>>>>> with
>>>>> same result.
>>>>>
>>>>>
>>>>>
>>>
>>>
>
>

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Re: R 3.0.3, Windows 7: Problem installing XML package

alpeshpandya
I have tried these sources (almost all US mirrors):

http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip

I have confirmed with IT that there is no restriction on downloading this
zip file from any of these sources. Also I am getting same error when I try
from my home network as well.


On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <[hidden email]
> wrote:

>
>
> On 13.04.2014 01:30, Alpesh Pandya wrote:
>
>> @Uwe I tried the same steps from office as well as home network with same
>> results. Are you using windows 7 with R 3.0.3?
>>
>> I have seen same question being asked by others without any resolution. Is
>> anything special about XML package? I am OK use older version of package
>> but in archives there are no zip files (only gz files). Is windows
>> platform
>> not recommended for R?
>>
>
> Right, and you can try to install these from sources.
> But I doubt you need it. You still have not told us if you tried another
> mirror to download the XML file from and what you local IT support tells
> you while your downloads are incomplete.
>
> Best,
> Uwe Ligges
>
>
>
>
>
>
>>
>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>> [hidden email]
>>
>>> wrote:
>>>
>>
>>
>>>
>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>>>
>>>  Thank you for response Uwe. I tried multiple times by downloading the
>>>> zip
>>>> file from many sources but still the same error. This is a major road
>>>> block
>>>> for me in using R. Appreciate any help on this.
>>>>
>>>>
>>> Please ask your local IT staff.
>>>
>>> I get, using the same mirror:
>>>
>>>  options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>>>> install.packages("XML", lib="d:/temp")
>>>>
>>>
>>> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>
>>> contrib/3.0/XML_3.98-1.1.zip'
>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>> opened URL
>>> downloaded 4.1 Mb
>>>
>>> package 'XML' successfully unpacked and MD5 sums checked
>>>
>>> The downloaded binary packages are in
>>>          d:\temp\RtmpqMqL8L\downloaded_packages
>>>
>>>
>>>
>>> Best,
>>> Uwe Ligges
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>> On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>>>> [hidden email]
>>>>
>>>>  wrote:
>>>>>
>>>>>
>>>>   Works for me.
>>>>
>>>>>
>>>>> Best,
>>>>> Uwe Ligges
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>>>
>>>>>   Using install.package('XML') command produces this error:
>>>>>
>>>>>>
>>>>>> trying URL
>>>>>> '
>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>>> '
>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>> opened URL
>>>>>> downloaded 4.1 Mb
>>>>>>
>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>> "Type")) :
>>>>>>      cannot open the connection
>>>>>> In addition: Warning messages:
>>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>>>>      downloaded length 4276224 != reported length 4288136
>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>>>>>> file
>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>> "Type"))
>>>>>> :
>>>>>>      cannot open compressed file 'XML/DESCRIPTION', probable reason
>>>>>> 'No
>>>>>> such
>>>>>> file or directory'
>>>>>>
>>>>>>
>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
>>>>>> cran
>>>>>> site. But this zip file is not a valid archive (cannot open using
>>>>>> winzip).
>>>>>> Also trying to install using this downloaded file produces the
>>>>>> following
>>>>>> error:
>>>>>>
>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>>>>>> win-library/3.0'
>>>>>> (as 'lib' is unspecified)
>>>>>> Warning in install.packages :
>>>>>>      error 1 in extracting from zip file
>>>>>> Warning in install.packages :
>>>>>>      cannot open compressed file 'XML/DESCRIPTION', probable reason
>>>>>> 'No
>>>>>> such
>>>>>> file or directory'
>>>>>> Error in install.packages : cannot open the connection
>>>>>>
>>>>>> I  downloaded this zip file from multiple sources and tried to install
>>>>>> with
>>>>>> same result.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>
>>


--
Thanks and Regards
Alpesh

        [[alternative HTML version deleted]]

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Re: R 3.0.3, Windows 7: Problem installing XML package

Rui Barradas
Hello,
I have package XML installed on Windows 7, R 3.0.3 and I had no problem
at all. Can't you try (it worked with me)

install.packages("XML", repos = "http://cran.dcc.fc.up.pt")

Hope this helps,

Rui Barradas

Em 14-04-2014 16:24, Alpesh Pandya escreveu:

> I have tried these sources (almost all US mirrors):
>
> http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://watson.nci.nih.gov/cran_mirror/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>
> I have confirmed with IT that there is no restriction on downloading this
> zip file from any of these sources. Also I am getting same error when I try
> from my home network as well.
>
>
> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <[hidden email]
>> wrote:
>
>>
>>
>> On 13.04.2014 01:30, Alpesh Pandya wrote:
>>
>>> @Uwe I tried the same steps from office as well as home network with same
>>> results. Are you using windows 7 with R 3.0.3?
>>>
>>> I have seen same question being asked by others without any resolution. Is
>>> anything special about XML package? I am OK use older version of package
>>> but in archives there are no zip files (only gz files). Is windows
>>> platform
>>> not recommended for R?
>>>
>>
>> Right, and you can try to install these from sources.
>> But I doubt you need it. You still have not told us if you tried another
>> mirror to download the XML file from and what you local IT support tells
>> you while your downloads are incomplete.
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>>
>>
>>
>>>
>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>>> [hidden email]
>>>
>>>> wrote:
>>>>
>>>
>>>
>>>>
>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>>>>
>>>>   Thank you for response Uwe. I tried multiple times by downloading the
>>>>> zip
>>>>> file from many sources but still the same error. This is a major road
>>>>> block
>>>>> for me in using R. Appreciate any help on this.
>>>>>
>>>>>
>>>> Please ask your local IT staff.
>>>>
>>>> I get, using the same mirror:
>>>>
>>>>   options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>>>>> install.packages("XML", lib="d:/temp")
>>>>>
>>>>
>>>> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>
>>>> contrib/3.0/XML_3.98-1.1.zip'
>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>> opened URL
>>>> downloaded 4.1 Mb
>>>>
>>>> package 'XML' successfully unpacked and MD5 sums checked
>>>>
>>>> The downloaded binary packages are in
>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
>>>>
>>>>
>>>>
>>>> Best,
>>>> Uwe Ligges
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>>>>> [hidden email]
>>>>>
>>>>>   wrote:
>>>>>>
>>>>>>
>>>>>    Works for me.
>>>>>
>>>>>>
>>>>>> Best,
>>>>>> Uwe Ligges
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>>>>
>>>>>>    Using install.package('XML') command produces this error:
>>>>>>
>>>>>>>
>>>>>>> trying URL
>>>>>>> '
>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>>>> '
>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>>> opened URL
>>>>>>> downloaded 4.1 Mb
>>>>>>>
>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>>> "Type")) :
>>>>>>>       cannot open the connection
>>>>>>> In addition: Warning messages:
>>>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>>>>>       downloaded length 4276224 != reported length 4288136
>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>>>>>>> file
>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>>> "Type"))
>>>>>>> :
>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable reason
>>>>>>> 'No
>>>>>>> such
>>>>>>> file or directory'
>>>>>>>
>>>>>>>
>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly from
>>>>>>> cran
>>>>>>> site. But this zip file is not a valid archive (cannot open using
>>>>>>> winzip).
>>>>>>> Also trying to install using this downloaded file produces the
>>>>>>> following
>>>>>>> error:
>>>>>>>
>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>>>>>>> win-library/3.0'
>>>>>>> (as 'lib' is unspecified)
>>>>>>> Warning in install.packages :
>>>>>>>       error 1 in extracting from zip file
>>>>>>> Warning in install.packages :
>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable reason
>>>>>>> 'No
>>>>>>> such
>>>>>>> file or directory'
>>>>>>> Error in install.packages : cannot open the connection
>>>>>>>
>>>>>>> I  downloaded this zip file from multiple sources and tried to install
>>>>>>> with
>>>>>>> same result.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>>>
>
>

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Re: R 3.0.3, Windows 7: Problem installing XML package

alpeshpandya
Thank you for response Rui.

I still get the same error with this repository.

Installing package into ‘C:/Users/APandya/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
trying URL '
http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4288136 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
:
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 4276224 != reported length 4288136
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
file or directory'



On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas <[hidden email]> wrote:

> Hello,
> I have package XML installed on Windows 7, R 3.0.3 and I had no problem at
> all. Can't you try (it worked with me)
>
> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
>
> Hope this helps,
>
> Rui Barradas
>
> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
>
>  I have tried these sources (almost all US mirrors):
>>
>> http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
>> 3.0/XML_3.98-1.1.zip
>> http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> contrib/3.0/XML_3.98-1.1.zip
>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>
>> I have confirmed with IT that there is no restriction on downloading this
>> zip file from any of these sources. Also I am getting same error when I
>> try
>> from my home network as well.
>>
>>
>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
>> [hidden email]
>>
>>> wrote:
>>>
>>
>>
>>>
>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
>>>
>>>  @Uwe I tried the same steps from office as well as home network with
>>>> same
>>>> results. Are you using windows 7 with R 3.0.3?
>>>>
>>>> I have seen same question being asked by others without any resolution.
>>>> Is
>>>> anything special about XML package? I am OK use older version of package
>>>> but in archives there are no zip files (only gz files). Is windows
>>>> platform
>>>> not recommended for R?
>>>>
>>>>
>>> Right, and you can try to install these from sources.
>>> But I doubt you need it. You still have not told us if you tried another
>>> mirror to download the XML file from and what you local IT support tells
>>> you while your downloads are incomplete.
>>>
>>> Best,
>>> Uwe Ligges
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>>>> [hidden email]
>>>>
>>>>  wrote:
>>>>>
>>>>>
>>>>
>>>>
>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>>>>>
>>>>>   Thank you for response Uwe. I tried multiple times by downloading the
>>>>>
>>>>>> zip
>>>>>> file from many sources but still the same error. This is a major road
>>>>>> block
>>>>>> for me in using R. Appreciate any help on this.
>>>>>>
>>>>>>
>>>>>>  Please ask your local IT staff.
>>>>>
>>>>> I get, using the same mirror:
>>>>>
>>>>>   options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>>>>>
>>>>>> install.packages("XML", lib="d:/temp")
>>>>>>
>>>>>>
>>>>> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>
>>>>> contrib/3.0/XML_3.98-1.1.zip'
>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>> opened URL
>>>>> downloaded 4.1 Mb
>>>>>
>>>>> package 'XML' successfully unpacked and MD5 sums checked
>>>>>
>>>>> The downloaded binary packages are in
>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
>>>>>
>>>>>
>>>>>
>>>>> Best,
>>>>> Uwe Ligges
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>>>>>> [hidden email]
>>>>>>
>>>>>>   wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>     Works for me.
>>>>>>
>>>>>>
>>>>>>> Best,
>>>>>>> Uwe Ligges
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>>>>>
>>>>>>>    Using install.package('XML') command produces this error:
>>>>>>>
>>>>>>>
>>>>>>>> trying URL
>>>>>>>> '
>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>>>>> '
>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>>>> opened URL
>>>>>>>> downloaded 4.1 Mb
>>>>>>>>
>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>>>> "Type")) :
>>>>>>>>       cannot open the connection
>>>>>>>> In addition: Warning messages:
>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>>>>>>       downloaded length 4276224 != reported length 4288136
>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>>>>>>>> file
>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>>>> "Type"))
>>>>>>>> :
>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable reason
>>>>>>>> 'No
>>>>>>>> such
>>>>>>>> file or directory'
>>>>>>>>
>>>>>>>>
>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly
>>>>>>>> from
>>>>>>>> cran
>>>>>>>> site. But this zip file is not a valid archive (cannot open using
>>>>>>>> winzip).
>>>>>>>> Also trying to install using this downloaded file produces the
>>>>>>>> following
>>>>>>>> error:
>>>>>>>>
>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>>>>>>>> win-library/3.0'
>>>>>>>> (as 'lib' is unspecified)
>>>>>>>> Warning in install.packages :
>>>>>>>>       error 1 in extracting from zip file
>>>>>>>> Warning in install.packages :
>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable reason
>>>>>>>> 'No
>>>>>>>> such
>>>>>>>> file or directory'
>>>>>>>> Error in install.packages : cannot open the connection
>>>>>>>>
>>>>>>>> I  downloaded this zip file from multiple sources and tried to
>>>>>>>> install
>>>>>>>> with
>>>>>>>> same result.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>
>>

--
Thanks and Regards
Alpesh

        [[alternative HTML version deleted]]


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Re: R 3.0.3, Windows 7: Problem installing XML package

alpeshpandya
I keep on trying from various networks but I still get the same error. I
don't this this has anything to do with network or ability to download the
package (as I can install other packages fine). This must be something in
base R or dependencies issues (that R is not spelling out).

I know R is geared for Mac and Windows is kind of looked down upon but I
have no option but use windows and need this XML package running to
complete my education. Any help on this would be appreciated.


On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya <[hidden email]>wrote:

> Thank you for response Rui.
>
> I still get the same error with this repository.
>
> Installing package into ‘C:/Users/APandya/Documents/R/win-library/3.0’
> (as ‘lib’ is unspecified)
> trying URL '
> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> opened URL
> downloaded 4.1 Mb
>
> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
> :
>   cannot open the connection
> In addition: Warning messages:
> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 4276224 != reported length 4288136
> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>   cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
> file or directory'
>
>
>
> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas <[hidden email]>wrote:
>
>> Hello,
>> I have package XML installed on Windows 7, R 3.0.3 and I had no problem
>> at all. Can't you try (it worked with me)
>>
>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
>>
>> Hope this helps,
>>
>> Rui Barradas
>>
>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
>>
>>  I have tried these sources (almost all US mirrors):
>>>
>>> http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>> http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
>>> 3.0/XML_3.98-1.1.zip
>>> http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>> http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>> contrib/3.0/XML_3.98-1.1.zip
>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>> http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>> http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>
>>> I have confirmed with IT that there is no restriction on downloading this
>>> zip file from any of these sources. Also I am getting same error when I
>>> try
>>> from my home network as well.
>>>
>>>
>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
>>> [hidden email]
>>>
>>>> wrote:
>>>>
>>>
>>>
>>>>
>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
>>>>
>>>>  @Uwe I tried the same steps from office as well as home network with
>>>>> same
>>>>> results. Are you using windows 7 with R 3.0.3?
>>>>>
>>>>> I have seen same question being asked by others without any
>>>>> resolution. Is
>>>>> anything special about XML package? I am OK use older version of
>>>>> package
>>>>> but in archives there are no zip files (only gz files). Is windows
>>>>> platform
>>>>> not recommended for R?
>>>>>
>>>>>
>>>> Right, and you can try to install these from sources.
>>>> But I doubt you need it. You still have not told us if you tried another
>>>> mirror to download the XML file from and what you local IT support tells
>>>> you while your downloads are incomplete.
>>>>
>>>> Best,
>>>> Uwe Ligges
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>>>>> [hidden email]
>>>>>
>>>>>  wrote:
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>>>>>>
>>>>>>   Thank you for response Uwe. I tried multiple times by downloading
>>>>>> the
>>>>>>
>>>>>>> zip
>>>>>>> file from many sources but still the same error. This is a major road
>>>>>>> block
>>>>>>> for me in using R. Appreciate any help on this.
>>>>>>>
>>>>>>>
>>>>>>>  Please ask your local IT staff.
>>>>>>
>>>>>> I get, using the same mirror:
>>>>>>
>>>>>>   options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>>>>>>
>>>>>>> install.packages("XML", lib="d:/temp")
>>>>>>>
>>>>>>>
>>>>>> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>
>>>>>> contrib/3.0/XML_3.98-1.1.zip'
>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>> opened URL
>>>>>> downloaded 4.1 Mb
>>>>>>
>>>>>> package 'XML' successfully unpacked and MD5 sums checked
>>>>>>
>>>>>> The downloaded binary packages are in
>>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
>>>>>>
>>>>>>
>>>>>>
>>>>>> Best,
>>>>>> Uwe Ligges
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>>>>>>> [hidden email]
>>>>>>>
>>>>>>>   wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>     Works for me.
>>>>>>>
>>>>>>>
>>>>>>>> Best,
>>>>>>>> Uwe Ligges
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>>>>>>
>>>>>>>>    Using install.package('XML') command produces this error:
>>>>>>>>
>>>>>>>>
>>>>>>>>> trying URL
>>>>>>>>> '
>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>>>>>> '
>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>>>>> opened URL
>>>>>>>>> downloaded 4.1 Mb
>>>>>>>>>
>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>>>>> "Type")) :
>>>>>>>>>       cannot open the connection
>>>>>>>>> In addition: Warning messages:
>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>>>>>>>       downloaded length 4276224 != reported length 4288136
>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>>>>>>>>> file
>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>>>>> "Type"))
>>>>>>>>> :
>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable
>>>>>>>>> reason
>>>>>>>>> 'No
>>>>>>>>> such
>>>>>>>>> file or directory'
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly
>>>>>>>>> from
>>>>>>>>> cran
>>>>>>>>> site. But this zip file is not a valid archive (cannot open using
>>>>>>>>> winzip).
>>>>>>>>> Also trying to install using this downloaded file produces the
>>>>>>>>> following
>>>>>>>>> error:
>>>>>>>>>
>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>>>>>>>>> win-library/3.0'
>>>>>>>>> (as 'lib' is unspecified)
>>>>>>>>> Warning in install.packages :
>>>>>>>>>       error 1 in extracting from zip file
>>>>>>>>> Warning in install.packages :
>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable
>>>>>>>>> reason
>>>>>>>>> 'No
>>>>>>>>> such
>>>>>>>>> file or directory'
>>>>>>>>> Error in install.packages : cannot open the connection
>>>>>>>>>
>>>>>>>>> I  downloaded this zip file from multiple sources and tried to
>>>>>>>>> install
>>>>>>>>> with
>>>>>>>>> same result.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>>>
>
>
> --
> Thanks and Regards
> Alpesh
>


--
Thanks and Regards
Alpesh

        [[alternative HTML version deleted]]


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Re: R 3.0.3, Windows 7: Problem installing XML package

Duncan Murdoch-2
On 20/04/2014, 2:45 PM, Alpesh Pandya wrote:
> I keep on trying from various networks but I still get the same error. I
> don't this this has anything to do with network or ability to download the
> package (as I can install other packages fine). This must be something in
> base R or dependencies issues (that R is not spelling out).

This is very clearly a problem with your setup, not with R:  nobody else
is reporting it.

What you should do is download the .zip file using some other means
(e.g. Firefox, etc.) and check whether the size comes out properly
(4,288,694 bytes; not sure why you saw the numbers you saw).  If it
does, then install the package from the .zip file.  If it doesn't, then
tell your IT people to fix your system.

Duncan Murdoch

>
> I know R is geared for Mac and Windows is kind of looked down upon but I
> have no option but use windows and need this XML package running to
> complete my education. Any help on this would be appreciated.
>
>
> On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya <[hidden email]>wrote:
>
>> Thank you for response Rui.
>>
>> I still get the same error with this repository.
>>
>> Installing package into ‘C:/Users/APandya/Documents/R/win-library/3.0’
>> (as ‘lib’ is unspecified)
>> trying URL '
>> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>> opened URL
>> downloaded 4.1 Mb
>>
>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
>> :
>>    cannot open the connection
>> In addition: Warning messages:
>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>    downloaded length 4276224 != reported length 4288136
>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>    cannot open compressed file 'XML/DESCRIPTION', probable reason 'No such
>> file or directory'
>>
>>
>>
>> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas <[hidden email]>wrote:
>>
>>> Hello,
>>> I have package XML installed on Windows 7, R 3.0.3 and I had no problem
>>> at all. Can't you try (it worked with me)
>>>
>>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
>>>
>>> Hope this helps,
>>>
>>> Rui Barradas
>>>
>>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
>>>
>>>   I have tried these sources (almost all US mirrors):
>>>>
>>>> http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
>>>> 3.0/XML_3.98-1.1.zip
>>>> http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>> contrib/3.0/XML_3.98-1.1.zip
>>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>
>>>> I have confirmed with IT that there is no restriction on downloading this
>>>> zip file from any of these sources. Also I am getting same error when I
>>>> try
>>>> from my home network as well.
>>>>
>>>>
>>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
>>>> [hidden email]
>>>>
>>>>> wrote:
>>>>>
>>>>
>>>>
>>>>>
>>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
>>>>>
>>>>>   @Uwe I tried the same steps from office as well as home network with
>>>>>> same
>>>>>> results. Are you using windows 7 with R 3.0.3?
>>>>>>
>>>>>> I have seen same question being asked by others without any
>>>>>> resolution. Is
>>>>>> anything special about XML package? I am OK use older version of
>>>>>> package
>>>>>> but in archives there are no zip files (only gz files). Is windows
>>>>>> platform
>>>>>> not recommended for R?
>>>>>>
>>>>>>
>>>>> Right, and you can try to install these from sources.
>>>>> But I doubt you need it. You still have not told us if you tried another
>>>>> mirror to download the XML file from and what you local IT support tells
>>>>> you while your downloads are incomplete.
>>>>>
>>>>> Best,
>>>>> Uwe Ligges
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>>>>>> [hidden email]
>>>>>>
>>>>>>   wrote:
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>>>>>>>
>>>>>>>    Thank you for response Uwe. I tried multiple times by downloading
>>>>>>> the
>>>>>>>
>>>>>>>> zip
>>>>>>>> file from many sources but still the same error. This is a major road
>>>>>>>> block
>>>>>>>> for me in using R. Appreciate any help on this.
>>>>>>>>
>>>>>>>>
>>>>>>>>   Please ask your local IT staff.
>>>>>>>
>>>>>>> I get, using the same mirror:
>>>>>>>
>>>>>>>    options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>>>>>>>
>>>>>>>> install.packages("XML", lib="d:/temp")
>>>>>>>>
>>>>>>>>
>>>>>>> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>
>>>>>>> contrib/3.0/XML_3.98-1.1.zip'
>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>>> opened URL
>>>>>>> downloaded 4.1 Mb
>>>>>>>
>>>>>>> package 'XML' successfully unpacked and MD5 sums checked
>>>>>>>
>>>>>>> The downloaded binary packages are in
>>>>>>>            d:\temp\RtmpqMqL8L\downloaded_packages
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>> Uwe Ligges
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>   On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>>>>>>>> [hidden email]
>>>>>>>>
>>>>>>>>    wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>      Works for me.
>>>>>>>>
>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> Uwe Ligges
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>>>>>>>
>>>>>>>>>     Using install.package('XML') command produces this error:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> trying URL
>>>>>>>>>> '
>>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>>>>>>> '
>>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>>>>>> opened URL
>>>>>>>>>> downloaded 4.1 Mb
>>>>>>>>>>
>>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>>>>>> "Type")) :
>>>>>>>>>>        cannot open the connection
>>>>>>>>>> In addition: Warning messages:
>>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>>>>>>>>        downloaded length 4276224 != reported length 4288136
>>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>>>>>>>>>> file
>>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>>>>>>> "Type"))
>>>>>>>>>> :
>>>>>>>>>>        cannot open compressed file 'XML/DESCRIPTION', probable
>>>>>>>>>> reason
>>>>>>>>>> 'No
>>>>>>>>>> such
>>>>>>>>>> file or directory'
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip directly
>>>>>>>>>> from
>>>>>>>>>> cran
>>>>>>>>>> site. But this zip file is not a valid archive (cannot open using
>>>>>>>>>> winzip).
>>>>>>>>>> Also trying to install using this downloaded file produces the
>>>>>>>>>> following
>>>>>>>>>> error:
>>>>>>>>>>
>>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>>>>>>>>>> win-library/3.0'
>>>>>>>>>> (as 'lib' is unspecified)
>>>>>>>>>> Warning in install.packages :
>>>>>>>>>>        error 1 in extracting from zip file
>>>>>>>>>> Warning in install.packages :
>>>>>>>>>>        cannot open compressed file 'XML/DESCRIPTION', probable
>>>>>>>>>> reason
>>>>>>>>>> 'No
>>>>>>>>>> such
>>>>>>>>>> file or directory'
>>>>>>>>>> Error in install.packages : cannot open the connection
>>>>>>>>>>
>>>>>>>>>> I  downloaded this zip file from multiple sources and tried to
>>>>>>>>>> install
>>>>>>>>>> with
>>>>>>>>>> same result.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>
>>
>> --
>> Thanks and Regards
>> Alpesh
>>
>
>
>
>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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Re: R 3.0.3, Windows 7: Problem installing XML package

Jeff Newmiller
In reply to this post by alpeshpandya
Hard to help you when the problem simply does not happen for others.

As for Windows being not a focus, that is not at all true. I use it regularly on Windows at work. That being said, there are thousands of packages and those each involve their own subset of R users. There are also many operating system configurations that may not all be fully tested. Blaming "R" or "Windows", or blaming us for "preventing" you from getting your education (isn't that something between you and your educational institution?) are not going to be effective strategies for problem solving.

Are you able to use other aspects of R beyond the XML package? Have you tried communicating with the maintainers of that package?
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/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
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Sent from my phone. Please excuse my brevity.

On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya <[hidden email]> wrote:

>I keep on trying from various networks but I still get the same error.
>I
>don't this this has anything to do with network or ability to download
>the
>package (as I can install other packages fine). This must be something
>in
>base R or dependencies issues (that R is not spelling out).
>
>I know R is geared for Mac and Windows is kind of looked down upon but
>I
>have no option but use windows and need this XML package running to
>complete my education. Any help on this would be appreciated.
>
>
>On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
><[hidden email]>wrote:
>
>> Thank you for response Rui.
>>
>> I still get the same error with this repository.
>>
>> Installing package into
>���C:/Users/APandya/Documents/R/win-library/3.0���
>> (as ���lib��� is unspecified)
>> trying URL '
>> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>> opened URL
>> downloaded 4.1 Mb
>>
>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>"Type"))
>> :
>>   cannot open the connection
>> In addition: Warning messages:
>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>   downloaded length 4276224 != reported length 4288136
>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>file
>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>"Type")) :
>>   cannot open compressed file 'XML/DESCRIPTION', probable reason 'No
>such
>> file or directory'
>>
>>
>>
>> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
><[hidden email]>wrote:
>>
>>> Hello,
>>> I have package XML installed on Windows 7, R 3.0.3 and I had no
>problem
>>> at all. Can't you try (it worked with me)
>>>
>>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
>>>
>>> Hope this helps,
>>>
>>> Rui Barradas
>>>
>>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
>>>
>>>  I have tried these sources (almost all US mirrors):
>>>>
>>>>
>http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
>>>> 3.0/XML_3.98-1.1.zip
>>>>
>http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>
>http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>> contrib/3.0/XML_3.98-1.1.zip
>>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>
>http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>
>http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>
>>>> I have confirmed with IT that there is no restriction on
>downloading this
>>>> zip file from any of these sources. Also I am getting same error
>when I
>>>> try
>>>> from my home network as well.
>>>>
>>>>
>>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
>>>> [hidden email]
>>>>
>>>>> wrote:
>>>>>
>>>>
>>>>
>>>>>
>>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
>>>>>
>>>>>  @Uwe I tried the same steps from office as well as home network
>with
>>>>>> same
>>>>>> results. Are you using windows 7 with R 3.0.3?
>>>>>>
>>>>>> I have seen same question being asked by others without any
>>>>>> resolution. Is
>>>>>> anything special about XML package? I am OK use older version of
>>>>>> package
>>>>>> but in archives there are no zip files (only gz files). Is
>windows
>>>>>> platform
>>>>>> not recommended for R?
>>>>>>
>>>>>>
>>>>> Right, and you can try to install these from sources.
>>>>> But I doubt you need it. You still have not told us if you tried
>another
>>>>> mirror to download the XML file from and what you local IT support
>tells
>>>>> you while your downloads are incomplete.
>>>>>
>>>>> Best,
>>>>> Uwe Ligges
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>>>>>> [hidden email]
>>>>>>
>>>>>>  wrote:
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>>>>>>>
>>>>>>>   Thank you for response Uwe. I tried multiple times by
>downloading
>>>>>>> the
>>>>>>>
>>>>>>>> zip
>>>>>>>> file from many sources but still the same error. This is a
>major road
>>>>>>>> block
>>>>>>>> for me in using R. Appreciate any help on this.
>>>>>>>>
>>>>>>>>
>>>>>>>>  Please ask your local IT staff.
>>>>>>>
>>>>>>> I get, using the same mirror:
>>>>>>>
>>>>>>>  
>options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>>>>>>>
>>>>>>>> install.packages("XML", lib="d:/temp")
>>>>>>>>
>>>>>>>>
>>>>>>> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>
>>>>>>> contrib/3.0/XML_3.98-1.1.zip'
>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>>> opened URL
>>>>>>> downloaded 4.1 Mb
>>>>>>>
>>>>>>> package 'XML' successfully unpacked and MD5 sums checked
>>>>>>>
>>>>>>> The downloaded binary packages are in
>>>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>> Uwe Ligges
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>>>>>>>> [hidden email]
>>>>>>>>
>>>>>>>>   wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>     Works for me.
>>>>>>>>
>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> Uwe Ligges
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>>>>>>>
>>>>>>>>>    Using install.package('XML') command produces this error:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> trying URL
>>>>>>>>>> '
>>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>>>>>>> '
>>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>>>>>> opened URL
>>>>>>>>>> downloaded 4.1 Mb
>>>>>>>>>>
>>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
>c("Package",
>>>>>>>>>> "Type")) :
>>>>>>>>>>       cannot open the connection
>>>>>>>>>> In addition: Warning messages:
>>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...)
>:
>>>>>>>>>>       downloaded length 4276224 != reported length 4288136
>>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
>from zip
>>>>>>>>>> file
>>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
>c("Package",
>>>>>>>>>> "Type"))
>>>>>>>>>> :
>>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable
>>>>>>>>>> reason
>>>>>>>>>> 'No
>>>>>>>>>> such
>>>>>>>>>> file or directory'
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
>directly
>>>>>>>>>> from
>>>>>>>>>> cran
>>>>>>>>>> site. But this zip file is not a valid archive (cannot open
>using
>>>>>>>>>> winzip).
>>>>>>>>>> Also trying to install using this downloaded file produces
>the
>>>>>>>>>> following
>>>>>>>>>> error:
>>>>>>>>>>
>>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>>>>>>>>>> win-library/3.0'
>>>>>>>>>> (as 'lib' is unspecified)
>>>>>>>>>> Warning in install.packages :
>>>>>>>>>>       error 1 in extracting from zip file
>>>>>>>>>> Warning in install.packages :
>>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable
>>>>>>>>>> reason
>>>>>>>>>> 'No
>>>>>>>>>> such
>>>>>>>>>> file or directory'
>>>>>>>>>> Error in install.packages : cannot open the connection
>>>>>>>>>>
>>>>>>>>>> I  downloaded this zip file from multiple sources and tried
>to
>>>>>>>>>> install
>>>>>>>>>> with
>>>>>>>>>> same result.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>
>>
>> --
>> Thanks and Regards
>> Alpesh
>>

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Re: R 3.0.3, Windows 7: Problem installing XML package

Frede Aakmann Tøgersen-2
Well now, I think I have seen something similar to Alpesh.

Recently I needed the climatol package that I have used some time ago. It is not maintained anymore but I downloaded the latest version, climatol_2.2.tar.gz,  from archives (http://cran.r-project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz ) . Trying to install that package from local file  using R-3.1.0 on Windows 8  resulted in this:

## From R Console
> utils:::menuInstallLocal()
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open the connection
In addition: Warning messages:
1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable reason 'No such file or directory'
>

And yes I know where the file is located, since choose.files() is used.

However I tried the same on our linux (R-3.0.2) cluster and it succeeded:

[frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz
* installing to library ?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library?
* installing *source* package ?climatol? ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (climatol)
[frtog@dkrdsfshn2 ~]$ R

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("climatol")
> ?rosavent
> q()
Save workspace image? [y/n/c]: n
[frtog@dkrdsfshn2 ~]$


Now unzipping and untaring climatol_2.2.tar.gz I thought to examine whether I could build the package on my Windows box. Only R stuff and no foreign language as C, FORTRAN, etc. so it should be easy.

## Command shell in Windows
Microsoft Windows [Version 6.2.9200]
(c) 2012 Microsoft Corporation. All rights reserved.

C:\Users\frtog>cd Desktop

C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build climatol
* checking for file 'climatol/DESCRIPTION' ... OK
* preparing 'climatol':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'climatol_2.2.tar.gz'

Now trying to install from that local file I Still got the same error as above.



Trying to do some debugging on read.dcf() (Emacs/ESS)


R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> > options(chmhelp=FALSE, help_type="text")
> options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient.exe', show.error.locations=TRUE)
> debug(read.dcf)
> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL)
debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
debug: {
    if (is.character(file)) {
        file <- gzfile(file)
        on.exit(close(file))
    }
    if (!inherits(file, "connection"))
        stop("'file' must be a character string or connection")
    if (!all)
        return(.Internal(readDCF(file, fields, keep.white)))
    .assemble_things_into_a_data_frame <- function(tags, vals,
        nums) {
        tf <- factor(tags, levels = unique(tags))
        cnts <- table(nums, tf)
        out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL,
            levels(tf)))
        if (all(cnts <= 1L)) {
            out[cbind(nums, tf)] <- vals
            out <- as.data.frame(out, stringsAsFactors = FALSE)
        }
        else {
            levs <- colSums(cnts > 1L) == 0L
            if (any(levs)) {
                inds <- tf %in% levels(tf)[levs]
                out[cbind(nums[inds], tf[inds])] <- vals[inds]
            }
            out <- as.data.frame(out, stringsAsFactors = FALSE)
            for (l in levels(tf)[!levs]) {
                out[[l]] <- rep.int(list(NA_character_), nrow(cnts))
                i <- tf == l
                out[[l]][unique(nums[i])] <- split(vals[i], nums[i])
            }
        }
        out
    }
    on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")),
        add = TRUE)
    Sys.setlocale("LC_CTYPE", "C")
    lines <- readLines(file)
    ind <- grep("^[^[:blank:]][^:]*$", lines)
    if (length(ind)) {
        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
        stop(gettextf("Invalid DCF format.\nRegular lines must have a tag.\nOffending lines start with:\n%s",
            paste0("  ", lines, collapse = "\n")), domain = NA)
    }
    line_is_not_empty <- !grepl("^[[:space:]]*$", lines)
    nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L)
    nums <- nums[line_is_not_empty]
    lines <- lines[line_is_not_empty]
    line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$",
        lines)
    if (any(line_is_escaped_blank))
        lines[line_is_escaped_blank] <- ""
    line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines)
    ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L])
    if (length(ind)) {
        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
        stop(gettextf("Invalid DCF format.\nContinuation lines must not start a record.\nOffending lines start with:\n%s",
            paste0("  ", lines, collapse = "\n")), domain = NA)
    }
    lengths <- rle(cumsum(line_has_tag))$lengths
    pos <- cumsum(lengths)
    tags <- sub(":.*", "", lines[line_has_tag])
    lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "", lines[line_has_tag])
    foldable <- rep.int(is.na(match(tags, keep.white)), lengths)
    lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable])
    lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable])
    vals <- mapply(function(from, to) paste(lines[from:to], collapse = "\n"),
        c(1L, pos[-length(pos)] + 1L), pos)
    out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos])
    if (!is.null(fields))
        out <- out[fields]
    out
}
Browse[2]> str(file)
 chr "climatol_2.2.tar.gz/DESCRIPTION"
Browse[2]> head(file)
[1] "climatol_2.2.tar.gz/DESCRIPTION"
Browse[2]>
debug: if (is.character(file)) {
    file <- gzfile(file)
    on.exit(close(file))
}
Browse[2]>
debug: file <- gzfile(file)
Browse[2]>
debug: on.exit(close(file))
Browse[2]>
debug: if (!inherits(file, "connection")) stop("'file' must be a character string or connection")
Browse[2]>
debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
Browse[2]> str(file)
Classes 'gzfile', 'connection'  atomic [1:1] 3
  ..- attr(*, "conn_id")=<externalptr>
Browse[2]> file
                      description                             class
"climatol_2.2.tar.gz/DESCRIPTION"                          "gzfile"
                             mode                              text
                             "rb"                            "text"
                           opened                          can read
                         "closed"                             "yes"
                        can write
                            "yes"
Browse[2]>
debug: return(.Internal(readDCF(file, fields, keep.white)))
Browse[2]>
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open the connection
In addition: Warning message:
In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable reason 'No such file or directory'
>

Well coming to debug: if (!all) return(.Internal(readDCF(file, fields, keep.white))) I loose control and R returns to prompt with an error.

Hopefully one of you can replicate this. If not then it must have something with Windows OS to do. But what?



Yours sincerely / Med venlig hilsen


Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant Performance & Modeling

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T +45 9730 5135
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> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]]
> On Behalf Of Jeff Newmiller
> Sent: 20. april 2014 23:33
> To: Alpesh Pandya; Rui Barradas
> Cc: [hidden email]; Uwe Ligges
> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
>
> Hard to help you when the problem simply does not happen for others.
>
> As for Windows being not a focus, that is not at all true. I use it regularly on
> Windows at work. That being said, there are thousands of packages and
> those each involve their own subset of R users. There are also many
> operating system configurations that may not all be fully tested. Blaming "R"
> or "Windows", or blaming us for "preventing" you from getting your
> education (isn't that something between you and your educational
> institution?) are not going to be effective strategies for problem solving.
>
> Are you able to use other aspects of R beyond the XML package? Have you
> tried communicating with the maintainers of that package?
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
>                                       Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya
> <[hidden email]> wrote:
> >I keep on trying from various networks but I still get the same error.
> >I
> >don't this this has anything to do with network or ability to download
> >the
> >package (as I can install other packages fine). This must be something
> >in
> >base R or dependencies issues (that R is not spelling out).
> >
> >I know R is geared for Mac and Windows is kind of looked down upon but
> >I
> >have no option but use windows and need this XML package running to
> >complete my education. Any help on this would be appreciated.
> >
> >
> >On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
> ><[hidden email]>wrote:
> >
> >> Thank you for response Rui.
> >>
> >> I still get the same error with this repository.
> >>
> >> Installing package into
> >���C:/Users/APandya/Documents/R/win-library/3.0���
> >> (as ���lib��� is unspecified)
> >> trying URL '
> >> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
> >> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >> opened URL
> >> downloaded 4.1 Mb
> >>
> >> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type"))
> >> :
> >>   cannot open the connection
> >> In addition: Warning messages:
> >> 1: In download.file(url, destfile, method, mode = "wb", ...) :
> >>   downloaded length 4276224 != reported length 4288136
> >> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
> >file
> >> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type")) :
> >>   cannot open compressed file 'XML/DESCRIPTION', probable reason 'No
> >such
> >> file or directory'
> >>
> >>
> >>
> >> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
> ><[hidden email]>wrote:
> >>
> >>> Hello,
> >>> I have package XML installed on Windows 7, R 3.0.3 and I had no
> >problem
> >>> at all. Can't you try (it worked with me)
> >>>
> >>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
> >>>
> >>> Hope this helps,
> >>>
> >>> Rui Barradas
> >>>
> >>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
> >>>
> >>>  I have tried these sources (almost all US mirrors):
> >>>>
> >>>>
> >http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>> http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
> >>>> 3.0/XML_3.98-1.1.zip
> >>>>
> >http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>>
> >http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >>>> contrib/3.0/XML_3.98-1.1.zip
> >>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>>
> >http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>>
> >http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-
> 1.1.zip
> >>>>
> >>>> I have confirmed with IT that there is no restriction on
> >downloading this
> >>>> zip file from any of these sources. Also I am getting same error
> >when I
> >>>> try
> >>>> from my home network as well.
> >>>>
> >>>>
> >>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
> >>>> [hidden email]
> >>>>
> >>>>> wrote:
> >>>>>
> >>>>
> >>>>
> >>>>>
> >>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
> >>>>>
> >>>>>  @Uwe I tried the same steps from office as well as home network
> >with
> >>>>>> same
> >>>>>> results. Are you using windows 7 with R 3.0.3?
> >>>>>>
> >>>>>> I have seen same question being asked by others without any
> >>>>>> resolution. Is
> >>>>>> anything special about XML package? I am OK use older version of
> >>>>>> package
> >>>>>> but in archives there are no zip files (only gz files). Is
> >windows
> >>>>>> platform
> >>>>>> not recommended for R?
> >>>>>>
> >>>>>>
> >>>>> Right, and you can try to install these from sources.
> >>>>> But I doubt you need it. You still have not told us if you tried
> >another
> >>>>> mirror to download the XML file from and what you local IT support
> >tells
> >>>>> you while your downloads are incomplete.
> >>>>>
> >>>>> Best,
> >>>>> Uwe Ligges
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
> >>>>>> [hidden email]
> >>>>>>
> >>>>>>  wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
> >>>>>>>
> >>>>>>>   Thank you for response Uwe. I tried multiple times by
> >downloading
> >>>>>>> the
> >>>>>>>
> >>>>>>>> zip
> >>>>>>>> file from many sources but still the same error. This is a
> >major road
> >>>>>>>> block
> >>>>>>>> for me in using R. Appreciate any help on this.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>  Please ask your local IT staff.
> >>>>>>>
> >>>>>>> I get, using the same mirror:
> >>>>>>>
> >>>>>>>
> >options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
> >>>>>>>
> >>>>>>>> install.packages("XML", lib="d:/temp")
> >>>>>>>>
> >>>>>>>>
> >>>>>>> trying URL 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >>>>>>>
> >>>>>>> contrib/3.0/XML_3.98-1.1.zip'
> >>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >>>>>>> opened URL
> >>>>>>> downloaded 4.1 Mb
> >>>>>>>
> >>>>>>> package 'XML' successfully unpacked and MD5 sums checked
> >>>>>>>
> >>>>>>> The downloaded binary packages are in
> >>>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Best,
> >>>>>>> Uwe Ligges
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
> >>>>>>>> [hidden email]
> >>>>>>>>
> >>>>>>>>   wrote:
> >>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>     Works for me.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> Best,
> >>>>>>>>> Uwe Ligges
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
> >>>>>>>>>
> >>>>>>>>>    Using install.package('XML') command produces this error:
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> trying URL
> >>>>>>>>>> '
> >>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
> >>>>>>>>>> '
> >>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >>>>>>>>>> opened URL
> >>>>>>>>>> downloaded 4.1 Mb
> >>>>>>>>>>
> >>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
> >c("Package",
> >>>>>>>>>> "Type")) :
> >>>>>>>>>>       cannot open the connection
> >>>>>>>>>> In addition: Warning messages:
> >>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...)
> >:
> >>>>>>>>>>       downloaded length 4276224 != reported length 4288136
> >>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
> >from zip
> >>>>>>>>>> file
> >>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
> >c("Package",
> >>>>>>>>>> "Type"))
> >>>>>>>>>> :
> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable
> >>>>>>>>>> reason
> >>>>>>>>>> 'No
> >>>>>>>>>> such
> >>>>>>>>>> file or directory'
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
> >directly
> >>>>>>>>>> from
> >>>>>>>>>> cran
> >>>>>>>>>> site. But this zip file is not a valid archive (cannot open
> >using
> >>>>>>>>>> winzip).
> >>>>>>>>>> Also trying to install using this downloaded file produces
> >the
> >>>>>>>>>> following
> >>>>>>>>>> error:
> >>>>>>>>>>
> >>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
> >>>>>>>>>> win-library/3.0'
> >>>>>>>>>> (as 'lib' is unspecified)
> >>>>>>>>>> Warning in install.packages :
> >>>>>>>>>>       error 1 in extracting from zip file
> >>>>>>>>>> Warning in install.packages :
> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION', probable
> >>>>>>>>>> reason
> >>>>>>>>>> 'No
> >>>>>>>>>> such
> >>>>>>>>>> file or directory'
> >>>>>>>>>> Error in install.packages : cannot open the connection
> >>>>>>>>>>
> >>>>>>>>>> I  downloaded this zip file from multiple sources and tried
> >to
> >>>>>>>>>> install
> >>>>>>>>>> with
> >>>>>>>>>> same result.
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>>>
> >>>>
> >>>>
> >>
> >>
> >> --
> >> Thanks and Regards
> >> Alpesh
> >>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Re: R 3.0.3, Windows 7: Problem installing XML package

Jeff Newmiller
Frede... Windows uses zip files (binary, aka pre-compiled format) for packages by default, because most installations don't have the development tools installed. You need to setup RTools and use the "source" option to install_package in order to handle the tar.gz package file, or download and install the zip file instead.
---------------------------------------------------------------------------
Jeff Newmiller                        The     .....       .....  Go Live...
DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
                                      Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
---------------------------------------------------------------------------
Sent from my phone. Please excuse my brevity.

On April 20, 2014 11:01:17 PM PDT, "Frede Aakmann Tøgersen" <[hidden email]> wrote:

>Well now, I think I have seen something similar to Alpesh.
>
>Recently I needed the climatol package that I have used some time ago.
>It is not maintained anymore but I downloaded the latest version,
>climatol_2.2.tar.gz,  from archives
>(http://cran.r-project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz
>) . Trying to install that package from local file  using R-3.1.0 on
>Windows 8  resulted in this:
>
>## From R Console
>> utils:::menuInstallLocal()
>Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>"Type")) :
>  cannot open the connection
>In addition: Warning messages:
>1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>file
>2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
>:
>cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
>reason 'No such file or directory'
>>
>
>And yes I know where the file is located, since choose.files() is used.
>
>However I tried the same on our linux (R-3.0.2) cluster and it
>succeeded:
>
>[frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz
>* installing to library
>?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library?
>* installing *source* package ?climatol? ...
>** R
>** data
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
>** building package indices
>** installing vignettes
>** testing if installed package can be loaded
>* DONE (climatol)
>[frtog@dkrdsfshn2 ~]$ R
>
>R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>Copyright (C) 2013 The R Foundation for Statistical Computing
>Platform: x86_64-unknown-linux-gnu (64-bit)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
>R is a collaborative project with many contributors.
>Type 'contributors()' for more information and
>'citation()' on how to cite R or R packages in publications.
>
>Type 'demo()' for some demos, 'help()' for on-line help, or
>'help.start()' for an HTML browser interface to help.
>Type 'q()' to quit R.
>
>> library("climatol")
>> ?rosavent
>> q()
>Save workspace image? [y/n/c]: n
>[frtog@dkrdsfshn2 ~]$
>
>
>Now unzipping and untaring climatol_2.2.tar.gz I thought to examine
>whether I could build the package on my Windows box. Only R stuff and
>no foreign language as C, FORTRAN, etc. so it should be easy.
>
>## Command shell in Windows
>Microsoft Windows [Version 6.2.9200]
>(c) 2012 Microsoft Corporation. All rights reserved.
>
>C:\Users\frtog>cd Desktop
>
>C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build
>climatol
>* checking for file 'climatol/DESCRIPTION' ... OK
>* preparing 'climatol':
>* checking DESCRIPTION meta-information ... OK
>* checking for LF line-endings in source and make files
>* checking for empty or unneeded directories
>* looking to see if a 'data/datalist' file should be added
>* building 'climatol_2.2.tar.gz'
>
>Now trying to install from that local file I Still got the same error
>as above.
>
>
>
>Trying to do some debugging on read.dcf() (Emacs/ESS)
>
>
>R version 3.1.0 (2014-04-10) -- "Spring Dance"
>Copyright (C) 2014 The R Foundation for Statistical Computing
>Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
>R is a collaborative project with many contributors.
>Type 'contributors()' for more information and
>'citation()' on how to cite R or R packages in publications.
>
>Type 'demo()' for some demos, 'help()' for on-line help, or
>'help.start()' for an HTML browser interface to help.
>Type 'q()' to quit R.
>
>> > options(chmhelp=FALSE, help_type="text")
>> options(STERM='iESS', str.dendrogram.last="'",
>editor='emacsclient.exe', show.error.locations=TRUE)
>> debug(read.dcf)
>> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL)
>debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>"Type"))
>debug: {
>    if (is.character(file)) {
>        file <- gzfile(file)
>        on.exit(close(file))
>    }
>    if (!inherits(file, "connection"))
>        stop("'file' must be a character string or connection")
>    if (!all)
>        return(.Internal(readDCF(file, fields, keep.white)))
>    .assemble_things_into_a_data_frame <- function(tags, vals,
>        nums) {
>        tf <- factor(tags, levels = unique(tags))
>        cnts <- table(nums, tf)
>     out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL,
>            levels(tf)))
>        if (all(cnts <= 1L)) {
>            out[cbind(nums, tf)] <- vals
>            out <- as.data.frame(out, stringsAsFactors = FALSE)
>        }
>        else {
>            levs <- colSums(cnts > 1L) == 0L
>            if (any(levs)) {
>                inds <- tf %in% levels(tf)[levs]
>                out[cbind(nums[inds], tf[inds])] <- vals[inds]
>            }
>            out <- as.data.frame(out, stringsAsFactors = FALSE)
>            for (l in levels(tf)[!levs]) {
>                out[[l]] <- rep.int(list(NA_character_), nrow(cnts))
>                i <- tf == l
>                out[[l]][unique(nums[i])] <- split(vals[i], nums[i])
>            }
>        }
>        out
>    }
>    on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")),
>        add = TRUE)
>    Sys.setlocale("LC_CTYPE", "C")
>    lines <- readLines(file)
>    ind <- grep("^[^[:blank:]][^:]*$", lines)
>    if (length(ind)) {
>        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
>stop(gettextf("Invalid DCF format.\nRegular lines must have a
>tag.\nOffending lines start with:\n%s",
>            paste0("  ", lines, collapse = "\n")), domain = NA)
>    }
>    line_is_not_empty <- !grepl("^[[:space:]]*$", lines)
>    nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L)
>    nums <- nums[line_is_not_empty]
>    lines <- lines[line_is_not_empty]
>    line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$",
>        lines)
>    if (any(line_is_escaped_blank))
>        lines[line_is_escaped_blank] <- ""
>    line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines)
>    ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L])
>    if (length(ind)) {
>        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
>stop(gettextf("Invalid DCF format.\nContinuation lines must not start a
>record.\nOffending lines start with:\n%s",
>            paste0("  ", lines, collapse = "\n")), domain = NA)
>    }
>    lengths <- rle(cumsum(line_has_tag))$lengths
>    pos <- cumsum(lengths)
>    tags <- sub(":.*", "", lines[line_has_tag])
>lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "",
>lines[line_has_tag])
>    foldable <- rep.int(is.na(match(tags, keep.white)), lengths)
>    lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable])
>    lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable])
>vals <- mapply(function(from, to) paste(lines[from:to], collapse =
>"\n"),
>        c(1L, pos[-length(pos)] + 1L), pos)
>    out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos])
>    if (!is.null(fields))
>        out <- out[fields]
>    out
>}
>Browse[2]> str(file)
> chr "climatol_2.2.tar.gz/DESCRIPTION"
>Browse[2]> head(file)
>[1] "climatol_2.2.tar.gz/DESCRIPTION"
>Browse[2]>
>debug: if (is.character(file)) {
>    file <- gzfile(file)
>    on.exit(close(file))
>}
>Browse[2]>
>debug: file <- gzfile(file)
>Browse[2]>
>debug: on.exit(close(file))
>Browse[2]>
>debug: if (!inherits(file, "connection")) stop("'file' must be a
>character string or connection")
>Browse[2]>
>debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
>Browse[2]> str(file)
>Classes 'gzfile', 'connection'  atomic [1:1] 3
>  ..- attr(*, "conn_id")=<externalptr>
>Browse[2]> file
>                      description                             class
>"climatol_2.2.tar.gz/DESCRIPTION"                          "gzfile"
>                             mode                              text
>                             "rb"                            "text"
>                           opened                          can read
>                         "closed"                             "yes"
>                        can write
>                            "yes"
>Browse[2]>
>debug: return(.Internal(readDCF(file, fields, keep.white)))
>Browse[2]>
>Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>"Type")) :
>  cannot open the connection
>In addition: Warning message:
>In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
>reason 'No such file or directory'
>>
>
>Well coming to debug: if (!all) return(.Internal(readDCF(file, fields,
>keep.white))) I loose control and R returns to prompt with an error.
>
>Hopefully one of you can replicate this. If not then it must have
>something with Windows OS to do. But what?
>
>
>
>Yours sincerely / Med venlig hilsen
>
>
>Frede Aakmann Tøgersen
>Specialist, M.Sc., Ph.D.
>Plant Performance & Modeling
>
>Technology & Service Solutions
>T +45 9730 5135
>M +45 2547 6050
>[hidden email]
>http://www.vestas.com
>
>Company reg. name: Vestas Wind Systems A/S
>This e-mail is subject to our e-mail disclaimer statement.
>Please refer to www.vestas.com/legal/notice
>If you have received this e-mail in error please contact the sender.
>
>> -----Original Message-----
>> From: [hidden email]
>[mailto:[hidden email]]
>> On Behalf Of Jeff Newmiller
>> Sent: 20. april 2014 23:33
>> To: Alpesh Pandya; Rui Barradas
>> Cc: [hidden email]; Uwe Ligges
>> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
>>
>> Hard to help you when the problem simply does not happen for others.
>>
>> As for Windows being not a focus, that is not at all true. I use it
>regularly on
>> Windows at work. That being said, there are thousands of packages and
>> those each involve their own subset of R users. There are also many
>> operating system configurations that may not all be fully tested.
>Blaming "R"
>> or "Windows", or blaming us for "preventing" you from getting your
>> education (isn't that something between you and your educational
>> institution?) are not going to be effective strategies for problem
>solving.
>>
>> Are you able to use other aspects of R beyond the XML package? Have
>you
>> tried communicating with the maintainers of that package?
>>
>---------------------------------------------------------------------------
>> Jeff Newmiller                        The     .....       .....  Go
>Live...
>> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
>Go...
>>                                       Live:   OO#.. Dead: OO#..
>Playing
>> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
>> /Software/Embedded Controllers)               .OO#.       .OO#.
>rocks...1k
>>
>---------------------------------------------------------------------------
>> Sent from my phone. Please excuse my brevity.
>>
>> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya
>> <[hidden email]> wrote:
>> >I keep on trying from various networks but I still get the same
>error.
>> >I
>> >don't this this has anything to do with network or ability to
>download
>> >the
>> >package (as I can install other packages fine). This must be
>something
>> >in
>> >base R or dependencies issues (that R is not spelling out).
>> >
>> >I know R is geared for Mac and Windows is kind of looked down upon
>but
>> >I
>> >have no option but use windows and need this XML package running to
>> >complete my education. Any help on this would be appreciated.
>> >
>> >
>> >On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
>> ><[hidden email]>wrote:
>> >
>> >> Thank you for response Rui.
>> >>
>> >> I still get the same error with this repository.
>> >>
>> >> Installing package into
>> >���C:/Users/APandya/Documents/R/win-library/3.0���
>> >> (as ���lib��� is unspecified)
>> >> trying URL '
>> >> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
>> >> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>> >> opened URL
>> >> downloaded 4.1 Mb
>> >>
>> >> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>> >"Type"))
>> >> :
>> >>   cannot open the connection
>> >> In addition: Warning messages:
>> >> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>> >>   downloaded length 4276224 != reported length 4288136
>> >> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from
>zip
>> >file
>> >> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>> >"Type")) :
>> >>   cannot open compressed file 'XML/DESCRIPTION', probable reason
>'No
>> >such
>> >> file or directory'
>> >>
>> >>
>> >>
>> >> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
>> ><[hidden email]>wrote:
>> >>
>> >>> Hello,
>> >>> I have package XML installed on Windows 7, R 3.0.3 and I had no
>> >problem
>> >>> at all. Can't you try (it worked with me)
>> >>>
>> >>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
>> >>>
>> >>> Hope this helps,
>> >>>
>> >>> Rui Barradas
>> >>>
>> >>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
>> >>>
>> >>>  I have tried these sources (almost all US mirrors):
>> >>>>
>> >>>>
>>
>>http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>>
>http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
>> >>>> 3.0/XML_3.98-1.1.zip
>> >>>>
>> >http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>>
>>
>>http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> >>>> contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>>
>>
>>http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>>
>> >http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-
>> 1.1.zip
>> >>>>
>> >>>> I have confirmed with IT that there is no restriction on
>> >downloading this
>> >>>> zip file from any of these sources. Also I am getting same error
>> >when I
>> >>>> try
>> >>>> from my home network as well.
>> >>>>
>> >>>>
>> >>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
>> >>>> [hidden email]
>> >>>>
>> >>>>> wrote:
>> >>>>>
>> >>>>
>> >>>>
>> >>>>>
>> >>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
>> >>>>>
>> >>>>>  @Uwe I tried the same steps from office as well as home
>network
>> >with
>> >>>>>> same
>> >>>>>> results. Are you using windows 7 with R 3.0.3?
>> >>>>>>
>> >>>>>> I have seen same question being asked by others without any
>> >>>>>> resolution. Is
>> >>>>>> anything special about XML package? I am OK use older version
>of
>> >>>>>> package
>> >>>>>> but in archives there are no zip files (only gz files). Is
>> >windows
>> >>>>>> platform
>> >>>>>> not recommended for R?
>> >>>>>>
>> >>>>>>
>> >>>>> Right, and you can try to install these from sources.
>> >>>>> But I doubt you need it. You still have not told us if you
>tried
>> >another
>> >>>>> mirror to download the XML file from and what you local IT
>support
>> >tells
>> >>>>> you while your downloads are incomplete.
>> >>>>>
>> >>>>> Best,
>> >>>>> Uwe Ligges
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>> >>>>>> [hidden email]
>> >>>>>>
>> >>>>>>  wrote:
>> >>>>>>>
>> >>>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>> >>>>>>>
>> >>>>>>>   Thank you for response Uwe. I tried multiple times by
>> >downloading
>> >>>>>>> the
>> >>>>>>>
>> >>>>>>>> zip
>> >>>>>>>> file from many sources but still the same error. This is a
>> >major road
>> >>>>>>>> block
>> >>>>>>>> for me in using R. Appreciate any help on this.
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>  Please ask your local IT staff.
>> >>>>>>>
>> >>>>>>> I get, using the same mirror:
>> >>>>>>>
>> >>>>>>>
>> >options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>> >>>>>>>
>> >>>>>>>> install.packages("XML", lib="d:/temp")
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>> trying URL
>'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> >>>>>>>
>> >>>>>>> contrib/3.0/XML_3.98-1.1.zip'
>> >>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>> >>>>>>> opened URL
>> >>>>>>> downloaded 4.1 Mb
>> >>>>>>>
>> >>>>>>> package 'XML' successfully unpacked and MD5 sums checked
>> >>>>>>>
>> >>>>>>> The downloaded binary packages are in
>> >>>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> Best,
>> >>>>>>> Uwe Ligges
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>> >>>>>>>> [hidden email]
>> >>>>>>>>
>> >>>>>>>>   wrote:
>> >>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>     Works for me.
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>> Best,
>> >>>>>>>>> Uwe Ligges
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>> >>>>>>>>>
>> >>>>>>>>>    Using install.package('XML') command produces this
>error:
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>> trying URL
>> >>>>>>>>>> '
>> >>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> >>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>> >>>>>>>>>> '
>> >>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1
>Mb)
>> >>>>>>>>>> opened URL
>> >>>>>>>>>> downloaded 4.1 Mb
>> >>>>>>>>>>
>> >>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
>> >c("Package",
>> >>>>>>>>>> "Type")) :
>> >>>>>>>>>>       cannot open the connection
>> >>>>>>>>>> In addition: Warning messages:
>> >>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb",
>...)
>> >:
>> >>>>>>>>>>       downloaded length 4276224 != reported length 4288136
>> >>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
>> >from zip
>> >>>>>>>>>> file
>> >>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
>> >c("Package",
>> >>>>>>>>>> "Type"))
>> >>>>>>>>>> :
>> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
>probable
>> >>>>>>>>>> reason
>> >>>>>>>>>> 'No
>> >>>>>>>>>> such
>> >>>>>>>>>> file or directory'
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
>> >directly
>> >>>>>>>>>> from
>> >>>>>>>>>> cran
>> >>>>>>>>>> site. But this zip file is not a valid archive (cannot
>open
>> >using
>> >>>>>>>>>> winzip).
>> >>>>>>>>>> Also trying to install using this downloaded file produces
>> >the
>> >>>>>>>>>> following
>> >>>>>>>>>> error:
>> >>>>>>>>>>
>> >>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>> >>>>>>>>>> win-library/3.0'
>> >>>>>>>>>> (as 'lib' is unspecified)
>> >>>>>>>>>> Warning in install.packages :
>> >>>>>>>>>>       error 1 in extracting from zip file
>> >>>>>>>>>> Warning in install.packages :
>> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
>probable
>> >>>>>>>>>> reason
>> >>>>>>>>>> 'No
>> >>>>>>>>>> such
>> >>>>>>>>>> file or directory'
>> >>>>>>>>>> Error in install.packages : cannot open the connection
>> >>>>>>>>>>
>> >>>>>>>>>> I  downloaded this zip file from multiple sources and
>tried
>> >to
>> >>>>>>>>>> install
>> >>>>>>>>>> with
>> >>>>>>>>>> same result.
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>
>> >>>>
>> >>
>> >>
>> >> --
>> >> Thanks and Regards
>> >> Alpesh
>> >>
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.html
>> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
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https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.
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Re: R 3.0.3, Windows 7: Problem installing XML package

Frede Aakmann Tøgersen-2
In reply to this post by alpeshpandya
Hi

Couldn't find a zip file in the archives.

Why didn't 'R CMD build' (in a command shell on Windows) not make a zip file? I did try to build from the climatol library that holds the typical files as DESCRIPTION, LICENSE, etc. as well as folders like R, etc.

Did you see the debug information on read.fcf? For me it seems like R has open a file handler to the DESCRIPTION file. Wouldn't the error already be thrown there and not when read.fcf is called if the .tar.gz format was the problem?

I'll try and locate a zip


Sendt fra Samsung mobil


-------- Oprindelig meddelelse --------
Fra: Jeff Newmiller
Dato:21/04/2014 09.44 (GMT+01:00)
Til: Frede Aakmann Tøgersen ,Alpesh Pandya ,Rui Barradas
Cc: [hidden email],Uwe Ligges ,Duncan Murdoch
Emne: RE: [R] R 3.0.3, Windows 7: Problem installing XML package

Frede... Windows uses zip files (binary, aka pre-compiled format) for packages by default, because most installations don't have the development tools installed. You need to setup RTools and use the "source" option to install_package in order to handle the tar.gz package file, or download and install the zip file instead.
---------------------------------------------------------------------------
Jeff Newmiller                        The     .....       .....  Go Live...
DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
                                      Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
---------------------------------------------------------------------------
Sent from my phone. Please excuse my brevity.

On April 20, 2014 11:01:17 PM PDT, "Frede Aakmann Tøgersen" <[hidden email]> wrote:

>Well now, I think I have seen something similar to Alpesh.
>
>Recently I needed the climatol package that I have used some time ago.
>It is not maintained anymore but I downloaded the latest version,
>climatol_2.2.tar.gz,  from archives
>(http://cran.r-project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz
>) . Trying to install that package from local file  using R-3.1.0 on
>Windows 8  resulted in this:
>
>## From R Console
>> utils:::menuInstallLocal()
>Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>"Type")) :
>  cannot open the connection
>In addition: Warning messages:
>1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>file
>2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
>:
>cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
>reason 'No such file or directory'
>>
>
>And yes I know where the file is located, since choose.files() is used.
>
>However I tried the same on our linux (R-3.0.2) cluster and it
>succeeded:
>
>[frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz
>* installing to library
>?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library?
>* installing *source* package ?climatol? ...
>** R
>** data
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
>** building package indices
>** installing vignettes
>** testing if installed package can be loaded
>* DONE (climatol)
>[frtog@dkrdsfshn2 ~]$ R
>
>R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>Copyright (C) 2013 The R Foundation for Statistical Computing
>Platform: x86_64-unknown-linux-gnu (64-bit)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
>R is a collaborative project with many contributors.
>Type 'contributors()' for more information and
>'citation()' on how to cite R or R packages in publications.
>
>Type 'demo()' for some demos, 'help()' for on-line help, or
>'help.start()' for an HTML browser interface to help.
>Type 'q()' to quit R.
>
>> library("climatol")
>> ?rosavent
>> q()
>Save workspace image? [y/n/c]: n
>[frtog@dkrdsfshn2 ~]$
>
>
>Now unzipping and untaring climatol_2.2.tar.gz I thought to examine
>whether I could build the package on my Windows box. Only R stuff and
>no foreign language as C, FORTRAN, etc. so it should be easy.
>
>## Command shell in Windows
>Microsoft Windows [Version 6.2.9200]
>(c) 2012 Microsoft Corporation. All rights reserved.
>
>C:\Users\frtog>cd Desktop
>
>C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build
>climatol
>* checking for file 'climatol/DESCRIPTION' ... OK
>* preparing 'climatol':
>* checking DESCRIPTION meta-information ... OK
>* checking for LF line-endings in source and make files
>* checking for empty or unneeded directories
>* looking to see if a 'data/datalist' file should be added
>* building 'climatol_2.2.tar.gz'
>
>Now trying to install from that local file I Still got the same error
>as above.
>
>
>
>Trying to do some debugging on read.dcf() (Emacs/ESS)
>
>
>R version 3.1.0 (2014-04-10) -- "Spring Dance"
>Copyright (C) 2014 The R Foundation for Statistical Computing
>Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
>R is a collaborative project with many contributors.
>Type 'contributors()' for more information and
>'citation()' on how to cite R or R packages in publications.
>
>Type 'demo()' for some demos, 'help()' for on-line help, or
>'help.start()' for an HTML browser interface to help.
>Type 'q()' to quit R.
>
>> > options(chmhelp=FALSE, help_type="text")
>> options(STERM='iESS', str.dendrogram.last="'",
>editor='emacsclient.exe', show.error.locations=TRUE)
>> debug(read.dcf)
>> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL)
>debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>"Type"))
>debug: {
>    if (is.character(file)) {
>        file <- gzfile(file)
>        on.exit(close(file))
>    }
>    if (!inherits(file, "connection"))
>        stop("'file' must be a character string or connection")
>    if (!all)
>        return(.Internal(readDCF(file, fields, keep.white)))
>    .assemble_things_into_a_data_frame <- function(tags, vals,
>        nums) {
>        tf <- factor(tags, levels = unique(tags))
>        cnts <- table(nums, tf)
>     out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL,
>            levels(tf)))
>        if (all(cnts <= 1L)) {
>            out[cbind(nums, tf)] <- vals
>            out <- as.data.frame(out, stringsAsFactors = FALSE)
>        }
>        else {
>            levs <- colSums(cnts > 1L) == 0L
>            if (any(levs)) {
>                inds <- tf %in% levels(tf)[levs]
>                out[cbind(nums[inds], tf[inds])] <- vals[inds]
>            }
>            out <- as.data.frame(out, stringsAsFactors = FALSE)
>            for (l in levels(tf)[!levs]) {
>                out[[l]] <- rep.int(list(NA_character_), nrow(cnts))
>                i <- tf == l
>                out[[l]][unique(nums[i])] <- split(vals[i], nums[i])
>            }
>        }
>        out
>    }
>    on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")),
>        add = TRUE)
>    Sys.setlocale("LC_CTYPE", "C")
>    lines <- readLines(file)
>    ind <- grep("^[^[:blank:]][^:]*$", lines)
>    if (length(ind)) {
>        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
>stop(gettextf("Invalid DCF format.\nRegular lines must have a
>tag.\nOffending lines start with:\n%s",
>            paste0("  ", lines, collapse = "\n")), domain = NA)
>    }
>    line_is_not_empty <- !grepl("^[[:space:]]*$", lines)
>    nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L)
>    nums <- nums[line_is_not_empty]
>    lines <- lines[line_is_not_empty]
>    line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$",
>        lines)
>    if (any(line_is_escaped_blank))
>        lines[line_is_escaped_blank] <- ""
>    line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines)
>    ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L])
>    if (length(ind)) {
>        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
>stop(gettextf("Invalid DCF format.\nContinuation lines must not start a
>record.\nOffending lines start with:\n%s",
>            paste0("  ", lines, collapse = "\n")), domain = NA)
>    }
>    lengths <- rle(cumsum(line_has_tag))$lengths
>    pos <- cumsum(lengths)
>    tags <- sub(":.*", "", lines[line_has_tag])
>lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "",
>lines[line_has_tag])
>    foldable <- rep.int(is.na(match(tags, keep.white)), lengths)
>    lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable])
>    lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable])
>vals <- mapply(function(from, to) paste(lines[from:to], collapse =
>"\n"),
>        c(1L, pos[-length(pos)] + 1L), pos)
>    out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos])
>    if (!is.null(fields))
>        out <- out[fields]
>    out
>}
>Browse[2]> str(file)
> chr "climatol_2.2.tar.gz/DESCRIPTION"
>Browse[2]> head(file)
>[1] "climatol_2.2.tar.gz/DESCRIPTION"
>Browse[2]>
>debug: if (is.character(file)) {
>    file <- gzfile(file)
>    on.exit(close(file))
>}
>Browse[2]>
>debug: file <- gzfile(file)
>Browse[2]>
>debug: on.exit(close(file))
>Browse[2]>
>debug: if (!inherits(file, "connection")) stop("'file' must be a
>character string or connection")
>Browse[2]>
>debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
>Browse[2]> str(file)
>Classes 'gzfile', 'connection'  atomic [1:1] 3
>  ..- attr(*, "conn_id")=<externalptr>
>Browse[2]> file
>                      description                             class
>"climatol_2.2.tar.gz/DESCRIPTION"                          "gzfile"
>                             mode                              text
>                             "rb"                            "text"
>                           opened                          can read
>                         "closed"                             "yes"
>                        can write
>                            "yes"
>Browse[2]>
>debug: return(.Internal(readDCF(file, fields, keep.white)))
>Browse[2]>
>Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>"Type")) :
>  cannot open the connection
>In addition: Warning message:
>In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
>reason 'No such file or directory'
>>
>
>Well coming to debug: if (!all) return(.Internal(readDCF(file, fields,
>keep.white))) I loose control and R returns to prompt with an error.
>
>Hopefully one of you can replicate this. If not then it must have
>something with Windows OS to do. But what?
>
>
>
>Yours sincerely / Med venlig hilsen
>
>
>Frede Aakmann Tøgersen
>Specialist, M.Sc., Ph.D.
>Plant Performance & Modeling
>
>Technology & Service Solutions
>T +45 9730 5135
>M +45 2547 6050
>[hidden email]
>http://www.vestas.com
>
>Company reg. name: Vestas Wind Systems A/S
>This e-mail is subject to our e-mail disclaimer statement.
>Please refer to www.vestas.com/legal/notice<http://www.vestas.com/legal/notice>
>If you have received this e-mail in error please contact the sender.
>
>> -----Original Message-----
>> From: [hidden email]
>[mailto:[hidden email]]
>> On Behalf Of Jeff Newmiller
>> Sent: 20. april 2014 23:33
>> To: Alpesh Pandya; Rui Barradas
>> Cc: [hidden email]; Uwe Ligges
>> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
>>
>> Hard to help you when the problem simply does not happen for others.
>>
>> As for Windows being not a focus, that is not at all true. I use it
>regularly on
>> Windows at work. That being said, there are thousands of packages and
>> those each involve their own subset of R users. There are also many
>> operating system configurations that may not all be fully tested.
>Blaming "R"
>> or "Windows", or blaming us for "preventing" you from getting your
>> education (isn't that something between you and your educational
>> institution?) are not going to be effective strategies for problem
>solving.
>>
>> Are you able to use other aspects of R beyond the XML package? Have
>you
>> tried communicating with the maintainers of that package?
>>
>---------------------------------------------------------------------------
>> Jeff Newmiller                        The     .....       .....  Go
>Live...
>> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
>Go...
>>                                       Live:   OO#.. Dead: OO#..
>Playing
>> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
>> /Software/Embedded Controllers)               .OO#.       .OO#.
>rocks...1k
>>
>---------------------------------------------------------------------------
>> Sent from my phone. Please excuse my brevity.
>>
>> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya
>> <[hidden email]> wrote:
>> >I keep on trying from various networks but I still get the same
>error.
>> >I
>> >don't this this has anything to do with network or ability to
>download
>> >the
>> >package (as I can install other packages fine). This must be
>something
>> >in
>> >base R or dependencies issues (that R is not spelling out).
>> >
>> >I know R is geared for Mac and Windows is kind of looked down upon
>but
>> >I
>> >have no option but use windows and need this XML package running to
>> >complete my education. Any help on this would be appreciated.
>> >
>> >
>> >On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
>> ><[hidden email]>wrote:
>> >
>> >> Thank you for response Rui.
>> >>
>> >> I still get the same error with this repository.
>> >>
>> >> Installing package into
>> >���C:/Users/APandya/Documents/R/win-library/3.0���
>> >> (as ���lib��� is unspecified)
>> >> trying URL '
>> >> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
>> >> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>> >> opened URL
>> >> downloaded 4.1 Mb
>> >>
>> >> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>> >"Type"))
>> >> :
>> >>   cannot open the connection
>> >> In addition: Warning messages:
>> >> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>> >>   downloaded length 4276224 != reported length 4288136
>> >> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from
>zip
>> >file
>> >> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>> >"Type")) :
>> >>   cannot open compressed file 'XML/DESCRIPTION', probable reason
>'No
>> >such
>> >> file or directory'
>> >>
>> >>
>> >>
>> >> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
>> ><[hidden email]>wrote:
>> >>
>> >>> Hello,
>> >>> I have package XML installed on Windows 7, R 3.0.3 and I had no
>> >problem
>> >>> at all. Can't you try (it worked with me)
>> >>>
>> >>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
>> >>>
>> >>> Hope this helps,
>> >>>
>> >>> Rui Barradas
>> >>>
>> >>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
>> >>>
>> >>>  I have tried these sources (almost all US mirrors):
>> >>>>
>> >>>>
>>
>>http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>>
>http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
>> >>>> 3.0/XML_3.98-1.1.zip
>> >>>>
>> >http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>>
>>
>>http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> >>>> contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>>
>>
>>http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>> >>>>
>> >http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-
>> 1.1.zip
>> >>>>
>> >>>> I have confirmed with IT that there is no restriction on
>> >downloading this
>> >>>> zip file from any of these sources. Also I am getting same error
>> >when I
>> >>>> try
>> >>>> from my home network as well.
>> >>>>
>> >>>>
>> >>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
>> >>>> [hidden email]
>> >>>>
>> >>>>> wrote:
>> >>>>>
>> >>>>
>> >>>>
>> >>>>>
>> >>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
>> >>>>>
>> >>>>>  @Uwe I tried the same steps from office as well as home
>network
>> >with
>> >>>>>> same
>> >>>>>> results. Are you using windows 7 with R 3.0.3?
>> >>>>>>
>> >>>>>> I have seen same question being asked by others without any
>> >>>>>> resolution. Is
>> >>>>>> anything special about XML package? I am OK use older version
>of
>> >>>>>> package
>> >>>>>> but in archives there are no zip files (only gz files). Is
>> >windows
>> >>>>>> platform
>> >>>>>> not recommended for R?
>> >>>>>>
>> >>>>>>
>> >>>>> Right, and you can try to install these from sources.
>> >>>>> But I doubt you need it. You still have not told us if you
>tried
>> >another
>> >>>>> mirror to download the XML file from and what you local IT
>support
>> >tells
>> >>>>> you while your downloads are incomplete.
>> >>>>>
>> >>>>> Best,
>> >>>>> Uwe Ligges
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>> >>>>>> [hidden email]
>> >>>>>>
>> >>>>>>  wrote:
>> >>>>>>>
>> >>>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>> >>>>>>>
>> >>>>>>>   Thank you for response Uwe. I tried multiple times by
>> >downloading
>> >>>>>>> the
>> >>>>>>>
>> >>>>>>>> zip
>> >>>>>>>> file from many sources but still the same error. This is a
>> >major road
>> >>>>>>>> block
>> >>>>>>>> for me in using R. Appreciate any help on this.
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>  Please ask your local IT staff.
>> >>>>>>>
>> >>>>>>> I get, using the same mirror:
>> >>>>>>>
>> >>>>>>>
>> >options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>> >>>>>>>
>> >>>>>>>> install.packages("XML", lib="d:/temp")
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>> trying URL
>'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> >>>>>>>
>> >>>>>>> contrib/3.0/XML_3.98-1.1.zip'
>> >>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>> >>>>>>> opened URL
>> >>>>>>> downloaded 4.1 Mb
>> >>>>>>>
>> >>>>>>> package 'XML' successfully unpacked and MD5 sums checked
>> >>>>>>>
>> >>>>>>> The downloaded binary packages are in
>> >>>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> Best,
>> >>>>>>> Uwe Ligges
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>> >>>>>>>> [hidden email]
>> >>>>>>>>
>> >>>>>>>>   wrote:
>> >>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>     Works for me.
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>> Best,
>> >>>>>>>>> Uwe Ligges
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>> >>>>>>>>>
>> >>>>>>>>>    Using install.package('XML') command produces this
>error:
>> >>>>>>>>>
>> >>>>>>>>>
>> >>>>>>>>>> trying URL
>> >>>>>>>>>> '
>> >>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>> >>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>> >>>>>>>>>> '
>> >>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1
>Mb)
>> >>>>>>>>>> opened URL
>> >>>>>>>>>> downloaded 4.1 Mb
>> >>>>>>>>>>
>> >>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
>> >c("Package",
>> >>>>>>>>>> "Type")) :
>> >>>>>>>>>>       cannot open the connection
>> >>>>>>>>>> In addition: Warning messages:
>> >>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb",
>...)
>> >:
>> >>>>>>>>>>       downloaded length 4276224 != reported length 4288136
>> >>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
>> >from zip
>> >>>>>>>>>> file
>> >>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
>> >c("Package",
>> >>>>>>>>>> "Type"))
>> >>>>>>>>>> :
>> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
>probable
>> >>>>>>>>>> reason
>> >>>>>>>>>> 'No
>> >>>>>>>>>> such
>> >>>>>>>>>> file or directory'
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
>> >directly
>> >>>>>>>>>> from
>> >>>>>>>>>> cran
>> >>>>>>>>>> site. But this zip file is not a valid archive (cannot
>open
>> >using
>> >>>>>>>>>> winzip).
>> >>>>>>>>>> Also trying to install using this downloaded file produces
>> >the
>> >>>>>>>>>> following
>> >>>>>>>>>> error:
>> >>>>>>>>>>
>> >>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>> >>>>>>>>>> win-library/3.0'
>> >>>>>>>>>> (as 'lib' is unspecified)
>> >>>>>>>>>> Warning in install.packages :
>> >>>>>>>>>>       error 1 in extracting from zip file
>> >>>>>>>>>> Warning in install.packages :
>> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
>probable
>> >>>>>>>>>> reason
>> >>>>>>>>>> 'No
>> >>>>>>>>>> such
>> >>>>>>>>>> file or directory'
>> >>>>>>>>>> Error in install.packages : cannot open the connection
>> >>>>>>>>>>
>> >>>>>>>>>> I  downloaded this zip file from multiple sources and
>tried
>> >to
>> >>>>>>>>>> install
>> >>>>>>>>>> with
>> >>>>>>>>>> same result.
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>
>> >>>>
>> >>
>> >>
>> >> --
>> >> Thanks and Regards
>> >> Alpesh
>> >>
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.html
>> and provide commented, minimal, self-contained, reproducible code.

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Re: R 3.0.3, Windows 7: Problem installing XML package

Michael Dewey
In reply to this post by Jeff Newmiller
At 08:43 21/04/2014, Jeff Newmiller wrote:
>Frede... Windows uses zip files (binary, aka
>pre-compiled format) for packages by default,
>because most installations don't have the
>development tools installed. You need to setup
>RTools and use the "source" option to
>install_package in order to handle the tar.gz
>package file, or download and install the zip file instead.

Jeff, Frede did say that there is no C or Fortran
in the package which suggests that it should be
possible to install it under Windows without
installing RTools first if I understand correctly.

>---------------------------------------------------------------------------
>Jeff Newmiller                        The     .....       .....  Go Live...
>DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
>                                       Live:   OO#.. Dead: OO#..  Playing
>Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
>/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
>---------------------------------------------------------------------------
>Sent from my phone. Please excuse my brevity.
>
>On April 20, 2014 11:01:17 PM PDT, "Frede
>Aakmann Tøgersen" <[hidden email]> wrote:
> >Well now, I think I have seen something similar to Alpesh.
> >
> >Recently I needed the climatol package that I have used some time ago.
> >It is not maintained anymore but I downloaded the latest version,
> >climatol_2.2.tar.gz,  from archives
> >(http://cran.r-project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz
> >) . Trying to install that package from local file  using R-3.1.0 on
> >Windows 8  resulted in this:
> >
> >## From R Console
> >> utils:::menuInstallLocal()
> >Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type")) :
> >  cannot open the connection
> >In addition: Warning messages:
> >1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
> >file
> >2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
> >:
> >cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
> >reason 'No such file or directory'
> >>
> >
> >And yes I know where the file is located, since choose.files() is used.
> >
> >However I tried the same on our linux (R-3.0.2) cluster and it
> >succeeded:
> >
> >[frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz
> >* installing to library
> >?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library?
> >* installing *source* package ?climatol? ...
> >** R
> >** data
> >** inst
> >** preparing package for lazy loading
> >** help
> >*** installing help indices
> >** building package indices
> >** installing vignettes
> >** testing if installed package can be loaded
> >* DONE (climatol)
> >[frtog@dkrdsfshn2 ~]$ R
> >
> >R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> >Copyright (C) 2013 The R Foundation for Statistical Computing
> >Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under certain conditions.
> >Type 'license()' or 'licence()' for distribution details.
> >
> >  Natural language support but running in an English locale
> >
> >R is a collaborative project with many contributors.
> >Type 'contributors()' for more information and
> >'citation()' on how to cite R or R packages in publications.
> >
> >Type 'demo()' for some demos, 'help()' for on-line help, or
> >'help.start()' for an HTML browser interface to help.
> >Type 'q()' to quit R.
> >
> >> library("climatol")
> >> ?rosavent
> >> q()
> >Save workspace image? [y/n/c]: n
> >[frtog@dkrdsfshn2 ~]$
> >
> >
> >Now unzipping and untaring climatol_2.2.tar.gz I thought to examine
> >whether I could build the package on my Windows box. Only R stuff and
> >no foreign language as C, FORTRAN, etc. so it should be easy.
> >
> >## Command shell in Windows
> >Microsoft Windows [Version 6.2.9200]
> >(c) 2012 Microsoft Corporation. All rights reserved.
> >
> >C:\Users\frtog>cd Desktop
> >
> >C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build
> >climatol
> >* checking for file 'climatol/DESCRIPTION' ... OK
> >* preparing 'climatol':
> >* checking DESCRIPTION meta-information ... OK
> >* checking for LF line-endings in source and make files
> >* checking for empty or unneeded directories
> >* looking to see if a 'data/datalist' file should be added
> >* building 'climatol_2.2.tar.gz'
> >
> >Now trying to install from that local file I Still got the same error
> >as above.
> >
> >
> >
> >Trying to do some debugging on read.dcf() (Emacs/ESS)
> >
> >
> >R version 3.1.0 (2014-04-10) -- "Spring Dance"
> >Copyright (C) 2014 The R Foundation for Statistical Computing
> >Platform: x86_64-w64-mingw32/x64 (64-bit)
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under certain conditions.
> >Type 'license()' or 'licence()' for distribution details.
> >
> >  Natural language support but running in an English locale
> >
> >R is a collaborative project with many contributors.
> >Type 'contributors()' for more information and
> >'citation()' on how to cite R or R packages in publications.
> >
> >Type 'demo()' for some demos, 'help()' for on-line help, or
> >'help.start()' for an HTML browser interface to help.
> >Type 'q()' to quit R.
> >
> >> > options(chmhelp=FALSE, help_type="text")
> >> options(STERM='iESS', str.dendrogram.last="'",
> >editor='emacsclient.exe', show.error.locations=TRUE)
> >> debug(read.dcf)
> >> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL)
> >debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type"))
> >debug: {
> >    if (is.character(file)) {
> >        file <- gzfile(file)
> >        on.exit(close(file))
> >    }
> >    if (!inherits(file, "connection"))
> >        stop("'file' must be a character string or connection")
> >    if (!all)
> >        return(.Internal(readDCF(file, fields, keep.white)))
> >    .assemble_things_into_a_data_frame <- function(tags, vals,
> >        nums) {
> >        tf <- factor(tags, levels = unique(tags))
> >        cnts <- table(nums, tf)
> >     out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL,
> >            levels(tf)))
> >        if (all(cnts <= 1L)) {
> >            out[cbind(nums, tf)] <- vals
> >            out <- as.data.frame(out, stringsAsFactors = FALSE)
> >        }
> >        else {
> >            levs <- colSums(cnts > 1L) == 0L
> >            if (any(levs)) {
> >                inds <- tf %in% levels(tf)[levs]
> >                out[cbind(nums[inds], tf[inds])] <- vals[inds]
> >            }
> >            out <- as.data.frame(out, stringsAsFactors = FALSE)
> >            for (l in levels(tf)[!levs]) {
> >                out[[l]] <- rep.int(list(NA_character_), nrow(cnts))
> >                i <- tf == l
> >                out[[l]][unique(nums[i])] <- split(vals[i], nums[i])
> >            }
> >        }
> >        out
> >    }
> >    on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")),
> >        add = TRUE)
> >    Sys.setlocale("LC_CTYPE", "C")
> >    lines <- readLines(file)
> >    ind <- grep("^[^[:blank:]][^:]*$", lines)
> >    if (length(ind)) {
> >        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
> >stop(gettextf("Invalid DCF format.\nRegular lines must have a
> >tag.\nOffending lines start with:\n%s",
> >            paste0("  ", lines, collapse = "\n")), domain = NA)
> >    }
> >    line_is_not_empty <- !grepl("^[[:space:]]*$", lines)
> >    nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L)
> >    nums <- nums[line_is_not_empty]
> >    lines <- lines[line_is_not_empty]
> >    line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$",
> >        lines)
> >    if (any(line_is_escaped_blank))
> >        lines[line_is_escaped_blank] <- ""
> >    line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines)
> >    ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L])
> >    if (length(ind)) {
> >        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
> >stop(gettextf("Invalid DCF format.\nContinuation lines must not start a
> >record.\nOffending lines start with:\n%s",
> >            paste0("  ", lines, collapse = "\n")), domain = NA)
> >    }
> >    lengths <- rle(cumsum(line_has_tag))$lengths
> >    pos <- cumsum(lengths)
> >    tags <- sub(":.*", "", lines[line_has_tag])
> >lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "",
> >lines[line_has_tag])
> >    foldable <- rep.int(is.na(match(tags, keep.white)), lengths)
> >    lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable])
> >    lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable])
> >vals <- mapply(function(from, to) paste(lines[from:to], collapse =
> >"\n"),
> >        c(1L, pos[-length(pos)] + 1L), pos)
> >    out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos])
> >    if (!is.null(fields))
> >        out <- out[fields]
> >    out
> >}
> >Browse[2]> str(file)
> > chr "climatol_2.2.tar.gz/DESCRIPTION"
> >Browse[2]> head(file)
> >[1] "climatol_2.2.tar.gz/DESCRIPTION"
> >Browse[2]>
> >debug: if (is.character(file)) {
> >    file <- gzfile(file)
> >    on.exit(close(file))
> >}
> >Browse[2]>
> >debug: file <- gzfile(file)
> >Browse[2]>
> >debug: on.exit(close(file))
> >Browse[2]>
> >debug: if (!inherits(file, "connection")) stop("'file' must be a
> >character string or connection")
> >Browse[2]>
> >debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
> >Browse[2]> str(file)
> >Classes 'gzfile', 'connection'  atomic [1:1] 3
> >  ..- attr(*, "conn_id")=<externalptr>
> >Browse[2]> file
> >                      description                             class
> >"climatol_2.2.tar.gz/DESCRIPTION"                          "gzfile"
> >                             mode                              text
> >                             "rb"                            "text"
> >                           opened                          can read
> >                         "closed"                             "yes"
> >                        can write
> >                            "yes"
> >Browse[2]>
> >debug: return(.Internal(readDCF(file, fields, keep.white)))
> >Browse[2]>
> >Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type")) :
> >  cannot open the connection
> >In addition: Warning message:
> >In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
> >cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
> >reason 'No such file or directory'
> >>
> >
> >Well coming to debug: if (!all) return(.Internal(readDCF(file, fields,
> >keep.white))) I loose control and R returns to prompt with an error.
> >
> >Hopefully one of you can replicate this. If not then it must have
> >something with Windows OS to do. But what?
> >
> >
> >
> >Yours sincerely / Med venlig hilsen
> >
> >
> >Frede Aakmann Tøgersen
> >Specialist, M.Sc., Ph.D.
> >Plant Performance & Modeling
> >
> >Technology & Service Solutions
> >T +45 9730 5135
> >M +45 2547 6050
> >[hidden email]
> >http://www.vestas.com
> >
> >Company reg. name: Vestas Wind Systems A/S
> >This e-mail is subject to our e-mail disclaimer statement.
> >Please refer to www.vestas.com/legal/notice
> >If you have received this e-mail in error please contact the sender.
> >
> >> -----Original Message-----
> >> From: [hidden email]
> >[mailto:[hidden email]]
> >> On Behalf Of Jeff Newmiller
> >> Sent: 20. april 2014 23:33
> >> To: Alpesh Pandya; Rui Barradas
> >> Cc: [hidden email]; Uwe Ligges
> >> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
> >>
> >> Hard to help you when the problem simply does not happen for others.
> >>
> >> As for Windows being not a focus, that is not at all true. I use it
> >regularly on
> >> Windows at work. That being said, there are thousands of packages and
> >> those each involve their own subset of R users. There are also many
> >> operating system configurations that may not all be fully tested.
> >Blaming "R"
> >> or "Windows", or blaming us for "preventing" you from getting your
> >> education (isn't that something between you and your educational
> >> institution?) are not going to be effective strategies for problem
> >solving.
> >>
> >> Are you able to use other aspects of R beyond the XML package? Have
> >you
> >> tried communicating with the maintainers of that package?
> >>
> >---------------------------------------------------------------------------
> >> Jeff Newmiller                        The     .....       .....  Go
> >Live...
> >> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
> >Go...
> >>                                       Live:   OO#.. Dead: OO#..
> >Playing
> >> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> >> /Software/Embedded Controllers)               .OO#.       .OO#.
> >rocks...1k
> >>
> >---------------------------------------------------------------------------
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya
> >> <[hidden email]> wrote:
> >> >I keep on trying from various networks but I still get the same
> >error.
> >> >I
> >> >don't this this has anything to do with network or ability to
> >download
> >> >the
> >> >package (as I can install other packages fine). This must be
> >something
> >> >in
> >> >base R or dependencies issues (that R is not spelling out).
> >> >
> >> >I know R is geared for Mac and Windows is kind of looked down upon
> >but
> >> >I
> >> >have no option but use windows and need this XML package running to
> >> >complete my education. Any help on this would be appreciated.
> >> >
> >> >
> >> >On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
> >> ><[hidden email]>wrote:
> >> >
> >> >> Thank you for response Rui.
> >> >>
> >> >> I still get the same error with this repository.
> >> >>
> >> >> Installing package into
> >> >���C:/Users/APandya/Documents/R/win-library/3.0���
> >> >> (as ���lib��� is unspecified)
> >> >> trying URL '
> >> >> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
> >> >> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >> >> opened URL
> >> >> downloaded 4.1 Mb
> >> >>
> >> >> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >> >"Type"))
> >> >> :
> >> >>   cannot open the connection
> >> >> In addition: Warning messages:
> >> >> 1: In download.file(url, destfile, method, mode = "wb", ...) :
> >> >>   downloaded length 4276224 != reported length 4288136
> >> >> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from
> >zip
> >> >file
> >> >> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >> >"Type")) :
> >> >>   cannot open compressed file 'XML/DESCRIPTION', probable reason
> >'No
> >> >such
> >> >> file or directory'
> >> >>
> >> >>
> >> >>
> >> >> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
> >> ><[hidden email]>wrote:
> >> >>
> >> >>> Hello,
> >> >>> I have package XML installed on Windows 7, R 3.0.3 and I had no
> >> >problem
> >> >>> at all. Can't you try (it worked with me)
> >> >>>
> >> >>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
> >> >>>
> >> >>> Hope this helps,
> >> >>>
> >> >>> Rui Barradas
> >> >>>
> >> >>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
> >> >>>
> >> >>>  I have tried these sources (almost all US mirrors):
> >> >>>>
> >> >>>>
> >>
> >>http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
> >> >>>> 3.0/XML_3.98-1.1.zip
> >> >>>>
> >> >http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >>
> >>http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>> contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >>
> >>http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >> >http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-
> >> 1.1.zip
> >> >>>>
> >> >>>> I have confirmed with IT that there is no restriction on
> >> >downloading this
> >> >>>> zip file from any of these sources. Also I am getting same error
> >> >when I
> >> >>>> try
> >> >>>> from my home network as well.
> >> >>>>
> >> >>>>
> >> >>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
> >> >>>> [hidden email]
> >> >>>>
> >> >>>>> wrote:
> >> >>>>>
> >> >>>>
> >> >>>>
> >> >>>>>
> >> >>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
> >> >>>>>
> >> >>>>>  @Uwe I tried the same steps from office as well as home
> >network
> >> >with
> >> >>>>>> same
> >> >>>>>> results. Are you using windows 7 with R 3.0.3?
> >> >>>>>>
> >> >>>>>> I have seen same question being asked by others without any
> >> >>>>>> resolution. Is
> >> >>>>>> anything special about XML package? I am OK use older version
> >of
> >> >>>>>> package
> >> >>>>>> but in archives there are no zip files (only gz files). Is
> >> >windows
> >> >>>>>> platform
> >> >>>>>> not recommended for R?
> >> >>>>>>
> >> >>>>>>
> >> >>>>> Right, and you can try to install these from sources.
> >> >>>>> But I doubt you need it. You still have not told us if you
> >tried
> >> >another
> >> >>>>> mirror to download the XML file from and what you local IT
> >support
> >> >tells
> >> >>>>> you while your downloads are incomplete.
> >> >>>>>
> >> >>>>> Best,
> >> >>>>> Uwe Ligges
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
> >> >>>>>> [hidden email]
> >> >>>>>>
> >> >>>>>>  wrote:
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>
> >> >>>>>>
> >> >>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
> >> >>>>>>>
> >> >>>>>>>   Thank you for response Uwe. I tried multiple times by
> >> >downloading
> >> >>>>>>> the
> >> >>>>>>>
> >> >>>>>>>> zip
> >> >>>>>>>> file from many sources but still the same error. This is a
> >> >major road
> >> >>>>>>>> block
> >> >>>>>>>> for me in using R. Appreciate any help on this.
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>  Please ask your local IT staff.
> >> >>>>>>>
> >> >>>>>>> I get, using the same mirror:
> >> >>>>>>>
> >> >>>>>>>
> >> >options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
> >> >>>>>>>
> >> >>>>>>>> install.packages("XML", lib="d:/temp")
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>> trying URL
> >'http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>>>>>
> >> >>>>>>> contrib/3.0/XML_3.98-1.1.zip'
> >> >>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >> >>>>>>> opened URL
> >> >>>>>>> downloaded 4.1 Mb
> >> >>>>>>>
> >> >>>>>>> package 'XML' successfully unpacked and MD5 sums checked
> >> >>>>>>>
> >> >>>>>>> The downloaded binary packages are in
> >> >>>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>> Best,
> >> >>>>>>> Uwe Ligges
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
> >> >>>>>>>> [hidden email]
> >> >>>>>>>>
> >> >>>>>>>>   wrote:
> >> >>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>     Works for me.
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>> Best,
> >> >>>>>>>>> Uwe Ligges
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
> >> >>>>>>>>>
> >> >>>>>>>>>    Using install.package('XML') command produces this
> >error:
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>> trying URL
> >> >>>>>>>>>> '
> >> >>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
> >> >>>>>>>>>> '
> >> >>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1
> >Mb)
> >> >>>>>>>>>> opened URL
> >> >>>>>>>>>> downloaded 4.1 Mb
> >> >>>>>>>>>>
> >> >>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
> >> >c("Package",
> >> >>>>>>>>>> "Type")) :
> >> >>>>>>>>>>       cannot open the connection
> >> >>>>>>>>>> In addition: Warning messages:
> >> >>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb",
> >...)
> >> >:
> >> >>>>>>>>>>       downloaded length 4276224 != reported length 4288136
> >> >>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
> >> >from zip
> >> >>>>>>>>>> file
> >> >>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
> >> >c("Package",
> >> >>>>>>>>>> "Type"))
> >> >>>>>>>>>> :
> >> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
> >probable
> >> >>>>>>>>>> reason
> >> >>>>>>>>>> 'No
> >> >>>>>>>>>> such
> >> >>>>>>>>>> file or directory'
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
> >> >directly
> >> >>>>>>>>>> from
> >> >>>>>>>>>> cran
> >> >>>>>>>>>> site. But this zip file is not a valid archive (cannot
> >open
> >> >using
> >> >>>>>>>>>> winzip).
> >> >>>>>>>>>> Also trying to install using this downloaded file produces
> >> >the
> >> >>>>>>>>>> following
> >> >>>>>>>>>> error:
> >> >>>>>>>>>>
> >> >>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
> >> >>>>>>>>>> win-library/3.0'
> >> >>>>>>>>>> (as 'lib' is unspecified)
> >> >>>>>>>>>> Warning in install.packages :
> >> >>>>>>>>>>       error 1 in extracting from zip file
> >> >>>>>>>>>> Warning in install.packages :
> >> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
> >probable
> >> >>>>>>>>>> reason
> >> >>>>>>>>>> 'No
> >> >>>>>>>>>> such
> >> >>>>>>>>>> file or directory'
> >> >>>>>>>>>> Error in install.packages : cannot open the connection
> >> >>>>>>>>>>
> >> >>>>>>>>>> I  downloaded this zip file from multiple sources and
> >tried
> >> >to
> >> >>>>>>>>>> install
> >> >>>>>>>>>> with
> >> >>>>>>>>>> same result.
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>
> >> >>>>>>
> >> >>>>
> >> >>>>
> >> >>
> >> >>
> >> >> --
> >> >> Thanks and Regards
> >> >> Alpesh
> >> >>
> >>
> >> ______________________________________________
> >> [hidden email] mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-
> >> guide.html
> >> and provide commented, minimal, self-contained, reproducible code.

Michael Dewey
[hidden email]
http://www.aghmed.fsnet.co.uk/home.html

______________________________________________
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: R 3.0.3, Windows 7: Problem installing XML package

Milan Bouchet-Valat
In reply to this post by Frede Aakmann Tøgersen-2
Le lundi 21 avril 2014 à 11:38 +0200, Frede Aakmann Tøgersen a écrit :
> Hi
>
> Couldn't find a zip file in the archives.
>
> Why didn't 'R CMD build' (in a command shell on Windows) not make a
> zip file? I did try to build from the climatol library that holds the
> typical files as DESCRIPTION, LICENSE, etc. as well as folders like R,
> etc.
R CMD build produces *source* packages, and .zip packages are *binary*.

> Did you see the debug information on read.fcf? For me it seems like R
> has open a file handler to the DESCRIPTION file. Wouldn't the error
> already be thrown there and not when read.fcf is called if the .tar.gz
> format was the problem?
>
> I'll try and locate a zip
Does install.packages(choose.file(), type="source") work? I'm not sure
what utils:::menuInstallLocal() does.


Regards


> Sendt fra Samsung mobil
>
>
> -------- Oprindelig meddelelse --------
> Fra: Jeff Newmiller
> Dato:21/04/2014 09.44 (GMT+01:00)
> Til: Frede Aakmann Tøgersen ,Alpesh Pandya ,Rui Barradas
> Cc: [hidden email],Uwe Ligges ,Duncan Murdoch
> Emne: RE: [R] R 3.0.3, Windows 7: Problem installing XML package
>
> Frede... Windows uses zip files (binary, aka pre-compiled format) for packages by default, because most installations don't have the development tools installed. You need to setup RTools and use the "source" option to install_package in order to handle the tar.gz package file, or download and install the zip file instead.
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
>                                       Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> On April 20, 2014 11:01:17 PM PDT, "Frede Aakmann Tøgersen" <[hidden email]> wrote:
> >Well now, I think I have seen something similar to Alpesh.
> >
> >Recently I needed the climatol package that I have used some time ago.
> >It is not maintained anymore but I downloaded the latest version,
> >climatol_2.2.tar.gz,  from archives
> >(http://cran.r-project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz
> >) . Trying to install that package from local file  using R-3.1.0 on
> >Windows 8  resulted in this:
> >
> >## From R Console
> >> utils:::menuInstallLocal()
> >Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type")) :
> >  cannot open the connection
> >In addition: Warning messages:
> >1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
> >file
> >2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
> >:
> >cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
> >reason 'No such file or directory'
> >>
> >
> >And yes I know where the file is located, since choose.files() is used.
> >
> >However I tried the same on our linux (R-3.0.2) cluster and it
> >succeeded:
> >
> >[frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz
> >* installing to library
> >?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library?
> >* installing *source* package ?climatol? ...
> >** R
> >** data
> >** inst
> >** preparing package for lazy loading
> >** help
> >*** installing help indices
> >** building package indices
> >** installing vignettes
> >** testing if installed package can be loaded
> >* DONE (climatol)
> >[frtog@dkrdsfshn2 ~]$ R
> >
> >R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> >Copyright (C) 2013 The R Foundation for Statistical Computing
> >Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under certain conditions.
> >Type 'license()' or 'licence()' for distribution details.
> >
> >  Natural language support but running in an English locale
> >
> >R is a collaborative project with many contributors.
> >Type 'contributors()' for more information and
> >'citation()' on how to cite R or R packages in publications.
> >
> >Type 'demo()' for some demos, 'help()' for on-line help, or
> >'help.start()' for an HTML browser interface to help.
> >Type 'q()' to quit R.
> >
> >> library("climatol")
> >> ?rosavent
> >> q()
> >Save workspace image? [y/n/c]: n
> >[frtog@dkrdsfshn2 ~]$
> >
> >
> >Now unzipping and untaring climatol_2.2.tar.gz I thought to examine
> >whether I could build the package on my Windows box. Only R stuff and
> >no foreign language as C, FORTRAN, etc. so it should be easy.
> >
> >## Command shell in Windows
> >Microsoft Windows [Version 6.2.9200]
> >(c) 2012 Microsoft Corporation. All rights reserved.
> >
> >C:\Users\frtog>cd Desktop
> >
> >C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build
> >climatol
> >* checking for file 'climatol/DESCRIPTION' ... OK
> >* preparing 'climatol':
> >* checking DESCRIPTION meta-information ... OK
> >* checking for LF line-endings in source and make files
> >* checking for empty or unneeded directories
> >* looking to see if a 'data/datalist' file should be added
> >* building 'climatol_2.2.tar.gz'
> >
> >Now trying to install from that local file I Still got the same error
> >as above.
> >
> >
> >
> >Trying to do some debugging on read.dcf() (Emacs/ESS)
> >
> >
> >R version 3.1.0 (2014-04-10) -- "Spring Dance"
> >Copyright (C) 2014 The R Foundation for Statistical Computing
> >Platform: x86_64-w64-mingw32/x64 (64-bit)
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under certain conditions.
> >Type 'license()' or 'licence()' for distribution details.
> >
> >  Natural language support but running in an English locale
> >
> >R is a collaborative project with many contributors.
> >Type 'contributors()' for more information and
> >'citation()' on how to cite R or R packages in publications.
> >
> >Type 'demo()' for some demos, 'help()' for on-line help, or
> >'help.start()' for an HTML browser interface to help.
> >Type 'q()' to quit R.
> >
> >> > options(chmhelp=FALSE, help_type="text")
> >> options(STERM='iESS', str.dendrogram.last="'",
> >editor='emacsclient.exe', show.error.locations=TRUE)
> >> debug(read.dcf)
> >> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL)
> >debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type"))
> >debug: {
> >    if (is.character(file)) {
> >        file <- gzfile(file)
> >        on.exit(close(file))
> >    }
> >    if (!inherits(file, "connection"))
> >        stop("'file' must be a character string or connection")
> >    if (!all)
> >        return(.Internal(readDCF(file, fields, keep.white)))
> >    .assemble_things_into_a_data_frame <- function(tags, vals,
> >        nums) {
> >        tf <- factor(tags, levels = unique(tags))
> >        cnts <- table(nums, tf)
> >     out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL,
> >            levels(tf)))
> >        if (all(cnts <= 1L)) {
> >            out[cbind(nums, tf)] <- vals
> >            out <- as.data.frame(out, stringsAsFactors = FALSE)
> >        }
> >        else {
> >            levs <- colSums(cnts > 1L) == 0L
> >            if (any(levs)) {
> >                inds <- tf %in% levels(tf)[levs]
> >                out[cbind(nums[inds], tf[inds])] <- vals[inds]
> >            }
> >            out <- as.data.frame(out, stringsAsFactors = FALSE)
> >            for (l in levels(tf)[!levs]) {
> >                out[[l]] <- rep.int(list(NA_character_), nrow(cnts))
> >                i <- tf == l
> >                out[[l]][unique(nums[i])] <- split(vals[i], nums[i])
> >            }
> >        }
> >        out
> >    }
> >    on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")),
> >        add = TRUE)
> >    Sys.setlocale("LC_CTYPE", "C")
> >    lines <- readLines(file)
> >    ind <- grep("^[^[:blank:]][^:]*$", lines)
> >    if (length(ind)) {
> >        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
> >stop(gettextf("Invalid DCF format.\nRegular lines must have a
> >tag.\nOffending lines start with:\n%s",
> >            paste0("  ", lines, collapse = "\n")), domain = NA)
> >    }
> >    line_is_not_empty <- !grepl("^[[:space:]]*$", lines)
> >    nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L)
> >    nums <- nums[line_is_not_empty]
> >    lines <- lines[line_is_not_empty]
> >    line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$",
> >        lines)
> >    if (any(line_is_escaped_blank))
> >        lines[line_is_escaped_blank] <- ""
> >    line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines)
> >    ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L])
> >    if (length(ind)) {
> >        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
> >stop(gettextf("Invalid DCF format.\nContinuation lines must not start a
> >record.\nOffending lines start with:\n%s",
> >            paste0("  ", lines, collapse = "\n")), domain = NA)
> >    }
> >    lengths <- rle(cumsum(line_has_tag))$lengths
> >    pos <- cumsum(lengths)
> >    tags <- sub(":.*", "", lines[line_has_tag])
> >lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "",
> >lines[line_has_tag])
> >    foldable <- rep.int(is.na(match(tags, keep.white)), lengths)
> >    lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable])
> >    lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable])
> >vals <- mapply(function(from, to) paste(lines[from:to], collapse =
> >"\n"),
> >        c(1L, pos[-length(pos)] + 1L), pos)
> >    out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos])
> >    if (!is.null(fields))
> >        out <- out[fields]
> >    out
> >}
> >Browse[2]> str(file)
> > chr "climatol_2.2.tar.gz/DESCRIPTION"
> >Browse[2]> head(file)
> >[1] "climatol_2.2.tar.gz/DESCRIPTION"
> >Browse[2]>
> >debug: if (is.character(file)) {
> >    file <- gzfile(file)
> >    on.exit(close(file))
> >}
> >Browse[2]>
> >debug: file <- gzfile(file)
> >Browse[2]>
> >debug: on.exit(close(file))
> >Browse[2]>
> >debug: if (!inherits(file, "connection")) stop("'file' must be a
> >character string or connection")
> >Browse[2]>
> >debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
> >Browse[2]> str(file)
> >Classes 'gzfile', 'connection'  atomic [1:1] 3
> >  ..- attr(*, "conn_id")=<externalptr>
> >Browse[2]> file
> >                      description                             class
> >"climatol_2.2.tar.gz/DESCRIPTION"                          "gzfile"
> >                             mode                              text
> >                             "rb"                            "text"
> >                           opened                          can read
> >                         "closed"                             "yes"
> >                        can write
> >                            "yes"
> >Browse[2]>
> >debug: return(.Internal(readDCF(file, fields, keep.white)))
> >Browse[2]>
> >Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type")) :
> >  cannot open the connection
> >In addition: Warning message:
> >In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
> >cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
> >reason 'No such file or directory'
> >>
> >
> >Well coming to debug: if (!all) return(.Internal(readDCF(file, fields,
> >keep.white))) I loose control and R returns to prompt with an error.
> >
> >Hopefully one of you can replicate this. If not then it must have
> >something with Windows OS to do. But what?
> >
> >
> >
> >Yours sincerely / Med venlig hilsen
> >
> >
> >Frede Aakmann Tøgersen
> >Specialist, M.Sc., Ph.D.
> >Plant Performance & Modeling
> >
> >Technology & Service Solutions
> >T +45 9730 5135
> >M +45 2547 6050
> >[hidden email]
> >http://www.vestas.com
> >
> >Company reg. name: Vestas Wind Systems A/S
> >This e-mail is subject to our e-mail disclaimer statement.
> >Please refer to www.vestas.com/legal/notice<http://www.vestas.com/legal/notice>
> >If you have received this e-mail in error please contact the sender.
> >
> >> -----Original Message-----
> >> From: [hidden email]
> >[mailto:[hidden email]]
> >> On Behalf Of Jeff Newmiller
> >> Sent: 20. april 2014 23:33
> >> To: Alpesh Pandya; Rui Barradas
> >> Cc: [hidden email]; Uwe Ligges
> >> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
> >>
> >> Hard to help you when the problem simply does not happen for others.
> >>
> >> As for Windows being not a focus, that is not at all true. I use it
> >regularly on
> >> Windows at work. That being said, there are thousands of packages and
> >> those each involve their own subset of R users. There are also many
> >> operating system configurations that may not all be fully tested.
> >Blaming "R"
> >> or "Windows", or blaming us for "preventing" you from getting your
> >> education (isn't that something between you and your educational
> >> institution?) are not going to be effective strategies for problem
> >solving.
> >>
> >> Are you able to use other aspects of R beyond the XML package? Have
> >you
> >> tried communicating with the maintainers of that package?
> >>
> >---------------------------------------------------------------------------
> >> Jeff Newmiller                        The     .....       .....  Go
> >Live...
> >> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
> >Go...
> >>                                       Live:   OO#.. Dead: OO#..
> >Playing
> >> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> >> /Software/Embedded Controllers)               .OO#.       .OO#.
> >rocks...1k
> >>
> >---------------------------------------------------------------------------
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya
> >> <[hidden email]> wrote:
> >> >I keep on trying from various networks but I still get the same
> >error.
> >> >I
> >> >don't this this has anything to do with network or ability to
> >download
> >> >the
> >> >package (as I can install other packages fine). This must be
> >something
> >> >in
> >> >base R or dependencies issues (that R is not spelling out).
> >> >
> >> >I know R is geared for Mac and Windows is kind of looked down upon
> >but
> >> >I
> >> >have no option but use windows and need this XML package running to
> >> >complete my education. Any help on this would be appreciated.
> >> >
> >> >
> >> >On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
> >> ><[hidden email]>wrote:
> >> >
> >> >> Thank you for response Rui.
> >> >>
> >> >> I still get the same error with this repository.
> >> >>
> >> >> Installing package into
> >> >���C:/Users/APandya/Documents/R/win-library/3.0���
> >> >> (as ���lib��� is unspecified)
> >> >> trying URL '
> >> >> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
> >> >> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >> >> opened URL
> >> >> downloaded 4.1 Mb
> >> >>
> >> >> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >> >"Type"))
> >> >> :
> >> >>   cannot open the connection
> >> >> In addition: Warning messages:
> >> >> 1: In download.file(url, destfile, method, mode = "wb", ...) :
> >> >>   downloaded length 4276224 != reported length 4288136
> >> >> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from
> >zip
> >> >file
> >> >> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >> >"Type")) :
> >> >>   cannot open compressed file 'XML/DESCRIPTION', probable reason
> >'No
> >> >such
> >> >> file or directory'
> >> >>
> >> >>
> >> >>
> >> >> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
> >> ><[hidden email]>wrote:
> >> >>
> >> >>> Hello,
> >> >>> I have package XML installed on Windows 7, R 3.0.3 and I had no
> >> >problem
> >> >>> at all. Can't you try (it worked with me)
> >> >>>
> >> >>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
> >> >>>
> >> >>> Hope this helps,
> >> >>>
> >> >>> Rui Barradas
> >> >>>
> >> >>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
> >> >>>
> >> >>>  I have tried these sources (almost all US mirrors):
> >> >>>>
> >> >>>>
> >>
> >>http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
> >> >>>> 3.0/XML_3.98-1.1.zip
> >> >>>>
> >> >http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >>
> >>http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>> contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >>
> >>http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >> >http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-
> >> 1.1.zip
> >> >>>>
> >> >>>> I have confirmed with IT that there is no restriction on
> >> >downloading this
> >> >>>> zip file from any of these sources. Also I am getting same error
> >> >when I
> >> >>>> try
> >> >>>> from my home network as well.
> >> >>>>
> >> >>>>
> >> >>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
> >> >>>> [hidden email]
> >> >>>>
> >> >>>>> wrote:
> >> >>>>>
> >> >>>>
> >> >>>>
> >> >>>>>
> >> >>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
> >> >>>>>
> >> >>>>>  @Uwe I tried the same steps from office as well as home
> >network
> >> >with
> >> >>>>>> same
> >> >>>>>> results. Are you using windows 7 with R 3.0.3?
> >> >>>>>>
> >> >>>>>> I have seen same question being asked by others without any
> >> >>>>>> resolution. Is
> >> >>>>>> anything special about XML package? I am OK use older version
> >of
> >> >>>>>> package
> >> >>>>>> but in archives there are no zip files (only gz files). Is
> >> >windows
> >> >>>>>> platform
> >> >>>>>> not recommended for R?
> >> >>>>>>
> >> >>>>>>
> >> >>>>> Right, and you can try to install these from sources.
> >> >>>>> But I doubt you need it. You still have not told us if you
> >tried
> >> >another
> >> >>>>> mirror to download the XML file from and what you local IT
> >support
> >> >tells
> >> >>>>> you while your downloads are incomplete.
> >> >>>>>
> >> >>>>> Best,
> >> >>>>> Uwe Ligges
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
> >> >>>>>> [hidden email]
> >> >>>>>>
> >> >>>>>>  wrote:
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>
> >> >>>>>>
> >> >>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
> >> >>>>>>>
> >> >>>>>>>   Thank you for response Uwe. I tried multiple times by
> >> >downloading
> >> >>>>>>> the
> >> >>>>>>>
> >> >>>>>>>> zip
> >> >>>>>>>> file from many sources but still the same error. This is a
> >> >major road
> >> >>>>>>>> block
> >> >>>>>>>> for me in using R. Appreciate any help on this.
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>  Please ask your local IT staff.
> >> >>>>>>>
> >> >>>>>>> I get, using the same mirror:
> >> >>>>>>>
> >> >>>>>>>
> >> >options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
> >> >>>>>>>
> >> >>>>>>>> install.packages("XML", lib="d:/temp")
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>> trying URL
> >'http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>>>>>
> >> >>>>>>> contrib/3.0/XML_3.98-1.1.zip'
> >> >>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >> >>>>>>> opened URL
> >> >>>>>>> downloaded 4.1 Mb
> >> >>>>>>>
> >> >>>>>>> package 'XML' successfully unpacked and MD5 sums checked
> >> >>>>>>>
> >> >>>>>>> The downloaded binary packages are in
> >> >>>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>> Best,
> >> >>>>>>> Uwe Ligges
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
> >> >>>>>>>> [hidden email]
> >> >>>>>>>>
> >> >>>>>>>>   wrote:
> >> >>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>     Works for me.
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>> Best,
> >> >>>>>>>>> Uwe Ligges
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
> >> >>>>>>>>>
> >> >>>>>>>>>    Using install.package('XML') command produces this
> >error:
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>> trying URL
> >> >>>>>>>>>> '
> >> >>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
> >> >>>>>>>>>> '
> >> >>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1
> >Mb)
> >> >>>>>>>>>> opened URL
> >> >>>>>>>>>> downloaded 4.1 Mb
> >> >>>>>>>>>>
> >> >>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
> >> >c("Package",
> >> >>>>>>>>>> "Type")) :
> >> >>>>>>>>>>       cannot open the connection
> >> >>>>>>>>>> In addition: Warning messages:
> >> >>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb",
> >...)
> >> >:
> >> >>>>>>>>>>       downloaded length 4276224 != reported length 4288136
> >> >>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
> >> >from zip
> >> >>>>>>>>>> file
> >> >>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
> >> >c("Package",
> >> >>>>>>>>>> "Type"))
> >> >>>>>>>>>> :
> >> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
> >probable
> >> >>>>>>>>>> reason
> >> >>>>>>>>>> 'No
> >> >>>>>>>>>> such
> >> >>>>>>>>>> file or directory'
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
> >> >directly
> >> >>>>>>>>>> from
> >> >>>>>>>>>> cran
> >> >>>>>>>>>> site. But this zip file is not a valid archive (cannot
> >open
> >> >using
> >> >>>>>>>>>> winzip).
> >> >>>>>>>>>> Also trying to install using this downloaded file produces
> >> >the
> >> >>>>>>>>>> following
> >> >>>>>>>>>> error:
> >> >>>>>>>>>>
> >> >>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
> >> >>>>>>>>>> win-library/3.0'
> >> >>>>>>>>>> (as 'lib' is unspecified)
> >> >>>>>>>>>> Warning in install.packages :
> >> >>>>>>>>>>       error 1 in extracting from zip file
> >> >>>>>>>>>> Warning in install.packages :
> >> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
> >probable
> >> >>>>>>>>>> reason
> >> >>>>>>>>>> 'No
> >> >>>>>>>>>> such
> >> >>>>>>>>>> file or directory'
> >> >>>>>>>>>> Error in install.packages : cannot open the connection
> >> >>>>>>>>>>
> >> >>>>>>>>>> I  downloaded this zip file from multiple sources and
> >tried
> >> >to
> >> >>>>>>>>>> install
> >> >>>>>>>>>> with
> >> >>>>>>>>>> same result.
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>
> >> >>>>>>
> >> >>>>
> >> >>>>
> >> >>
> >> >>
> >> >> --
> >> >> Thanks and Regards
> >> >> Alpesh
> >> >>
> >>
> >> ______________________________________________
> >> [hidden email] mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-
> >> guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: R 3.0.3, Windows 7: Problem installing XML package

Milan Bouchet-Valat
In reply to this post by Frede Aakmann Tøgersen-2
Le lundi 21 avril 2014 à 11:38 +0200, Frede Aakmann Tøgersen a écrit :
> Hi
>
> Couldn't find a zip file in the archives.
>
> Why didn't 'R CMD build' (in a command shell on Windows) not make a
> zip file? I did try to build from the climatol library that holds the
> typical files as DESCRIPTION, LICENSE, etc. as well as folders like R,
> etc.
R CMD build produces *source* packages, and .zip packages are *binary*.

> Did you see the debug information on read.fcf? For me it seems like R
> has open a file handler to the DESCRIPTION file. Wouldn't the error
> already be thrown there and not when read.fcf is called if the .tar.gz
> format was the problem?
>
> I'll try and locate a zip
Does install.packages(choose.file(), type="source") work? I'm not sure
what utils:::menuInstallLocal() does.


Regards


> Sendt fra Samsung mobil
>
>
> -------- Oprindelig meddelelse --------
> Fra: Jeff Newmiller
> Dato:21/04/2014 09.44 (GMT+01:00)
> Til: Frede Aakmann Tøgersen ,Alpesh Pandya ,Rui Barradas
> Cc: [hidden email],Uwe Ligges ,Duncan Murdoch
> Emne: RE: [R] R 3.0.3, Windows 7: Problem installing XML package
>
> Frede... Windows uses zip files (binary, aka pre-compiled format) for packages by default, because most installations don't have the development tools installed. You need to setup RTools and use the "source" option to install_package in order to handle the tar.gz package file, or download and install the zip file instead.
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
>                                       Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> On April 20, 2014 11:01:17 PM PDT, "Frede Aakmann Tøgersen" <[hidden email]> wrote:
> >Well now, I think I have seen something similar to Alpesh.
> >
> >Recently I needed the climatol package that I have used some time ago.
> >It is not maintained anymore but I downloaded the latest version,
> >climatol_2.2.tar.gz,  from archives
> >(http://cran.r-project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz
> >) . Trying to install that package from local file  using R-3.1.0 on
> >Windows 8  resulted in this:
> >
> >## From R Console
> >> utils:::menuInstallLocal()
> >Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type")) :
> >  cannot open the connection
> >In addition: Warning messages:
> >1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
> >file
> >2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
> >:
> >cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
> >reason 'No such file or directory'
> >>
> >
> >And yes I know where the file is located, since choose.files() is used.
> >
> >However I tried the same on our linux (R-3.0.2) cluster and it
> >succeeded:
> >
> >[frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz
> >* installing to library
> >?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library?
> >* installing *source* package ?climatol? ...
> >** R
> >** data
> >** inst
> >** preparing package for lazy loading
> >** help
> >*** installing help indices
> >** building package indices
> >** installing vignettes
> >** testing if installed package can be loaded
> >* DONE (climatol)
> >[frtog@dkrdsfshn2 ~]$ R
> >
> >R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> >Copyright (C) 2013 The R Foundation for Statistical Computing
> >Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under certain conditions.
> >Type 'license()' or 'licence()' for distribution details.
> >
> >  Natural language support but running in an English locale
> >
> >R is a collaborative project with many contributors.
> >Type 'contributors()' for more information and
> >'citation()' on how to cite R or R packages in publications.
> >
> >Type 'demo()' for some demos, 'help()' for on-line help, or
> >'help.start()' for an HTML browser interface to help.
> >Type 'q()' to quit R.
> >
> >> library("climatol")
> >> ?rosavent
> >> q()
> >Save workspace image? [y/n/c]: n
> >[frtog@dkrdsfshn2 ~]$
> >
> >
> >Now unzipping and untaring climatol_2.2.tar.gz I thought to examine
> >whether I could build the package on my Windows box. Only R stuff and
> >no foreign language as C, FORTRAN, etc. so it should be easy.
> >
> >## Command shell in Windows
> >Microsoft Windows [Version 6.2.9200]
> >(c) 2012 Microsoft Corporation. All rights reserved.
> >
> >C:\Users\frtog>cd Desktop
> >
> >C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build
> >climatol
> >* checking for file 'climatol/DESCRIPTION' ... OK
> >* preparing 'climatol':
> >* checking DESCRIPTION meta-information ... OK
> >* checking for LF line-endings in source and make files
> >* checking for empty or unneeded directories
> >* looking to see if a 'data/datalist' file should be added
> >* building 'climatol_2.2.tar.gz'
> >
> >Now trying to install from that local file I Still got the same error
> >as above.
> >
> >
> >
> >Trying to do some debugging on read.dcf() (Emacs/ESS)
> >
> >
> >R version 3.1.0 (2014-04-10) -- "Spring Dance"
> >Copyright (C) 2014 The R Foundation for Statistical Computing
> >Platform: x86_64-w64-mingw32/x64 (64-bit)
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under certain conditions.
> >Type 'license()' or 'licence()' for distribution details.
> >
> >  Natural language support but running in an English locale
> >
> >R is a collaborative project with many contributors.
> >Type 'contributors()' for more information and
> >'citation()' on how to cite R or R packages in publications.
> >
> >Type 'demo()' for some demos, 'help()' for on-line help, or
> >'help.start()' for an HTML browser interface to help.
> >Type 'q()' to quit R.
> >
> >> > options(chmhelp=FALSE, help_type="text")
> >> options(STERM='iESS', str.dendrogram.last="'",
> >editor='emacsclient.exe', show.error.locations=TRUE)
> >> debug(read.dcf)
> >> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL)
> >debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type"))
> >debug: {
> >    if (is.character(file)) {
> >        file <- gzfile(file)
> >        on.exit(close(file))
> >    }
> >    if (!inherits(file, "connection"))
> >        stop("'file' must be a character string or connection")
> >    if (!all)
> >        return(.Internal(readDCF(file, fields, keep.white)))
> >    .assemble_things_into_a_data_frame <- function(tags, vals,
> >        nums) {
> >        tf <- factor(tags, levels = unique(tags))
> >        cnts <- table(nums, tf)
> >     out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL,
> >            levels(tf)))
> >        if (all(cnts <= 1L)) {
> >            out[cbind(nums, tf)] <- vals
> >            out <- as.data.frame(out, stringsAsFactors = FALSE)
> >        }
> >        else {
> >            levs <- colSums(cnts > 1L) == 0L
> >            if (any(levs)) {
> >                inds <- tf %in% levels(tf)[levs]
> >                out[cbind(nums[inds], tf[inds])] <- vals[inds]
> >            }
> >            out <- as.data.frame(out, stringsAsFactors = FALSE)
> >            for (l in levels(tf)[!levs]) {
> >                out[[l]] <- rep.int(list(NA_character_), nrow(cnts))
> >                i <- tf == l
> >                out[[l]][unique(nums[i])] <- split(vals[i], nums[i])
> >            }
> >        }
> >        out
> >    }
> >    on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")),
> >        add = TRUE)
> >    Sys.setlocale("LC_CTYPE", "C")
> >    lines <- readLines(file)
> >    ind <- grep("^[^[:blank:]][^:]*$", lines)
> >    if (length(ind)) {
> >        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
> >stop(gettextf("Invalid DCF format.\nRegular lines must have a
> >tag.\nOffending lines start with:\n%s",
> >            paste0("  ", lines, collapse = "\n")), domain = NA)
> >    }
> >    line_is_not_empty <- !grepl("^[[:space:]]*$", lines)
> >    nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L)
> >    nums <- nums[line_is_not_empty]
> >    lines <- lines[line_is_not_empty]
> >    line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$",
> >        lines)
> >    if (any(line_is_escaped_blank))
> >        lines[line_is_escaped_blank] <- ""
> >    line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines)
> >    ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L])
> >    if (length(ind)) {
> >        lines <- strtrim(lines[ind], 0.7 * getOption("width"))
> >stop(gettextf("Invalid DCF format.\nContinuation lines must not start a
> >record.\nOffending lines start with:\n%s",
> >            paste0("  ", lines, collapse = "\n")), domain = NA)
> >    }
> >    lengths <- rle(cumsum(line_has_tag))$lengths
> >    pos <- cumsum(lengths)
> >    tags <- sub(":.*", "", lines[line_has_tag])
> >lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "",
> >lines[line_has_tag])
> >    foldable <- rep.int(is.na(match(tags, keep.white)), lengths)
> >    lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable])
> >    lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable])
> >vals <- mapply(function(from, to) paste(lines[from:to], collapse =
> >"\n"),
> >        c(1L, pos[-length(pos)] + 1L), pos)
> >    out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos])
> >    if (!is.null(fields))
> >        out <- out[fields]
> >    out
> >}
> >Browse[2]> str(file)
> > chr "climatol_2.2.tar.gz/DESCRIPTION"
> >Browse[2]> head(file)
> >[1] "climatol_2.2.tar.gz/DESCRIPTION"
> >Browse[2]>
> >debug: if (is.character(file)) {
> >    file <- gzfile(file)
> >    on.exit(close(file))
> >}
> >Browse[2]>
> >debug: file <- gzfile(file)
> >Browse[2]>
> >debug: on.exit(close(file))
> >Browse[2]>
> >debug: if (!inherits(file, "connection")) stop("'file' must be a
> >character string or connection")
> >Browse[2]>
> >debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
> >Browse[2]> str(file)
> >Classes 'gzfile', 'connection'  atomic [1:1] 3
> >  ..- attr(*, "conn_id")=<externalptr>
> >Browse[2]> file
> >                      description                             class
> >"climatol_2.2.tar.gz/DESCRIPTION"                          "gzfile"
> >                             mode                              text
> >                             "rb"                            "text"
> >                           opened                          can read
> >                         "closed"                             "yes"
> >                        can write
> >                            "yes"
> >Browse[2]>
> >debug: return(.Internal(readDCF(file, fields, keep.white)))
> >Browse[2]>
> >Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >"Type")) :
> >  cannot open the connection
> >In addition: Warning message:
> >In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
> >cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
> >reason 'No such file or directory'
> >>
> >
> >Well coming to debug: if (!all) return(.Internal(readDCF(file, fields,
> >keep.white))) I loose control and R returns to prompt with an error.
> >
> >Hopefully one of you can replicate this. If not then it must have
> >something with Windows OS to do. But what?
> >
> >
> >
> >Yours sincerely / Med venlig hilsen
> >
> >
> >Frede Aakmann Tøgersen
> >Specialist, M.Sc., Ph.D.
> >Plant Performance & Modeling
> >
> >Technology & Service Solutions
> >T +45 9730 5135
> >M +45 2547 6050
> >[hidden email]
> >http://www.vestas.com
> >
> >Company reg. name: Vestas Wind Systems A/S
> >This e-mail is subject to our e-mail disclaimer statement.
> >Please refer to www.vestas.com/legal/notice<http://www.vestas.com/legal/notice>
> >If you have received this e-mail in error please contact the sender.
> >
> >> -----Original Message-----
> >> From: [hidden email]
> >[mailto:[hidden email]]
> >> On Behalf Of Jeff Newmiller
> >> Sent: 20. april 2014 23:33
> >> To: Alpesh Pandya; Rui Barradas
> >> Cc: [hidden email]; Uwe Ligges
> >> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
> >>
> >> Hard to help you when the problem simply does not happen for others.
> >>
> >> As for Windows being not a focus, that is not at all true. I use it
> >regularly on
> >> Windows at work. That being said, there are thousands of packages and
> >> those each involve their own subset of R users. There are also many
> >> operating system configurations that may not all be fully tested.
> >Blaming "R"
> >> or "Windows", or blaming us for "preventing" you from getting your
> >> education (isn't that something between you and your educational
> >> institution?) are not going to be effective strategies for problem
> >solving.
> >>
> >> Are you able to use other aspects of R beyond the XML package? Have
> >you
> >> tried communicating with the maintainers of that package?
> >>
> >---------------------------------------------------------------------------
> >> Jeff Newmiller                        The     .....       .....  Go
> >Live...
> >> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
> >Go...
> >>                                       Live:   OO#.. Dead: OO#..
> >Playing
> >> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> >> /Software/Embedded Controllers)               .OO#.       .OO#.
> >rocks...1k
> >>
> >---------------------------------------------------------------------------
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya
> >> <[hidden email]> wrote:
> >> >I keep on trying from various networks but I still get the same
> >error.
> >> >I
> >> >don't this this has anything to do with network or ability to
> >download
> >> >the
> >> >package (as I can install other packages fine). This must be
> >something
> >> >in
> >> >base R or dependencies issues (that R is not spelling out).
> >> >
> >> >I know R is geared for Mac and Windows is kind of looked down upon
> >but
> >> >I
> >> >have no option but use windows and need this XML package running to
> >> >complete my education. Any help on this would be appreciated.
> >> >
> >> >
> >> >On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
> >> ><[hidden email]>wrote:
> >> >
> >> >> Thank you for response Rui.
> >> >>
> >> >> I still get the same error with this repository.
> >> >>
> >> >> Installing package into
> >> >���C:/Users/APandya/Documents/R/win-library/3.0���
> >> >> (as ���lib��� is unspecified)
> >> >> trying URL '
> >> >> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
> >> >> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >> >> opened URL
> >> >> downloaded 4.1 Mb
> >> >>
> >> >> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >> >"Type"))
> >> >> :
> >> >>   cannot open the connection
> >> >> In addition: Warning messages:
> >> >> 1: In download.file(url, destfile, method, mode = "wb", ...) :
> >> >>   downloaded length 4276224 != reported length 4288136
> >> >> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from
> >zip
> >> >file
> >> >> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >> >"Type")) :
> >> >>   cannot open compressed file 'XML/DESCRIPTION', probable reason
> >'No
> >> >such
> >> >> file or directory'
> >> >>
> >> >>
> >> >>
> >> >> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
> >> ><[hidden email]>wrote:
> >> >>
> >> >>> Hello,
> >> >>> I have package XML installed on Windows 7, R 3.0.3 and I had no
> >> >problem
> >> >>> at all. Can't you try (it worked with me)
> >> >>>
> >> >>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
> >> >>>
> >> >>> Hope this helps,
> >> >>>
> >> >>> Rui Barradas
> >> >>>
> >> >>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
> >> >>>
> >> >>>  I have tried these sources (almost all US mirrors):
> >> >>>>
> >> >>>>
> >>
> >>http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
> >> >>>> 3.0/XML_3.98-1.1.zip
> >> >>>>
> >> >http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >>
> >>http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>> contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >>
> >>http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >> >>>>
> >> >http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-
> >> 1.1.zip
> >> >>>>
> >> >>>> I have confirmed with IT that there is no restriction on
> >> >downloading this
> >> >>>> zip file from any of these sources. Also I am getting same error
> >> >when I
> >> >>>> try
> >> >>>> from my home network as well.
> >> >>>>
> >> >>>>
> >> >>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
> >> >>>> [hidden email]
> >> >>>>
> >> >>>>> wrote:
> >> >>>>>
> >> >>>>
> >> >>>>
> >> >>>>>
> >> >>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
> >> >>>>>
> >> >>>>>  @Uwe I tried the same steps from office as well as home
> >network
> >> >with
> >> >>>>>> same
> >> >>>>>> results. Are you using windows 7 with R 3.0.3?
> >> >>>>>>
> >> >>>>>> I have seen same question being asked by others without any
> >> >>>>>> resolution. Is
> >> >>>>>> anything special about XML package? I am OK use older version
> >of
> >> >>>>>> package
> >> >>>>>> but in archives there are no zip files (only gz files). Is
> >> >windows
> >> >>>>>> platform
> >> >>>>>> not recommended for R?
> >> >>>>>>
> >> >>>>>>
> >> >>>>> Right, and you can try to install these from sources.
> >> >>>>> But I doubt you need it. You still have not told us if you
> >tried
> >> >another
> >> >>>>> mirror to download the XML file from and what you local IT
> >support
> >> >tells
> >> >>>>> you while your downloads are incomplete.
> >> >>>>>
> >> >>>>> Best,
> >> >>>>> Uwe Ligges
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
> >> >>>>>> [hidden email]
> >> >>>>>>
> >> >>>>>>  wrote:
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>
> >> >>>>>>
> >> >>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
> >> >>>>>>>
> >> >>>>>>>   Thank you for response Uwe. I tried multiple times by
> >> >downloading
> >> >>>>>>> the
> >> >>>>>>>
> >> >>>>>>>> zip
> >> >>>>>>>> file from many sources but still the same error. This is a
> >> >major road
> >> >>>>>>>> block
> >> >>>>>>>> for me in using R. Appreciate any help on this.
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>  Please ask your local IT staff.
> >> >>>>>>>
> >> >>>>>>> I get, using the same mirror:
> >> >>>>>>>
> >> >>>>>>>
> >> >options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
> >> >>>>>>>
> >> >>>>>>>> install.packages("XML", lib="d:/temp")
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>> trying URL
> >'http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>>>>>
> >> >>>>>>> contrib/3.0/XML_3.98-1.1.zip'
> >> >>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >> >>>>>>> opened URL
> >> >>>>>>> downloaded 4.1 Mb
> >> >>>>>>>
> >> >>>>>>> package 'XML' successfully unpacked and MD5 sums checked
> >> >>>>>>>
> >> >>>>>>> The downloaded binary packages are in
> >> >>>>>>>           d:\temp\RtmpqMqL8L\downloaded_packages
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>> Best,
> >> >>>>>>> Uwe Ligges
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>  On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
> >> >>>>>>>> [hidden email]
> >> >>>>>>>>
> >> >>>>>>>>   wrote:
> >> >>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>     Works for me.
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>> Best,
> >> >>>>>>>>> Uwe Ligges
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
> >> >>>>>>>>>
> >> >>>>>>>>>    Using install.package('XML') command produces this
> >error:
> >> >>>>>>>>>
> >> >>>>>>>>>
> >> >>>>>>>>>> trying URL
> >> >>>>>>>>>> '
> >> >>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >> >>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
> >> >>>>>>>>>> '
> >> >>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1
> >Mb)
> >> >>>>>>>>>> opened URL
> >> >>>>>>>>>> downloaded 4.1 Mb
> >> >>>>>>>>>>
> >> >>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
> >> >c("Package",
> >> >>>>>>>>>> "Type")) :
> >> >>>>>>>>>>       cannot open the connection
> >> >>>>>>>>>> In addition: Warning messages:
> >> >>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb",
> >...)
> >> >:
> >> >>>>>>>>>>       downloaded length 4276224 != reported length 4288136
> >> >>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
> >> >from zip
> >> >>>>>>>>>> file
> >> >>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
> >> >c("Package",
> >> >>>>>>>>>> "Type"))
> >> >>>>>>>>>> :
> >> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
> >probable
> >> >>>>>>>>>> reason
> >> >>>>>>>>>> 'No
> >> >>>>>>>>>> such
> >> >>>>>>>>>> file or directory'
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
> >> >directly
> >> >>>>>>>>>> from
> >> >>>>>>>>>> cran
> >> >>>>>>>>>> site. But this zip file is not a valid archive (cannot
> >open
> >> >using
> >> >>>>>>>>>> winzip).
> >> >>>>>>>>>> Also trying to install using this downloaded file produces
> >> >the
> >> >>>>>>>>>> following
> >> >>>>>>>>>> error:
> >> >>>>>>>>>>
> >> >>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
> >> >>>>>>>>>> win-library/3.0'
> >> >>>>>>>>>> (as 'lib' is unspecified)
> >> >>>>>>>>>> Warning in install.packages :
> >> >>>>>>>>>>       error 1 in extracting from zip file
> >> >>>>>>>>>> Warning in install.packages :
> >> >>>>>>>>>>       cannot open compressed file 'XML/DESCRIPTION',
> >probable
> >> >>>>>>>>>> reason
> >> >>>>>>>>>> 'No
> >> >>>>>>>>>> such
> >> >>>>>>>>>> file or directory'
> >> >>>>>>>>>> Error in install.packages : cannot open the connection
> >> >>>>>>>>>>
> >> >>>>>>>>>> I  downloaded this zip file from multiple sources and
> >tried
> >> >to
> >> >>>>>>>>>> install
> >> >>>>>>>>>> with
> >> >>>>>>>>>> same result.
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>>>
> >> >>>>>>>>
> >> >>>>>>>>
> >> >>>>>>
> >> >>>>>>
> >> >>>>
> >> >>>>
> >> >>
> >> >>
> >> >> --
> >> >> Thanks and Regards
> >> >> Alpesh
> >> >>
> >>
> >> ______________________________________________
> >> [hidden email] mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-
> >> guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
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Re: R 3.0.3, Windows 7: Problem installing XML package

Duncan Murdoch-2
In reply to this post by Milan Bouchet-Valat
On 21/04/2014, 7:10 AM, Milan Bouchet-Valat wrote:

> Le lundi 21 avril 2014 à 11:38 +0200, Frede Aakmann Tøgersen a écrit :
>> Hi
>>
>> Couldn't find a zip file in the archives.
>>
>> Why didn't 'R CMD build' (in a command shell on Windows) not make a
>> zip file? I did try to build from the climatol library that holds the
>> typical files as DESCRIPTION, LICENSE, etc. as well as folders like R,
>> etc.
> R CMD build produces *source* packages, and .zip packages are *binary*.
>
>> Did you see the debug information on read.fcf? For me it seems like R
>> has open a file handler to the DESCRIPTION file. Wouldn't the error
>> already be thrown there and not when read.fcf is called if the .tar.gz
>> format was the problem?
>>
>> I'll try and locate a zip
> Does install.packages(choose.file(), type="source") work?

That will also need "repos=NULL", or it will go out to a repository to
look for the package.

That should work if the package doesn't have compiled code.  It will
handle compiled code only if Frede has the appropriate tools installed.


I'm not sure
> what utils:::menuInstallLocal() does.

It is essentially

install.packages(choose.file(), type="binary", repos=NULL)

so it's not what Frede needs.

Duncan

>
>
> Regards
>
>
>> Sendt fra Samsung mobil
>>
>>
>> -------- Oprindelig meddelelse --------
>> Fra: Jeff Newmiller
>> Dato:21/04/2014 09.44 (GMT+01:00)
>> Til: Frede Aakmann Tøgersen ,Alpesh Pandya ,Rui Barradas
>> Cc: [hidden email],Uwe Ligges ,Duncan Murdoch
>> Emne: RE: [R] R 3.0.3, Windows 7: Problem installing XML package
>>
>> Frede... Windows uses zip files (binary, aka pre-compiled format) for packages by default, because most installations don't have the development tools installed. You need to setup RTools and use the "source" option to install_package in order to handle the tar.gz package file, or download and install the zip file instead.
>> ---------------------------------------------------------------------------
>> Jeff Newmiller                        The     .....       .....  Go Live...
>> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
>>                                        Live:   OO#.. Dead: OO#..  Playing
>> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
>> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
>> ---------------------------------------------------------------------------
>> Sent from my phone. Please excuse my brevity.
>>
>> On April 20, 2014 11:01:17 PM PDT, "Frede Aakmann Tøgersen" <[hidden email]> wrote:
>>> Well now, I think I have seen something similar to Alpesh.
>>>
>>> Recently I needed the climatol package that I have used some time ago.
>>> It is not maintained anymore but I downloaded the latest version,
>>> climatol_2.2.tar.gz,  from archives
>>> (http://cran.r-project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz
>>> ) . Trying to install that package from local file  using R-3.1.0 on
>>> Windows 8  resulted in this:
>>>
>>> ## From R Console
>>>> utils:::menuInstallLocal()
>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>> "Type")) :
>>>   cannot open the connection
>>> In addition: Warning messages:
>>> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
>>> file
>>> 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
>>> :
>>> cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
>>> reason 'No such file or directory'
>>>>
>>>
>>> And yes I know where the file is located, since choose.files() is used.
>>>
>>> However I tried the same on our linux (R-3.0.2) cluster and it
>>> succeeded:
>>>
>>> [frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz
>>> * installing to library
>>> ?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library?
>>> * installing *source* package ?climatol? ...
>>> ** R
>>> ** data
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** installing vignettes
>>> ** testing if installed package can be loaded
>>> * DONE (climatol)
>>> [frtog@dkrdsfshn2 ~]$ R
>>>
>>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>>> Copyright (C) 2013 The R Foundation for Statistical Computing
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>>   Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>> library("climatol")
>>>> ?rosavent
>>>> q()
>>> Save workspace image? [y/n/c]: n
>>> [frtog@dkrdsfshn2 ~]$
>>>
>>>
>>> Now unzipping and untaring climatol_2.2.tar.gz I thought to examine
>>> whether I could build the package on my Windows box. Only R stuff and
>>> no foreign language as C, FORTRAN, etc. so it should be easy.
>>>
>>> ## Command shell in Windows
>>> Microsoft Windows [Version 6.2.9200]
>>> (c) 2012 Microsoft Corporation. All rights reserved.
>>>
>>> C:\Users\frtog>cd Desktop
>>>
>>> C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build
>>> climatol
>>> * checking for file 'climatol/DESCRIPTION' ... OK
>>> * preparing 'climatol':
>>> * checking DESCRIPTION meta-information ... OK
>>> * checking for LF line-endings in source and make files
>>> * checking for empty or unneeded directories
>>> * looking to see if a 'data/datalist' file should be added
>>> * building 'climatol_2.2.tar.gz'
>>>
>>> Now trying to install from that local file I Still got the same error
>>> as above.
>>>
>>>
>>>
>>> Trying to do some debugging on read.dcf() (Emacs/ESS)
>>>
>>>
>>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>>> Copyright (C) 2014 The R Foundation for Statistical Computing
>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>>   Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>>> options(chmhelp=FALSE, help_type="text")
>>>> options(STERM='iESS', str.dendrogram.last="'",
>>> editor='emacsclient.exe', show.error.locations=TRUE)
>>>> debug(read.dcf)
>>>> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL)
>>> debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>> "Type"))
>>> debug: {
>>>     if (is.character(file)) {
>>>         file <- gzfile(file)
>>>         on.exit(close(file))
>>>     }
>>>     if (!inherits(file, "connection"))
>>>         stop("'file' must be a character string or connection")
>>>     if (!all)
>>>         return(.Internal(readDCF(file, fields, keep.white)))
>>>     .assemble_things_into_a_data_frame <- function(tags, vals,
>>>         nums) {
>>>         tf <- factor(tags, levels = unique(tags))
>>>         cnts <- table(nums, tf)
>>>      out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL,
>>>             levels(tf)))
>>>         if (all(cnts <= 1L)) {
>>>             out[cbind(nums, tf)] <- vals
>>>             out <- as.data.frame(out, stringsAsFactors = FALSE)
>>>         }
>>>         else {
>>>             levs <- colSums(cnts > 1L) == 0L
>>>             if (any(levs)) {
>>>                 inds <- tf %in% levels(tf)[levs]
>>>                 out[cbind(nums[inds], tf[inds])] <- vals[inds]
>>>             }
>>>             out <- as.data.frame(out, stringsAsFactors = FALSE)
>>>             for (l in levels(tf)[!levs]) {
>>>                 out[[l]] <- rep.int(list(NA_character_), nrow(cnts))
>>>                 i <- tf == l
>>>                 out[[l]][unique(nums[i])] <- split(vals[i], nums[i])
>>>             }
>>>         }
>>>         out
>>>     }
>>>     on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")),
>>>         add = TRUE)
>>>     Sys.setlocale("LC_CTYPE", "C")
>>>     lines <- readLines(file)
>>>     ind <- grep("^[^[:blank:]][^:]*$", lines)
>>>     if (length(ind)) {
>>>         lines <- strtrim(lines[ind], 0.7 * getOption("width"))
>>> stop(gettextf("Invalid DCF format.\nRegular lines must have a
>>> tag.\nOffending lines start with:\n%s",
>>>             paste0("  ", lines, collapse = "\n")), domain = NA)
>>>     }
>>>     line_is_not_empty <- !grepl("^[[:space:]]*$", lines)
>>>     nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L)
>>>     nums <- nums[line_is_not_empty]
>>>     lines <- lines[line_is_not_empty]
>>>     line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$",
>>>         lines)
>>>     if (any(line_is_escaped_blank))
>>>         lines[line_is_escaped_blank] <- ""
>>>     line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines)
>>>     ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L])
>>>     if (length(ind)) {
>>>         lines <- strtrim(lines[ind], 0.7 * getOption("width"))
>>> stop(gettextf("Invalid DCF format.\nContinuation lines must not start a
>>> record.\nOffending lines start with:\n%s",
>>>             paste0("  ", lines, collapse = "\n")), domain = NA)
>>>     }
>>>     lengths <- rle(cumsum(line_has_tag))$lengths
>>>     pos <- cumsum(lengths)
>>>     tags <- sub(":.*", "", lines[line_has_tag])
>>> lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "",
>>> lines[line_has_tag])
>>>     foldable <- rep.int(is.na(match(tags, keep.white)), lengths)
>>>     lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable])
>>>     lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable])
>>> vals <- mapply(function(from, to) paste(lines[from:to], collapse =
>>> "\n"),
>>>         c(1L, pos[-length(pos)] + 1L), pos)
>>>     out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos])
>>>     if (!is.null(fields))
>>>         out <- out[fields]
>>>     out
>>> }
>>> Browse[2]> str(file)
>>> chr "climatol_2.2.tar.gz/DESCRIPTION"
>>> Browse[2]> head(file)
>>> [1] "climatol_2.2.tar.gz/DESCRIPTION"
>>> Browse[2]>
>>> debug: if (is.character(file)) {
>>>     file <- gzfile(file)
>>>     on.exit(close(file))
>>> }
>>> Browse[2]>
>>> debug: file <- gzfile(file)
>>> Browse[2]>
>>> debug: on.exit(close(file))
>>> Browse[2]>
>>> debug: if (!inherits(file, "connection")) stop("'file' must be a
>>> character string or connection")
>>> Browse[2]>
>>> debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
>>> Browse[2]> str(file)
>>> Classes 'gzfile', 'connection'  atomic [1:1] 3
>>>   ..- attr(*, "conn_id")=<externalptr>
>>> Browse[2]> file
>>>                       description                             class
>>> "climatol_2.2.tar.gz/DESCRIPTION"                          "gzfile"
>>>                              mode                              text
>>>                              "rb"                            "text"
>>>                            opened                          can read
>>>                          "closed"                             "yes"
>>>                         can write
>>>                             "yes"
>>> Browse[2]>
>>> debug: return(.Internal(readDCF(file, fields, keep.white)))
>>> Browse[2]>
>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>> "Type")) :
>>>   cannot open the connection
>>> In addition: Warning message:
>>> In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>>> cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION', probable
>>> reason 'No such file or directory'
>>>>
>>>
>>> Well coming to debug: if (!all) return(.Internal(readDCF(file, fields,
>>> keep.white))) I loose control and R returns to prompt with an error.
>>>
>>> Hopefully one of you can replicate this. If not then it must have
>>> something with Windows OS to do. But what?
>>>
>>>
>>>
>>> Yours sincerely / Med venlig hilsen
>>>
>>>
>>> Frede Aakmann Tøgersen
>>> Specialist, M.Sc., Ph.D.
>>> Plant Performance & Modeling
>>>
>>> Technology & Service Solutions
>>> T +45 9730 5135
>>> M +45 2547 6050
>>> [hidden email]
>>> http://www.vestas.com
>>>
>>> Company reg. name: Vestas Wind Systems A/S
>>> This e-mail is subject to our e-mail disclaimer statement.
>>> Please refer to www.vestas.com/legal/notice<http://www.vestas.com/legal/notice>
>>> If you have received this e-mail in error please contact the sender.
>>>
>>>> -----Original Message-----
>>>> From: [hidden email]
>>> [mailto:[hidden email]]
>>>> On Behalf Of Jeff Newmiller
>>>> Sent: 20. april 2014 23:33
>>>> To: Alpesh Pandya; Rui Barradas
>>>> Cc: [hidden email]; Uwe Ligges
>>>> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
>>>>
>>>> Hard to help you when the problem simply does not happen for others.
>>>>
>>>> As for Windows being not a focus, that is not at all true. I use it
>>> regularly on
>>>> Windows at work. That being said, there are thousands of packages and
>>>> those each involve their own subset of R users. There are also many
>>>> operating system configurations that may not all be fully tested.
>>> Blaming "R"
>>>> or "Windows", or blaming us for "preventing" you from getting your
>>>> education (isn't that something between you and your educational
>>>> institution?) are not going to be effective strategies for problem
>>> solving.
>>>>
>>>> Are you able to use other aspects of R beyond the XML package? Have
>>> you
>>>> tried communicating with the maintainers of that package?
>>>>
>>> ---------------------------------------------------------------------------
>>>> Jeff Newmiller                        The     .....       .....  Go
>>> Live...
>>>> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
>>> Go...
>>>>                                        Live:   OO#.. Dead: OO#..
>>> Playing
>>>> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
>>>> /Software/Embedded Controllers)               .OO#.       .OO#.
>>> rocks...1k
>>>>
>>> ---------------------------------------------------------------------------
>>>> Sent from my phone. Please excuse my brevity.
>>>>
>>>> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya
>>>> <[hidden email]> wrote:
>>>>> I keep on trying from various networks but I still get the same
>>> error.
>>>>> I
>>>>> don't this this has anything to do with network or ability to
>>> download
>>>>> the
>>>>> package (as I can install other packages fine). This must be
>>> something
>>>>> in
>>>>> base R or dependencies issues (that R is not spelling out).
>>>>>
>>>>> I know R is geared for Mac and Windows is kind of looked down upon
>>> but
>>>>> I
>>>>> have no option but use windows and need this XML package running to
>>>>> complete my education. Any help on this would be appreciated.
>>>>>
>>>>>
>>>>> On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
>>>>> <[hidden email]>wrote:
>>>>>
>>>>>> Thank you for response Rui.
>>>>>>
>>>>>> I still get the same error with this repository.
>>>>>>
>>>>>> Installing package into
>>>>> ���C:/Users/APandya/Documents/R/win-library/3.0���
>>>>>> (as ���lib��� is unspecified)
>>>>>> trying URL '
>>>>>> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>> opened URL
>>>>>> downloaded 4.1 Mb
>>>>>>
>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>> "Type"))
>>>>>> :
>>>>>>    cannot open the connection
>>>>>> In addition: Warning messages:
>>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>>>>>>    downloaded length 4276224 != reported length 4288136
>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from
>>> zip
>>>>> file
>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
>>>>> "Type")) :
>>>>>>    cannot open compressed file 'XML/DESCRIPTION', probable reason
>>> 'No
>>>>> such
>>>>>> file or directory'
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
>>>>> <[hidden email]>wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>> I have package XML installed on Windows 7, R 3.0.3 and I had no
>>>>> problem
>>>>>>> at all. Can't you try (it worked with me)
>>>>>>>
>>>>>>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
>>>>>>>
>>>>>>> Hope this helps,
>>>>>>>
>>>>>>> Rui Barradas
>>>>>>>
>>>>>>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
>>>>>>>
>>>>>>>   I have tried these sources (almost all US mirrors):
>>>>>>>>
>>>>>>>>
>>>>
>>>> http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>>>>>
>>> http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>>>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
>>>>>>>> 3.0/XML_3.98-1.1.zip
>>>>>>>>
>>>>> http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>>>>>
>>>>
>>>> http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>>>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>>>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>>>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>>>>>
>>>>
>>>> http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-1.1.zip
>>>>>>>>
>>>>> http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-
>>>> 1.1.zip
>>>>>>>>
>>>>>>>> I have confirmed with IT that there is no restriction on
>>>>> downloading this
>>>>>>>> zip file from any of these sources. Also I am getting same error
>>>>> when I
>>>>>>>> try
>>>>>>>> from my home network as well.
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
>>>>>>>> [hidden email]
>>>>>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
>>>>>>>>>
>>>>>>>>>   @Uwe I tried the same steps from office as well as home
>>> network
>>>>> with
>>>>>>>>>> same
>>>>>>>>>> results. Are you using windows 7 with R 3.0.3?
>>>>>>>>>>
>>>>>>>>>> I have seen same question being asked by others without any
>>>>>>>>>> resolution. Is
>>>>>>>>>> anything special about XML package? I am OK use older version
>>> of
>>>>>>>>>> package
>>>>>>>>>> but in archives there are no zip files (only gz files). Is
>>>>> windows
>>>>>>>>>> platform
>>>>>>>>>> not recommended for R?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> Right, and you can try to install these from sources.
>>>>>>>>> But I doubt you need it. You still have not told us if you
>>> tried
>>>>> another
>>>>>>>>> mirror to download the XML file from and what you local IT
>>> support
>>>>> tells
>>>>>>>>> you while your downloads are incomplete.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> Uwe Ligges
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
>>>>>>>>>> [hidden email]
>>>>>>>>>>
>>>>>>>>>>   wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
>>>>>>>>>>>
>>>>>>>>>>>    Thank you for response Uwe. I tried multiple times by
>>>>> downloading
>>>>>>>>>>> the
>>>>>>>>>>>
>>>>>>>>>>>> zip
>>>>>>>>>>>> file from many sources but still the same error. This is a
>>>>> major road
>>>>>>>>>>>> block
>>>>>>>>>>>> for me in using R. Appreciate any help on this.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>   Please ask your local IT staff.
>>>>>>>>>>>
>>>>>>>>>>> I get, using the same mirror:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>> options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
>>>>>>>>>>>
>>>>>>>>>>>> install.packages("XML", lib="d:/temp")
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> trying URL
>>> 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>>>>>
>>>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip'
>>>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
>>>>>>>>>>> opened URL
>>>>>>>>>>> downloaded 4.1 Mb
>>>>>>>>>>>
>>>>>>>>>>> package 'XML' successfully unpacked and MD5 sums checked
>>>>>>>>>>>
>>>>>>>>>>> The downloaded binary packages are in
>>>>>>>>>>>            d:\temp\RtmpqMqL8L\downloaded_packages
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> Uwe Ligges
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>   On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>
>>>>>>>>>>>>    wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>      Works for me.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> Uwe Ligges
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>     Using install.package('XML') command produces this
>>> error:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> trying URL
>>>>>>>>>>>>>> '
>>>>>>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
>>>>>>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
>>>>>>>>>>>>>> '
>>>>>>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1
>>> Mb)
>>>>>>>>>>>>>> opened URL
>>>>>>>>>>>>>> downloaded 4.1 Mb
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
>>>>> c("Package",
>>>>>>>>>>>>>> "Type")) :
>>>>>>>>>>>>>>        cannot open the connection
>>>>>>>>>>>>>> In addition: Warning messages:
>>>>>>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb",
>>> ...)
>>>>> :
>>>>>>>>>>>>>>        downloaded length 4276224 != reported length 4288136
>>>>>>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
>>>> >from zip
>>>>>>>>>>>>>> file
>>>>>>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
>>>>> c("Package",
>>>>>>>>>>>>>> "Type"))
>>>>>>>>>>>>>> :
>>>>>>>>>>>>>>        cannot open compressed file 'XML/DESCRIPTION',
>>> probable
>>>>>>>>>>>>>> reason
>>>>>>>>>>>>>> 'No
>>>>>>>>>>>>>> such
>>>>>>>>>>>>>> file or directory'
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
>>>>> directly
>>>>>>>>>>>>>> from
>>>>>>>>>>>>>> cran
>>>>>>>>>>>>>> site. But this zip file is not a valid archive (cannot
>>> open
>>>>> using
>>>>>>>>>>>>>> winzip).
>>>>>>>>>>>>>> Also trying to install using this downloaded file produces
>>>>> the
>>>>>>>>>>>>>> following
>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
>>>>>>>>>>>>>> win-library/3.0'
>>>>>>>>>>>>>> (as 'lib' is unspecified)
>>>>>>>>>>>>>> Warning in install.packages :
>>>>>>>>>>>>>>        error 1 in extracting from zip file
>>>>>>>>>>>>>> Warning in install.packages :
>>>>>>>>>>>>>>        cannot open compressed file 'XML/DESCRIPTION',
>>> probable
>>>>>>>>>>>>>> reason
>>>>>>>>>>>>>> 'No
>>>>>>>>>>>>>> such
>>>>>>>>>>>>>> file or directory'
>>>>>>>>>>>>>> Error in install.packages : cannot open the connection
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I  downloaded this zip file from multiple sources and
>>> tried
>>>>> to
>>>>>>>>>>>>>> install
>>>>>>>>>>>>>> with
>>>>>>>>>>>>>> same result.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Thanks and Regards
>>>>>> Alpesh
>>>>>>
>>>>
>>>> ______________________________________________
>>>> [hidden email] mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/posting-
>>>> guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
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https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.
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Re: R 3.0.3, Windows 7: Problem installing XML package

Frede Aakmann Tøgersen-2
Sorry guys

I didn't do my homework, sorry for cluttering the list. I did know about the source argument.

This worked like a charm:

> install.packages(choose.files(), type="source", repos=NULL)
* installing *source* package 'climatol' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (climatol)

when choosing the cmiatol_2.2.tar.gz file.

Thanks for your help. That still leaves Alpesh out in the limbo :-(

Yours sincerely / Med venlig hilsen


Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant Performance & Modeling

Technology & Service Solutions
T +45 9730 5135
M +45 2547 6050
[hidden email]
http://www.vestas.com

Company reg. name: Vestas Wind Systems A/S
This e-mail is subject to our e-mail disclaimer statement.
Please refer to www.vestas.com/legal/notice
If you have received this e-mail in error please contact the sender.

> -----Original Message-----
> From: Duncan Murdoch [mailto:[hidden email]]
> Sent: 21. april 2014 13:21
> To: Milan Bouchet-Valat; Frede Aakmann Tøgersen
> Cc: [hidden email]; Uwe Ligges; Alpesh Pandya
> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
>
> On 21/04/2014, 7:10 AM, Milan Bouchet-Valat wrote:
> > Le lundi 21 avril 2014 à 11:38 +0200, Frede Aakmann Tøgersen a écrit :
> >> Hi
> >>
> >> Couldn't find a zip file in the archives.
> >>
> >> Why didn't 'R CMD build' (in a command shell on Windows) not make a
> >> zip file? I did try to build from the climatol library that holds the
> >> typical files as DESCRIPTION, LICENSE, etc. as well as folders like R,
> >> etc.
> > R CMD build produces *source* packages, and .zip packages are *binary*.
> >
> >> Did you see the debug information on read.fcf? For me it seems like R
> >> has open a file handler to the DESCRIPTION file. Wouldn't the error
> >> already be thrown there and not when read.fcf is called if the .tar.gz
> >> format was the problem?
> >>
> >> I'll try and locate a zip
> > Does install.packages(choose.file(), type="source") work?
>
> That will also need "repos=NULL", or it will go out to a repository to
> look for the package.
>
> That should work if the package doesn't have compiled code.  It will
> handle compiled code only if Frede has the appropriate tools installed.
>
>
> I'm not sure
> > what utils:::menuInstallLocal() does.
>
> It is essentially
>
> install.packages(choose.file(), type="binary", repos=NULL)
>
> so it's not what Frede needs.
>
> Duncan
> >
> >
> > Regards
> >
> >
> >> Sendt fra Samsung mobil
> >>
> >>
> >> -------- Oprindelig meddelelse --------
> >> Fra: Jeff Newmiller
> >> Dato:21/04/2014 09.44 (GMT+01:00)
> >> Til: Frede Aakmann Tøgersen ,Alpesh Pandya ,Rui Barradas
> >> Cc: [hidden email],Uwe Ligges ,Duncan Murdoch
> >> Emne: RE: [R] R 3.0.3, Windows 7: Problem installing XML package
> >>
> >> Frede... Windows uses zip files (binary, aka pre-compiled format) for
> packages by default, because most installations don't have the development
> tools installed. You need to setup RTools and use the "source" option to
> install_package in order to handle the tar.gz package file, or download and
> install the zip file instead.
> >> ---------------------------------------------------------------------------
> >> Jeff Newmiller                        The     .....       .....  Go Live...
> >> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live Go...
> >>                                        Live:   OO#.. Dead: OO#..  Playing
> >> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> >> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> >> ---------------------------------------------------------------------------
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> On April 20, 2014 11:01:17 PM PDT, "Frede Aakmann Tøgersen"
> <[hidden email]> wrote:
> >>> Well now, I think I have seen something similar to Alpesh.
> >>>
> >>> Recently I needed the climatol package that I have used some time ago.
> >>> It is not maintained anymore but I downloaded the latest version,
> >>> climatol_2.2.tar.gz,  from archives
> >>> (http://cran.r-
> project.org/src/contrib/Archive/climatol/climatol_2.2.tar.gz
> >>> ) . Trying to install that package from local file  using R-3.1.0 on
> >>> Windows 8  resulted in this:
> >>>
> >>> ## From R Console
> >>>> utils:::menuInstallLocal()
> >>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >>> "Type")) :
> >>>   cannot open the connection
> >>> In addition: Warning messages:
> >>> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
> >>> file
> >>> 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
> >>> :
> >>> cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION',
> probable
> >>> reason 'No such file or directory'
> >>>>
> >>>
> >>> And yes I know where the file is located, since choose.files() is used.
> >>>
> >>> However I tried the same on our linux (R-3.0.2) cluster and it
> >>> succeeded:
> >>>
> >>> [frtog@dkrdsfshn2 ~]$ R CMD INSTALL climatol_2.2.tar.gz
> >>> * installing to library
> >>> ?/gpfs02/gcdistro/app/R/3.0.2-gcc4.8.2/lib64/R/library?
> >>> * installing *source* package ?climatol? ...
> >>> ** R
> >>> ** data
> >>> ** inst
> >>> ** preparing package for lazy loading
> >>> ** help
> >>> *** installing help indices
> >>> ** building package indices
> >>> ** installing vignettes
> >>> ** testing if installed package can be loaded
> >>> * DONE (climatol)
> >>> [frtog@dkrdsfshn2 ~]$ R
> >>>
> >>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> >>> Copyright (C) 2013 The R Foundation for Statistical Computing
> >>> Platform: x86_64-unknown-linux-gnu (64-bit)
> >>>
> >>> R is free software and comes with ABSOLUTELY NO WARRANTY.
> >>> You are welcome to redistribute it under certain conditions.
> >>> Type 'license()' or 'licence()' for distribution details.
> >>>
> >>>   Natural language support but running in an English locale
> >>>
> >>> R is a collaborative project with many contributors.
> >>> Type 'contributors()' for more information and
> >>> 'citation()' on how to cite R or R packages in publications.
> >>>
> >>> Type 'demo()' for some demos, 'help()' for on-line help, or
> >>> 'help.start()' for an HTML browser interface to help.
> >>> Type 'q()' to quit R.
> >>>
> >>>> library("climatol")
> >>>> ?rosavent
> >>>> q()
> >>> Save workspace image? [y/n/c]: n
> >>> [frtog@dkrdsfshn2 ~]$
> >>>
> >>>
> >>> Now unzipping and untaring climatol_2.2.tar.gz I thought to examine
> >>> whether I could build the package on my Windows box. Only R stuff and
> >>> no foreign language as C, FORTRAN, etc. so it should be easy.
> >>>
> >>> ## Command shell in Windows
> >>> Microsoft Windows [Version 6.2.9200]
> >>> (c) 2012 Microsoft Corporation. All rights reserved.
> >>>
> >>> C:\Users\frtog>cd Desktop
> >>>
> >>> C:\Users\frtog\Desktop>c:\Programmer\R\R-3.1.0\bin\x64\R CMD build
> >>> climatol
> >>> * checking for file 'climatol/DESCRIPTION' ... OK
> >>> * preparing 'climatol':
> >>> * checking DESCRIPTION meta-information ... OK
> >>> * checking for LF line-endings in source and make files
> >>> * checking for empty or unneeded directories
> >>> * looking to see if a 'data/datalist' file should be added
> >>> * building 'climatol_2.2.tar.gz'
> >>>
> >>> Now trying to install from that local file I Still got the same error
> >>> as above.
> >>>
> >>>
> >>>
> >>> Trying to do some debugging on read.dcf() (Emacs/ESS)
> >>>
> >>>
> >>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
> >>> Copyright (C) 2014 The R Foundation for Statistical Computing
> >>> Platform: x86_64-w64-mingw32/x64 (64-bit)
> >>>
> >>> R is free software and comes with ABSOLUTELY NO WARRANTY.
> >>> You are welcome to redistribute it under certain conditions.
> >>> Type 'license()' or 'licence()' for distribution details.
> >>>
> >>>   Natural language support but running in an English locale
> >>>
> >>> R is a collaborative project with many contributors.
> >>> Type 'contributors()' for more information and
> >>> 'citation()' on how to cite R or R packages in publications.
> >>>
> >>> Type 'demo()' for some demos, 'help()' for on-line help, or
> >>> 'help.start()' for an HTML browser interface to help.
> >>> Type 'q()' to quit R.
> >>>
> >>>>> options(chmhelp=FALSE, help_type="text")
> >>>> options(STERM='iESS', str.dendrogram.last="'",
> >>> editor='emacsclient.exe', show.error.locations=TRUE)
> >>>> debug(read.dcf)
> >>>> install.packages("~/Desktop/climatol_2.2.tar.gz", repos = NULL)
> >>> debugging in: read.dcf(file.path(pkgname, "DESCRIPTION"),
> c("Package",
> >>> "Type"))
> >>> debug: {
> >>>     if (is.character(file)) {
> >>>         file <- gzfile(file)
> >>>         on.exit(close(file))
> >>>     }
> >>>     if (!inherits(file, "connection"))
> >>>         stop("'file' must be a character string or connection")
> >>>     if (!all)
> >>>         return(.Internal(readDCF(file, fields, keep.white)))
> >>>     .assemble_things_into_a_data_frame <- function(tags, vals,
> >>>         nums) {
> >>>         tf <- factor(tags, levels = unique(tags))
> >>>         cnts <- table(nums, tf)
> >>>      out <- array(NA_character_, dim = dim(cnts), dimnames = list(NULL,
> >>>             levels(tf)))
> >>>         if (all(cnts <= 1L)) {
> >>>             out[cbind(nums, tf)] <- vals
> >>>             out <- as.data.frame(out, stringsAsFactors = FALSE)
> >>>         }
> >>>         else {
> >>>             levs <- colSums(cnts > 1L) == 0L
> >>>             if (any(levs)) {
> >>>                 inds <- tf %in% levels(tf)[levs]
> >>>                 out[cbind(nums[inds], tf[inds])] <- vals[inds]
> >>>             }
> >>>             out <- as.data.frame(out, stringsAsFactors = FALSE)
> >>>             for (l in levels(tf)[!levs]) {
> >>>                 out[[l]] <- rep.int(list(NA_character_), nrow(cnts))
> >>>                 i <- tf == l
> >>>                 out[[l]][unique(nums[i])] <- split(vals[i], nums[i])
> >>>             }
> >>>         }
> >>>         out
> >>>     }
> >>>     on.exit(Sys.setlocale("LC_CTYPE", Sys.getlocale("LC_CTYPE")),
> >>>         add = TRUE)
> >>>     Sys.setlocale("LC_CTYPE", "C")
> >>>     lines <- readLines(file)
> >>>     ind <- grep("^[^[:blank:]][^:]*$", lines)
> >>>     if (length(ind)) {
> >>>         lines <- strtrim(lines[ind], 0.7 * getOption("width"))
> >>> stop(gettextf("Invalid DCF format.\nRegular lines must have a
> >>> tag.\nOffending lines start with:\n%s",
> >>>             paste0("  ", lines, collapse = "\n")), domain = NA)
> >>>     }
> >>>     line_is_not_empty <- !grepl("^[[:space:]]*$", lines)
> >>>     nums <- cumsum(diff(c(FALSE, line_is_not_empty) > 0L) > 0L)
> >>>     nums <- nums[line_is_not_empty]
> >>>     lines <- lines[line_is_not_empty]
> >>>     line_is_escaped_blank <- grepl("^[[:space:]]+\\.[[:space:]]*$",
> >>>         lines)
> >>>     if (any(line_is_escaped_blank))
> >>>         lines[line_is_escaped_blank] <- ""
> >>>     line_has_tag <- grepl("^[^[:blank:]][^:]*:", lines)
> >>>     ind <- which(!line_has_tag[which(diff(nums) > 0L) + 1L])
> >>>     if (length(ind)) {
> >>>         lines <- strtrim(lines[ind], 0.7 * getOption("width"))
> >>> stop(gettextf("Invalid DCF format.\nContinuation lines must not start a
> >>> record.\nOffending lines start with:\n%s",
> >>>             paste0("  ", lines, collapse = "\n")), domain = NA)
> >>>     }
> >>>     lengths <- rle(cumsum(line_has_tag))$lengths
> >>>     pos <- cumsum(lengths)
> >>>     tags <- sub(":.*", "", lines[line_has_tag])
> >>> lines[line_has_tag] <- sub("[^:]*:[[:space:]]*", "",
> >>> lines[line_has_tag])
> >>>     foldable <- rep.int(is.na(match(tags, keep.white)), lengths)
> >>>     lines[foldable] <- sub("^[[:space:]]*", "", lines[foldable])
> >>>     lines[foldable] <- sub("[[:space:]]*$", "", lines[foldable])
> >>> vals <- mapply(function(from, to) paste(lines[from:to], collapse =
> >>> "\n"),
> >>>         c(1L, pos[-length(pos)] + 1L), pos)
> >>>     out <- .assemble_things_into_a_data_frame(tags, vals, nums[pos])
> >>>     if (!is.null(fields))
> >>>         out <- out[fields]
> >>>     out
> >>> }
> >>> Browse[2]> str(file)
> >>> chr "climatol_2.2.tar.gz/DESCRIPTION"
> >>> Browse[2]> head(file)
> >>> [1] "climatol_2.2.tar.gz/DESCRIPTION"
> >>> Browse[2]>
> >>> debug: if (is.character(file)) {
> >>>     file <- gzfile(file)
> >>>     on.exit(close(file))
> >>> }
> >>> Browse[2]>
> >>> debug: file <- gzfile(file)
> >>> Browse[2]>
> >>> debug: on.exit(close(file))
> >>> Browse[2]>
> >>> debug: if (!inherits(file, "connection")) stop("'file' must be a
> >>> character string or connection")
> >>> Browse[2]>
> >>> debug: if (!all) return(.Internal(readDCF(file, fields, keep.white)))
> >>> Browse[2]> str(file)
> >>> Classes 'gzfile', 'connection'  atomic [1:1] 3
> >>>   ..- attr(*, "conn_id")=<externalptr>
> >>> Browse[2]> file
> >>>                       description                             class
> >>> "climatol_2.2.tar.gz/DESCRIPTION"                          "gzfile"
> >>>                              mode                              text
> >>>                              "rb"                            "text"
> >>>                            opened                          can read
> >>>                          "closed"                             "yes"
> >>>                         can write
> >>>                             "yes"
> >>> Browse[2]>
> >>> debug: return(.Internal(readDCF(file, fields, keep.white)))
> >>> Browse[2]>
> >>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >>> "Type")) :
> >>>   cannot open the connection
> >>> In addition: Warning message:
> >>> In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
> >>> cannot open compressed file 'climatol_2.2.tar.gz/DESCRIPTION',
> probable
> >>> reason 'No such file or directory'
> >>>>
> >>>
> >>> Well coming to debug: if (!all) return(.Internal(readDCF(file, fields,
> >>> keep.white))) I loose control and R returns to prompt with an error.
> >>>
> >>> Hopefully one of you can replicate this. If not then it must have
> >>> something with Windows OS to do. But what?
> >>>
> >>>
> >>>
> >>> Yours sincerely / Med venlig hilsen
> >>>
> >>>
> >>> Frede Aakmann Tøgersen
> >>> Specialist, M.Sc., Ph.D.
> >>> Plant Performance & Modeling
> >>>
> >>> Technology & Service Solutions
> >>> T +45 9730 5135
> >>> M +45 2547 6050
> >>> [hidden email]
> >>> http://www.vestas.com
> >>>
> >>> Company reg. name: Vestas Wind Systems A/S
> >>> This e-mail is subject to our e-mail disclaimer statement.
> >>> Please refer to
> www.vestas.com/legal/notice<http://www.vestas.com/legal/notice>
> >>> If you have received this e-mail in error please contact the sender.
> >>>
> >>>> -----Original Message-----
> >>>> From: [hidden email]
> >>> [mailto:[hidden email]]
> >>>> On Behalf Of Jeff Newmiller
> >>>> Sent: 20. april 2014 23:33
> >>>> To: Alpesh Pandya; Rui Barradas
> >>>> Cc: [hidden email]; Uwe Ligges
> >>>> Subject: Re: [R] R 3.0.3, Windows 7: Problem installing XML package
> >>>>
> >>>> Hard to help you when the problem simply does not happen for others.
> >>>>
> >>>> As for Windows being not a focus, that is not at all true. I use it
> >>> regularly on
> >>>> Windows at work. That being said, there are thousands of packages
> and
> >>>> those each involve their own subset of R users. There are also many
> >>>> operating system configurations that may not all be fully tested.
> >>> Blaming "R"
> >>>> or "Windows", or blaming us for "preventing" you from getting your
> >>>> education (isn't that something between you and your educational
> >>>> institution?) are not going to be effective strategies for problem
> >>> solving.
> >>>>
> >>>> Are you able to use other aspects of R beyond the XML package? Have
> >>> you
> >>>> tried communicating with the maintainers of that package?
> >>>>
> >>> ---------------------------------------------------------------------------
> >>>> Jeff Newmiller                        The     .....       .....  Go
> >>> Live...
> >>>> DCN:<[hidden email]>        Basics: ##.#.       ##.#.  Live
> >>> Go...
> >>>>                                        Live:   OO#.. Dead: OO#..
> >>> Playing
> >>>> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> >>>> /Software/Embedded Controllers)               .OO#.       .OO#.
> >>> rocks...1k
> >>>>
> >>> ---------------------------------------------------------------------------
> >>>> Sent from my phone. Please excuse my brevity.
> >>>>
> >>>> On April 20, 2014 11:45:44 AM PDT, Alpesh Pandya
> >>>> <[hidden email]> wrote:
> >>>>> I keep on trying from various networks but I still get the same
> >>> error.
> >>>>> I
> >>>>> don't this this has anything to do with network or ability to
> >>> download
> >>>>> the
> >>>>> package (as I can install other packages fine). This must be
> >>> something
> >>>>> in
> >>>>> base R or dependencies issues (that R is not spelling out).
> >>>>>
> >>>>> I know R is geared for Mac and Windows is kind of looked down upon
> >>> but
> >>>>> I
> >>>>> have no option but use windows and need this XML package running
> to
> >>>>> complete my education. Any help on this would be appreciated.
> >>>>>
> >>>>>
> >>>>> On Mon, Apr 14, 2014 at 2:24 PM, Alpesh Pandya
> >>>>> <[hidden email]>wrote:
> >>>>>
> >>>>>> Thank you for response Rui.
> >>>>>>
> >>>>>> I still get the same error with this repository.
> >>>>>>
> >>>>>> Installing package into
> >>>>> ���C:/Users/APandya/Documents/R/win-library/3.0���
> >>>>>> (as ���lib��� is unspecified)
> >>>>>> trying URL '
> >>>>>> http://cran.dcc.fc.up.pt/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
> >>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >>>>>> opened URL
> >>>>>> downloaded 4.1 Mb
> >>>>>>
> >>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >>>>> "Type"))
> >>>>>> :
> >>>>>>    cannot open the connection
> >>>>>> In addition: Warning messages:
> >>>>>> 1: In download.file(url, destfile, method, mode = "wb", ...) :
> >>>>>>    downloaded length 4276224 != reported length 4288136
> >>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting from
> >>> zip
> >>>>> file
> >>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
> >>>>> "Type")) :
> >>>>>>    cannot open compressed file 'XML/DESCRIPTION', probable reason
> >>> 'No
> >>>>> such
> >>>>>> file or directory'
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Mon, Apr 14, 2014 at 2:17 PM, Rui Barradas
> >>>>> <[hidden email]>wrote:
> >>>>>>
> >>>>>>> Hello,
> >>>>>>> I have package XML installed on Windows 7, R 3.0.3 and I had no
> >>>>> problem
> >>>>>>> at all. Can't you try (it worked with me)
> >>>>>>>
> >>>>>>> install.packages("XML", repos = "http://cran.dcc.fc.up.pt")
> >>>>>>>
> >>>>>>> Hope this helps,
> >>>>>>>
> >>>>>>> Rui Barradas
> >>>>>>>
> >>>>>>> Em 14-04-2014 16:24, Alpesh Pandya escreveu:
> >>>>>>>
> >>>>>>>   I have tried these sources (almost all US mirrors):
> >>>>>>>>
> >>>>>>>>
> >>>>
> >>>> http://cran.cnr.Berkeley.edu/bin/windows/contrib/3.0/XML_3.98-
> 1.1.zip
> >>>>>>>>
> >>> http://cran.stat.ucla.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>>>>>> http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/
> >>>>>>>> 3.0/XML_3.98-1.1.zip
> >>>>>>>>
> >>>>> http://ftp.ussg.iu.edu/CRAN/bin/windows/contrib/3.0/XML_3.98-
> 1.1.zip
> >>>>>>>>
> >>>>
> >>>> http://rweb.quant.ku.edu/cran/bin/windows/contrib/3.0/XML_3.98-
> 1.1.zip
> >>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >>>>>>>> contrib/3.0/XML_3.98-1.1.zip
> >>>>>>>> http://cran.mtu.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>>>>>> http://cran.wustl.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>>>>>> http://cran.case.edu/bin/windows/contrib/3.0/XML_3.98-1.1.zip
> >>>>>>>>
> >>>>
> >>>> http://ftp.osuosl.org/pub/cran/bin/windows/contrib/3.0/XML_3.98-
> 1.1.zip
> >>>>>>>>
> >>>>> http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/3.0/XML_3.98-
> >>>> 1.1.zip
> >>>>>>>>
> >>>>>>>> I have confirmed with IT that there is no restriction on
> >>>>> downloading this
> >>>>>>>> zip file from any of these sources. Also I am getting same error
> >>>>> when I
> >>>>>>>> try
> >>>>>>>> from my home network as well.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Sun, Apr 13, 2014 at 9:46 AM, Uwe Ligges <
> >>>>>>>> [hidden email]
> >>>>>>>>
> >>>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On 13.04.2014 01:30, Alpesh Pandya wrote:
> >>>>>>>>>
> >>>>>>>>>   @Uwe I tried the same steps from office as well as home
> >>> network
> >>>>> with
> >>>>>>>>>> same
> >>>>>>>>>> results. Are you using windows 7 with R 3.0.3?
> >>>>>>>>>>
> >>>>>>>>>> I have seen same question being asked by others without any
> >>>>>>>>>> resolution. Is
> >>>>>>>>>> anything special about XML package? I am OK use older version
> >>> of
> >>>>>>>>>> package
> >>>>>>>>>> but in archives there are no zip files (only gz files). Is
> >>>>> windows
> >>>>>>>>>> platform
> >>>>>>>>>> not recommended for R?
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>> Right, and you can try to install these from sources.
> >>>>>>>>> But I doubt you need it. You still have not told us if you
> >>> tried
> >>>>> another
> >>>>>>>>> mirror to download the XML file from and what you local IT
> >>> support
> >>>>> tells
> >>>>>>>>> you while your downloads are incomplete.
> >>>>>>>>>
> >>>>>>>>> Best,
> >>>>>>>>> Uwe Ligges
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> On Sat, Apr 12, 2014 at 7:22 PM, Uwe Ligges <
> >>>>>>>>>> [hidden email]
> >>>>>>>>>>
> >>>>>>>>>>   wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>> On 12.04.2014 22:39, Alpesh Pandya wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>    Thank you for response Uwe. I tried multiple times by
> >>>>> downloading
> >>>>>>>>>>> the
> >>>>>>>>>>>
> >>>>>>>>>>>> zip
> >>>>>>>>>>>> file from many sources but still the same error. This is a
> >>>>> major road
> >>>>>>>>>>>> block
> >>>>>>>>>>>> for me in using R. Appreciate any help on this.
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>   Please ask your local IT staff.
> >>>>>>>>>>>
> >>>>>>>>>>> I get, using the same mirror:
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>> options("repos"=c(CRAN="http://watson.nci.nih.gov/cran_mirror"))
> >>>>>>>>>>>
> >>>>>>>>>>>> install.packages("XML", lib="d:/temp")
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>> trying URL
> >>> 'http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >>>>>>>>>>>
> >>>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip'
> >>>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1 Mb)
> >>>>>>>>>>> opened URL
> >>>>>>>>>>> downloaded 4.1 Mb
> >>>>>>>>>>>
> >>>>>>>>>>> package 'XML' successfully unpacked and MD5 sums checked
> >>>>>>>>>>>
> >>>>>>>>>>> The downloaded binary packages are in
> >>>>>>>>>>>            d:\temp\RtmpqMqL8L\downloaded_packages
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> Best,
> >>>>>>>>>>> Uwe Ligges
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>   On Fri, Apr 11, 2014 at 6:53 PM, Uwe Ligges <
> >>>>>>>>>>>> [hidden email]
> >>>>>>>>>>>>
> >>>>>>>>>>>>    wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>      Works for me.
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>> Best,
> >>>>>>>>>>>>> Uwe Ligges
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On 11.04.2014 17:10, Alpesh Pandya wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>     Using install.package('XML') command produces this
> >>> error:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> trying URL
> >>>>>>>>>>>>>> '
> >>>>>>>>>>>>>> http://watson.nci.nih.gov/cran_mirror/bin/windows/
> >>>>>>>>>>>>>> contrib/3.0/XML_3.98-1.1.zip
> >>>>>>>>>>>>>> '
> >>>>>>>>>>>>>> Content type 'application/zip' length 4288136 bytes (4.1
> >>> Mb)
> >>>>>>>>>>>>>> opened URL
> >>>>>>>>>>>>>> downloaded 4.1 Mb
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Error in read.dcf(file.path(pkgname, "DESCRIPTION"),
> >>>>> c("Package",
> >>>>>>>>>>>>>> "Type")) :
> >>>>>>>>>>>>>>        cannot open the connection
> >>>>>>>>>>>>>> In addition: Warning messages:
> >>>>>>>>>>>>>> 1: In download.file(url, destfile, method, mode = "wb",
> >>> ...)
> >>>>> :
> >>>>>>>>>>>>>>        downloaded length 4276224 != reported length
> 4288136
> >>>>>>>>>>>>>> 2: In unzip(zipname, exdir = dest) : error 1 in extracting
> >>>> >from zip
> >>>>>>>>>>>>>> file
> >>>>>>>>>>>>>> 3: In read.dcf(file.path(pkgname, "DESCRIPTION"),
> >>>>> c("Package",
> >>>>>>>>>>>>>> "Type"))
> >>>>>>>>>>>>>> :
> >>>>>>>>>>>>>>        cannot open compressed file 'XML/DESCRIPTION',
> >>> probable
> >>>>>>>>>>>>>> reason
> >>>>>>>>>>>>>> 'No
> >>>>>>>>>>>>>> such
> >>>>>>>>>>>>>> file or directory'
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Upon receiving this error, I downloaded XML_3.98-1.1.zip
> >>>>> directly
> >>>>>>>>>>>>>> from
> >>>>>>>>>>>>>> cran
> >>>>>>>>>>>>>> site. But this zip file is not a valid archive (cannot
> >>> open
> >>>>> using
> >>>>>>>>>>>>>> winzip).
> >>>>>>>>>>>>>> Also trying to install using this downloaded file produces
> >>>>> the
> >>>>>>>>>>>>>> following
> >>>>>>>>>>>>>> error:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Installing package into 'C:/Users/APandya/Documents/R/
> >>>>>>>>>>>>>> win-library/3.0'
> >>>>>>>>>>>>>> (as 'lib' is unspecified)
> >>>>>>>>>>>>>> Warning in install.packages :
> >>>>>>>>>>>>>>        error 1 in extracting from zip file
> >>>>>>>>>>>>>> Warning in install.packages :
> >>>>>>>>>>>>>>        cannot open compressed file 'XML/DESCRIPTION',
> >>> probable
> >>>>>>>>>>>>>> reason
> >>>>>>>>>>>>>> 'No
> >>>>>>>>>>>>>> such
> >>>>>>>>>>>>>> file or directory'
> >>>>>>>>>>>>>> Error in install.packages : cannot open the connection
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> I  downloaded this zip file from multiple sources and
> >>> tried
> >>>>> to
> >>>>>>>>>>>>>> install
> >>>>>>>>>>>>>> with
> >>>>>>>>>>>>>> same result.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Thanks and Regards
> >>>>>> Alpesh
> >>>>>>
> >>>>
> >>>> ______________________________________________
> >>>> [hidden email] mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>>> PLEASE do read the posting guide http://www.R-project.org/posting-
> >>>> guide.html
> >>>> and provide commented, minimal, self-contained, reproducible code.
> >>
> >>
> >>    [[alternative HTML version deleted]]
> >>
> >> ______________________________________________
> >> [hidden email] mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > ______________________________________________
> > [hidden email] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >

______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
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