Error with installed.packages with R 3.4.0 on Windows

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Error with installed.packages with R 3.4.0 on Windows

Jean-Claude Arbaut
Hello,

I am currently getting a strange error when I call installed.packages():

Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
  missing value where TRUE/FALSE needed
Calls: installed.packages


I am working with R 3.4.0 on Windows. I didn't get this error with R 3.3.3.
Apparently, file.mtime() is returning NA well applied to a directory, and
this causes the entire && expression to be NA, then the "if" fails because
it needs either T or F.
The source of "installed.packages" seems to be roughly the same as in R
3.3.3, so I wonder if there have been other changes in R, maybe the logical
operators, that would make this function fail.

Any idea?

Best regards,

Jean-Claude Arbaut

        [[alternative HTML version deleted]]

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Re: Error with installed.packages with R 3.4.0 on Windows

Thierry Onkelinx
We have several computers with the same problem.

Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <[hidden email]>:

Hello,

I am currently getting a strange error when I call installed.packages():

Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
  missing value where TRUE/FALSE needed
Calls: installed.packages


I am working with R 3.4.0 on Windows. I didn't get this error with R 3.3.3.
Apparently, file.mtime() is returning NA well applied to a directory, and
this causes the entire && expression to be NA, then the "if" fails because
it needs either T or F.
The source of "installed.packages" seems to be roughly the same as in R
3.3.3, so I wonder if there have been other changes in R, maybe the logical
operators, that would make this function fail.

Any idea?

Best regards,

Jean-Claude Arbaut

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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]]

______________________________________________
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Re: Error with installed.packages with R 3.4.0 on Windows

Peter Dalgaard-2
Yes, we noticed this in the last days of the code freeze before release and shied away from inserting a workaround, partly because we couldn't see what the root of the problem might be.

For the purposes of installed.packages it is relatively harmless to treat the NA condition as FALSE, since it is just a matter of whether a cache is valid. I.e., it might cause an unnecessary cache rebuild. For other situations it might be more of an issue.

The workaround (NA -> FALSE, basically) is in place in R-patched and R-devel.

-pd

> On 28 Apr 2017, at 07:47 , Thierry Onkelinx <[hidden email]> wrote:
>
> We have several computers with the same problem.
>
> Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <[hidden email]>:
>
> Hello,
>
> I am currently getting a strange error when I call installed.packages():
>
> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>  missing value where TRUE/FALSE needed
> Calls: installed.packages
>
>
> I am working with R 3.4.0 on Windows. I didn't get this error with R 3.3.3.
> Apparently, file.mtime() is returning NA well applied to a directory, and
> this causes the entire && expression to be NA, then the "if" fails because
> it needs either T or F.
> The source of "installed.packages" seems to be roughly the same as in R
> 3.3.3, so I wonder if there have been other changes in R, maybe the logical
> operators, that would make this function fail.
>
> Any idea?
>
> Best regards,
>
> Jean-Claude Arbaut
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
> 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.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Error with installed.packages with R 3.4.0 on Windows

Thierry Onkelinx
Dear Peter,

It actually breaks install.packages(). So it is not that innocent.

Best regards,

Thierry


Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard" <[hidden email]>:

Yes, we noticed this in the last days of the code freeze before release and
shied away from inserting a workaround, partly because we couldn't see what
the root of the problem might be.

For the purposes of installed.packages it is relatively harmless to treat
the NA condition as FALSE, since it is just a matter of whether a cache is
valid. I.e., it might cause an unnecessary cache rebuild. For other
situations it might be more of an issue.

The workaround (NA -> FALSE, basically) is in place in R-patched and
R-devel.

-pd

> On 28 Apr 2017, at 07:47 , Thierry Onkelinx <[hidden email]>
wrote:

>
> We have several computers with the same problem.
>
> Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <[hidden email]
>:
>
> Hello,
>
> I am currently getting a strange error when I call installed.packages():
>
> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>  missing value where TRUE/FALSE needed
> Calls: installed.packages
>
>
> I am working with R 3.4.0 on Windows. I didn't get this error with R
3.3.3.
> Apparently, file.mtime() is returning NA well applied to a directory, and
> this causes the entire && expression to be NA, then the "if" fails because
> it needs either T or F.
> The source of "installed.packages" seems to be roughly the same as in R
> 3.3.3, so I wonder if there have been other changes in R, maybe the
logical

> operators, that would make this function fail.
>
> Any idea?
>
> Best regards,
>
> Jean-Claude Arbaut
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
> 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.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Error with installed.packages with R 3.4.0 on Windows

Duncan Murdoch-2
On 28/04/2017 4:45 AM, Thierry Onkelinx wrote:
> Dear Peter,
>
> It actually breaks install.packages(). So it is not that innocent.

I don't think he meant that it is harmless, he meant that the fix is
easy, and is in place in R-patched and R-devel.  You should use
R-patched and you won't have the problem.

More generally, there's a lot more variety of systems in the wild than
on our test machines, so we really do rely on people testing things in
the alpha/beta/rc phase.  In this case we saw the error too late to fix
it (as I recall, it was very late in rc).  If more people had tested, we
might have found it earlier.

Duncan Murdoch

>
> Best regards,
>
> Thierry
>
>
> Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard" <[hidden email]>:
>
> Yes, we noticed this in the last days of the code freeze before release and
> shied away from inserting a workaround, partly because we couldn't see what
> the root of the problem might be.
>
> For the purposes of installed.packages it is relatively harmless to treat
> the NA condition as FALSE, since it is just a matter of whether a cache is
> valid. I.e., it might cause an unnecessary cache rebuild. For other
> situations it might be more of an issue.
>
> The workaround (NA -> FALSE, basically) is in place in R-patched and
> R-devel.
>
> -pd
>
>> On 28 Apr 2017, at 07:47 , Thierry Onkelinx <[hidden email]>
> wrote:
>>
>> We have several computers with the same problem.
>>
>> Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <[hidden email]
>> :
>>
>> Hello,
>>
>> I am currently getting a strange error when I call installed.packages():
>>
>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>>  missing value where TRUE/FALSE needed
>> Calls: installed.packages
>>
>>
>> I am working with R 3.4.0 on Windows. I didn't get this error with R
> 3.3.3.
>> Apparently, file.mtime() is returning NA well applied to a directory, and
>> this causes the entire && expression to be NA, then the "if" fails because
>> it needs either T or F.
>> The source of "installed.packages" seems to be roughly the same as in R
>> 3.3.3, so I wonder if there have been other changes in R, maybe the
> logical
>> operators, that would make this function fail.
>>
>> Any idea?
>>
>> Best regards,
>>
>> Jean-Claude Arbaut
>>
>>        [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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 -- To UNSUBSCRIBE and more, see
>> 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.
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: [hidden email]  Priv: [hidden email]
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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: Error with installed.packages with R 3.4.0 on Windows

Uwe Ligges-3
In reply to this post by Thierry Onkelinx


On 28.04.2017 10:45, Thierry Onkelinx wrote:
> Dear Peter,
>
> It actually breaks install.packages(). So it is not that innocent.

And hence, as Peter exoplained, it is already fixed inn R-patched,
thanks to Tomas Kalibera.

Best,
Uwe Ligges





> Best regards,
>
> Thierry
>
>
> Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard" <[hidden email]>:
>
> Yes, we noticed this in the last days of the code freeze before release and
> shied away from inserting a workaround, partly because we couldn't see what
> the root of the problem might be.
>
> For the purposes of installed.packages it is relatively harmless to treat
> the NA condition as FALSE, since it is just a matter of whether a cache is
> valid. I.e., it might cause an unnecessary cache rebuild. For other
> situations it might be more of an issue.
>
> The workaround (NA -> FALSE, basically) is in place in R-patched and
> R-devel.
>
> -pd
>
>> On 28 Apr 2017, at 07:47 , Thierry Onkelinx <[hidden email]>
> wrote:
>>
>> We have several computers with the same problem.
>>
>> Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <[hidden email]
>> :
>>
>> Hello,
>>
>> I am currently getting a strange error when I call installed.packages():
>>
>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>>  missing value where TRUE/FALSE needed
>> Calls: installed.packages
>>
>>
>> I am working with R 3.4.0 on Windows. I didn't get this error with R
> 3.3.3.
>> Apparently, file.mtime() is returning NA well applied to a directory, and
>> this causes the entire && expression to be NA, then the "if" fails because
>> it needs either T or F.
>> The source of "installed.packages" seems to be roughly the same as in R
>> 3.3.3, so I wonder if there have been other changes in R, maybe the
> logical
>> operators, that would make this function fail.
>>
>> Any idea?
>>
>> Best regards,
>>
>> Jean-Claude Arbaut
>>
>>        [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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 -- To UNSUBSCRIBE and more, see
>> 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.
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: [hidden email]  Priv: [hidden email]
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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: Error with installed.packages with R 3.4.0 on Windows

Dimitri Liakhovitski-2
When I click on "r patched snapshot build" here
<https://cran.r-project.org/bin/windows/base/>, it take me here
<https://cran.r-project.org/bin/windows/base/rpatched.html> , it says: Download
R-3.3.3 Patched build for Windows
<https://cran.r-project.org/bin/windows/base/R-3.3.3patched-win.exe>
However, I am unclear how can one get to the patched 3.4.0 version?
Thank you!

On Fri, Apr 28, 2017 at 7:58 AM, Uwe Ligges <[hidden email]
> wrote:

>
>
> On 28.04.2017 10:45, Thierry Onkelinx wrote:
>
>> Dear Peter,
>>
>> It actually breaks install.packages(). So it is not that innocent.
>>
>
> And hence, as Peter exoplained, it is already fixed inn R-patched, thanks
> to Tomas Kalibera.
>
> Best,
> Uwe Ligges
>
>
>
>
>
>
> Best regards,
>>
>> Thierry
>>
>>
>> Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard" <[hidden email]>:
>>
>> Yes, we noticed this in the last days of the code freeze before release
>> and
>> shied away from inserting a workaround, partly because we couldn't see
>> what
>> the root of the problem might be.
>>
>> For the purposes of installed.packages it is relatively harmless to treat
>> the NA condition as FALSE, since it is just a matter of whether a cache is
>> valid. I.e., it might cause an unnecessary cache rebuild. For other
>> situations it might be more of an issue.
>>
>> The workaround (NA -> FALSE, basically) is in place in R-patched and
>> R-devel.
>>
>> -pd
>>
>> On 28 Apr 2017, at 07:47 , Thierry Onkelinx <[hidden email]>
>>>
>> wrote:
>>
>>>
>>> We have several computers with the same problem.
>>>
>>> Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <
>>> [hidden email]
>>> :
>>>
>>> Hello,
>>>
>>> I am currently getting a strange error when I call installed.packages():
>>>
>>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&
>>> :
>>>  missing value where TRUE/FALSE needed
>>> Calls: installed.packages
>>>
>>>
>>> I am working with R 3.4.0 on Windows. I didn't get this error with R
>>>
>> 3.3.3.
>>
>>> Apparently, file.mtime() is returning NA well applied to a directory, and
>>> this causes the entire && expression to be NA, then the "if" fails
>>> because
>>> it needs either T or F.
>>> The source of "installed.packages" seems to be roughly the same as in R
>>> 3.3.3, so I wonder if there have been other changes in R, maybe the
>>>
>> logical
>>
>>> operators, that would make this function fail.
>>>
>>> Any idea?
>>>
>>> Best regards,
>>>
>>> Jean-Claude Arbaut
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> 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 -- To UNSUBSCRIBE and more, see
>>> 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.
>>>
>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: [hidden email]  Priv: [hidden email]
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posti
> ng-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



--
Dimitri Liakhovitski

        [[alternative HTML version deleted]]

______________________________________________
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Re: Error with installed.packages with R 3.4.0 on Windows

Peter Dalgaard-2
In reply to this post by Duncan Murdoch-2

> On 28 Apr 2017, at 12:08 , Duncan Murdoch <[hidden email]> wrote:
>
> On 28/04/2017 4:45 AM, Thierry Onkelinx wrote:
>> Dear Peter,
>>
>> It actually breaks install.packages(). So it is not that innocent.
>
> I don't think he meant that it is harmless, he meant that the fix is easy, and is in place in R-patched and R-devel.  You should use R-patched and you won't have the problem.

Read more carefully: I said that the _fix_ is harmless for this case, but might not be so in general.

-pd

>
> More generally, there's a lot more variety of systems in the wild than on our test machines, so we really do rely on people testing things in the alpha/beta/rc phase.  In this case we saw the error too late to fix it (as I recall, it was very late in rc).  If more people had tested, we might have found it earlier.
>
> Duncan Murdoch
>
>>
>> Best regards,
>>
>> Thierry
>>
>>
>> Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard" <[hidden email]>:
>>
>> Yes, we noticed this in the last days of the code freeze before release and
>> shied away from inserting a workaround, partly because we couldn't see what
>> the root of the problem might be.
>>
>> For the purposes of installed.packages it is relatively harmless to treat
>> the NA condition as FALSE, since it is just a matter of whether a cache is
>> valid. I.e., it might cause an unnecessary cache rebuild. For other
>> situations it might be more of an issue.
>>
>> The workaround (NA -> FALSE, basically) is in place in R-patched and
>> R-devel.
>>
>> -pd
>>
>>> On 28 Apr 2017, at 07:47 , Thierry Onkelinx <[hidden email]>
>> wrote:
>>>
>>> We have several computers with the same problem.
>>>
>>> Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut" <[hidden email]
>>> :
>>>
>>> Hello,
>>>
>>> I am currently getting a strange error when I call installed.packages():
>>>
>>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>>> missing value where TRUE/FALSE needed
>>> Calls: installed.packages
>>>
>>>
>>> I am working with R 3.4.0 on Windows. I didn't get this error with R
>> 3.3.3.
>>> Apparently, file.mtime() is returning NA well applied to a directory, and
>>> this causes the entire && expression to be NA, then the "if" fails because
>>> it needs either T or F.
>>> The source of "installed.packages" seems to be roughly the same as in R
>>> 3.3.3, so I wonder if there have been other changes in R, maybe the
>> logical
>>> operators, that would make this function fail.
>>>
>>> Any idea?
>>>
>>> Best regards,
>>>
>>> Jean-Claude Arbaut
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> 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 -- To UNSUBSCRIBE and more, see
>>> 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.
>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: [hidden email]  Priv: [hidden email]
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

______________________________________________
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Re: Error with installed.packages with R 3.4.0 on Windows

Uwe Ligges-3
In reply to this post by Dimitri Liakhovitski-2


On 28.04.2017 19:10, Dimitri Liakhovitski wrote:
> When I click on "r patched snapshot build" here
> <https://cran.r-project.org/bin/windows/base/>, it take me here
> <https://cran.r-project.org/bin/windows/base/rpatched.html> , it
> says: Download R-3.3.3 Patched build for Windows
> <https://cran.r-project.org/bin/windows/base/R-3.3.3patched-win.exe>
> However, I am unclear how can one get to the patched 3.4.0 version?

If you are on Windows, you did the roight things, but the page has to be
updated.CCing Duncan who maintains these pages.

Best,
Uwe



> Thank you!
>
> On Fri, Apr 28, 2017 at 7:58 AM, Uwe Ligges
> <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>
>
>     On 28.04.2017 10:45, Thierry Onkelinx wrote:
>
>         Dear Peter,
>
>         It actually breaks install.packages(). So it is not that innocent.
>
>
>     And hence, as Peter exoplained, it is already fixed inn R-patched,
>     thanks to Tomas Kalibera.
>
>     Best,
>     Uwe Ligges
>
>
>
>
>
>
>         Best regards,
>
>         Thierry
>
>
>         Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard"
>         <[hidden email] <mailto:[hidden email]>>:
>
>         Yes, we noticed this in the last days of the code freeze before
>         release and
>         shied away from inserting a workaround, partly because we
>         couldn't see what
>         the root of the problem might be.
>
>         For the purposes of installed.packages it is relatively harmless
>         to treat
>         the NA condition as FALSE, since it is just a matter of whether
>         a cache is
>         valid. I.e., it might cause an unnecessary cache rebuild. For other
>         situations it might be more of an issue.
>
>         The workaround (NA -> FALSE, basically) is in place in R-patched and
>         R-devel.
>
>         -pd
>
>             On 28 Apr 2017, at 07:47 , Thierry Onkelinx
>             <[hidden email] <mailto:[hidden email]>>
>
>         wrote:
>
>
>             We have several computers with the same problem.
>
>             Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut"
>             <[hidden email] <mailto:[hidden email]>
>             :
>
>             Hello,
>
>             I am currently getting a strange error when I call
>             installed.packages():
>
>             Error in if (file.exists(dest) && file.mtime(dest) >
>             file.mtime(lib) &&  :
>              missing value where TRUE/FALSE needed
>             Calls: installed.packages
>
>
>             I am working with R 3.4.0 on Windows. I didn't get this
>             error with R
>
>         3.3.3.
>
>             Apparently, file.mtime() is returning NA well applied to a
>             directory, and
>             this causes the entire && expression to be NA, then the "if"
>             fails because
>             it needs either T or F.
>             The source of "installed.packages" seems to be roughly the
>             same as in R
>             3.3.3, so I wonder if there have been other changes in R,
>             maybe the
>
>         logical
>
>             operators, that would make this function fail.
>
>             Any idea?
>
>             Best regards,
>
>             Jean-Claude Arbaut
>
>                    [[alternative HTML version deleted]]
>
>             ______________________________________________
>             [hidden email] <mailto:[hidden email]> mailing
>             list -- To UNSUBSCRIBE and more, see
>             https://stat.ethz.ch/mailman/listinfo/r-help
>             <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] <mailto:[hidden email]> mailing
>             list -- To UNSUBSCRIBE and more, see
>             https://stat.ethz.ch/mailman/listinfo/r-help
>             <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.
>
>
>         --
>         Peter Dalgaard, Professor,
>         Center for Statistics, Copenhagen Business School
>         Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>         Phone: (+45)38153501 <tel:%28%2B45%2938153501>
>         Office: A 4.23
>         Email: [hidden email] <mailto:[hidden email]>  Priv:
>         [hidden email] <mailto:[hidden email]>
>
>                 [[alternative HTML version deleted]]
>
>         ______________________________________________
>         [hidden email] <mailto:[hidden email]> mailing list
>         -- To UNSUBSCRIBE and more, see
>         https://stat.ethz.ch/mailman/listinfo/r-help
>         <https://stat.ethz.ch/mailman/listinfo/r-help>
>         PLEASE do read the posting guide
>         http://www.R-project.org/posting-guide.html
>         <http://www.R-project.org/posting-guide.html>
>         and provide commented, minimal, self-contained, reproducible code.
>
>
>     ______________________________________________
>     [hidden email] <mailto:[hidden email]> mailing list --
>     To UNSUBSCRIBE and more, see
>     https://stat.ethz.ch/mailman/listinfo/r-help
>     <https://stat.ethz.ch/mailman/listinfo/r-help>
>     PLEASE do read the posting guide
>     http://www.R-project.org/posting-guide.html
>     <http://www.R-project.org/posting-guide.html>
>     and provide commented, minimal, self-contained, reproducible code.
>
>
>
>
> --
> Dimitri Liakhovitski

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Error with installed.packages with R 3.4.0 on Windows

Duncan Murdoch-2
On 28/04/2017 5:58 PM, Uwe Ligges wrote:

>
>
> On 28.04.2017 19:10, Dimitri Liakhovitski wrote:
>> When I click on "r patched snapshot build" here
>> <https://cran.r-project.org/bin/windows/base/>, it take me here
>> <https://cran.r-project.org/bin/windows/base/rpatched.html> , it
>> says: Download R-3.3.3 Patched build for Windows
>> <https://cran.r-project.org/bin/windows/base/R-3.3.3patched-win.exe>
>> However, I am unclear how can one get to the patched 3.4.0 version?
>
> If you are on Windows, you did the roight things, but the page has to be
> updated.CCing Duncan who maintains these pages.

Thanks, I missed that update.  It is now building 3.4.0-patched, so that
version should be available on the mirrors in a few hours.

Duncan Murdoch

>
> Best,
> Uwe
>
>
>
>> Thank you!
>>
>> On Fri, Apr 28, 2017 at 7:58 AM, Uwe Ligges
>> <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>
>>
>>     On 28.04.2017 10:45, Thierry Onkelinx wrote:
>>
>>         Dear Peter,
>>
>>         It actually breaks install.packages(). So it is not that innocent.
>>
>>
>>     And hence, as Peter exoplained, it is already fixed inn R-patched,
>>     thanks to Tomas Kalibera.
>>
>>     Best,
>>     Uwe Ligges
>>
>>
>>
>>
>>
>>
>>         Best regards,
>>
>>         Thierry
>>
>>
>>         Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard"
>>         <[hidden email] <mailto:[hidden email]>>:
>>
>>         Yes, we noticed this in the last days of the code freeze before
>>         release and
>>         shied away from inserting a workaround, partly because we
>>         couldn't see what
>>         the root of the problem might be.
>>
>>         For the purposes of installed.packages it is relatively harmless
>>         to treat
>>         the NA condition as FALSE, since it is just a matter of whether
>>         a cache is
>>         valid. I.e., it might cause an unnecessary cache rebuild. For other
>>         situations it might be more of an issue.
>>
>>         The workaround (NA -> FALSE, basically) is in place in R-patched and
>>         R-devel.
>>
>>         -pd
>>
>>             On 28 Apr 2017, at 07:47 , Thierry Onkelinx
>>             <[hidden email] <mailto:[hidden email]>>
>>
>>         wrote:
>>
>>
>>             We have several computers with the same problem.
>>
>>             Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut"
>>             <[hidden email] <mailto:[hidden email]>
>>             :
>>
>>             Hello,
>>
>>             I am currently getting a strange error when I call
>>             installed.packages():
>>
>>             Error in if (file.exists(dest) && file.mtime(dest) >
>>             file.mtime(lib) &&  :
>>              missing value where TRUE/FALSE needed
>>             Calls: installed.packages
>>
>>
>>             I am working with R 3.4.0 on Windows. I didn't get this
>>             error with R
>>
>>         3.3.3.
>>
>>             Apparently, file.mtime() is returning NA well applied to a
>>             directory, and
>>             this causes the entire && expression to be NA, then the "if"
>>             fails because
>>             it needs either T or F.
>>             The source of "installed.packages" seems to be roughly the
>>             same as in R
>>             3.3.3, so I wonder if there have been other changes in R,
>>             maybe the
>>
>>         logical
>>
>>             operators, that would make this function fail.
>>
>>             Any idea?
>>
>>             Best regards,
>>
>>             Jean-Claude Arbaut
>>
>>                    [[alternative HTML version deleted]]
>>
>>             ______________________________________________
>>             [hidden email] <mailto:[hidden email]> mailing
>>             list -- To UNSUBSCRIBE and more, see
>>             https://stat.ethz.ch/mailman/listinfo/r-help
>>             <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] <mailto:[hidden email]> mailing
>>             list -- To UNSUBSCRIBE and more, see
>>             https://stat.ethz.ch/mailman/listinfo/r-help
>>             <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.
>>
>>
>>         --
>>         Peter Dalgaard, Professor,
>>         Center for Statistics, Copenhagen Business School
>>         Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>         Phone: (+45)38153501 <tel:%28%2B45%2938153501>
>>         Office: A 4.23
>>         Email: [hidden email] <mailto:[hidden email]>  Priv:
>>         [hidden email] <mailto:[hidden email]>
>>
>>                 [[alternative HTML version deleted]]
>>
>>         ______________________________________________
>>         [hidden email] <mailto:[hidden email]> mailing list
>>         -- To UNSUBSCRIBE and more, see
>>         https://stat.ethz.ch/mailman/listinfo/r-help
>>         <https://stat.ethz.ch/mailman/listinfo/r-help>
>>         PLEASE do read the posting guide
>>         http://www.R-project.org/posting-guide.html
>>         <http://www.R-project.org/posting-guide.html>
>>         and provide commented, minimal, self-contained, reproducible code.
>>
>>
>>     ______________________________________________
>>     [hidden email] <mailto:[hidden email]> mailing list --
>>     To UNSUBSCRIBE and more, see
>>     https://stat.ethz.ch/mailman/listinfo/r-help
>>     <https://stat.ethz.ch/mailman/listinfo/r-help>
>>     PLEASE do read the posting guide
>>     http://www.R-project.org/posting-guide.html
>>     <http://www.R-project.org/posting-guide.html>
>>     and provide commented, minimal, self-contained, reproducible code.
>>
>>
>>
>>
>> --
>> Dimitri Liakhovitski

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: Error with installed.packages with R 3.4.0 on Windows

Jean-Claude Arbaut
Thank you all for the help. I will try the patch.

Best regards,

Jean-Claude Arbaut

2017-04-29 0:33 GMT+02:00 Duncan Murdoch <[hidden email]>:

> On 28/04/2017 5:58 PM, Uwe Ligges wrote:
>
>>
>>
>> On 28.04.2017 19:10, Dimitri Liakhovitski wrote:
>>
>>> When I click on "r patched snapshot build" here
>>> <https://cran.r-project.org/bin/windows/base/>, it take me here
>>> <https://cran.r-project.org/bin/windows/base/rpatched.html> , it
>>> says: Download R-3.3.3 Patched build for Windows
>>> <https://cran.r-project.org/bin/windows/base/R-3.3.3patched-win.exe>
>>> However, I am unclear how can one get to the patched 3.4.0 version?
>>>
>>
>> If you are on Windows, you did the roight things, but the page has to be
>> updated.CCing Duncan who maintains these pages.
>>
>
> Thanks, I missed that update.  It is now building 3.4.0-patched, so that
> version should be available on the mirrors in a few hours.
>
> Duncan Murdoch
>
>
>> Best,
>> Uwe
>>
>>
>>
>> Thank you!
>>>
>>> On Fri, Apr 28, 2017 at 7:58 AM, Uwe Ligges
>>> <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>>
>>>
>>>     On 28.04.2017 10:45, Thierry Onkelinx wrote:
>>>
>>>         Dear Peter,
>>>
>>>         It actually breaks install.packages(). So it is not that
>>> innocent.
>>>
>>>
>>>     And hence, as Peter exoplained, it is already fixed inn R-patched,
>>>     thanks to Tomas Kalibera.
>>>
>>>     Best,
>>>     Uwe Ligges
>>>
>>>
>>>
>>>
>>>
>>>
>>>         Best regards,
>>>
>>>         Thierry
>>>
>>>
>>>         Op 28 apr. 2017 10:36 a.m. schreef "peter dalgaard"
>>>         <[hidden email] <mailto:[hidden email]>>:
>>>
>>>         Yes, we noticed this in the last days of the code freeze before
>>>         release and
>>>         shied away from inserting a workaround, partly because we
>>>         couldn't see what
>>>         the root of the problem might be.
>>>
>>>         For the purposes of installed.packages it is relatively harmless
>>>         to treat
>>>         the NA condition as FALSE, since it is just a matter of whether
>>>         a cache is
>>>         valid. I.e., it might cause an unnecessary cache rebuild. For
>>> other
>>>         situations it might be more of an issue.
>>>
>>>         The workaround (NA -> FALSE, basically) is in place in R-patched
>>> and
>>>         R-devel.
>>>
>>>         -pd
>>>
>>>             On 28 Apr 2017, at 07:47 , Thierry Onkelinx
>>>             <[hidden email] <mailto:[hidden email]>>
>>>
>>>         wrote:
>>>
>>>
>>>             We have several computers with the same problem.
>>>
>>>             Op 28 apr. 2017 7:25 a.m. schreef "Jean-Claude Arbaut"
>>>             <[hidden email] <mailto:[hidden email]>
>>>             :
>>>
>>>             Hello,
>>>
>>>             I am currently getting a strange error when I call
>>>             installed.packages():
>>>
>>>             Error in if (file.exists(dest) && file.mtime(dest) >
>>>             file.mtime(lib) &&  :
>>>              missing value where TRUE/FALSE needed
>>>             Calls: installed.packages
>>>
>>>
>>>             I am working with R 3.4.0 on Windows. I didn't get this
>>>             error with R
>>>
>>>         3.3.3.
>>>
>>>             Apparently, file.mtime() is returning NA well applied to a
>>>             directory, and
>>>             this causes the entire && expression to be NA, then the "if"
>>>             fails because
>>>             it needs either T or F.
>>>             The source of "installed.packages" seems to be roughly the
>>>             same as in R
>>>             3.3.3, so I wonder if there have been other changes in R,
>>>             maybe the
>>>
>>>         logical
>>>
>>>             operators, that would make this function fail.
>>>
>>>             Any idea?
>>>
>>>             Best regards,
>>>
>>>             Jean-Claude Arbaut
>>>
>>>                    [[alternative HTML version deleted]]
>>>
>>>             ______________________________________________
>>>             [hidden email] <mailto:[hidden email]> mailing
>>>             list -- To UNSUBSCRIBE and more, see
>>>             https://stat.ethz.ch/mailman/listinfo/r-help
>>>             <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] <mailto:[hidden email]> mailing
>>>             list -- To UNSUBSCRIBE and more, see
>>>             https://stat.ethz.ch/mailman/listinfo/r-help
>>>             <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.
>>>
>>>
>>>         --
>>>         Peter Dalgaard, Professor,
>>>         Center for Statistics, Copenhagen Business School
>>>         Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>>         Phone: (+45)38153501 <tel:%28%2B45%2938153501>
>>>         Office: A 4.23
>>>         Email: [hidden email] <mailto:[hidden email]>  Priv:
>>>         [hidden email] <mailto:[hidden email]>
>>>
>>>                 [[alternative HTML version deleted]]
>>>
>>>         ______________________________________________
>>>         [hidden email] <mailto:[hidden email]> mailing list
>>>         -- To UNSUBSCRIBE and more, see
>>>         https://stat.ethz.ch/mailman/listinfo/r-help
>>>         <https://stat.ethz.ch/mailman/listinfo/r-help>
>>>         PLEASE do read the posting guide
>>>         http://www.R-project.org/posting-guide.html
>>>         <http://www.R-project.org/posting-guide.html>
>>>         and provide commented, minimal, self-contained, reproducible
>>> code.
>>>
>>>
>>>     ______________________________________________
>>>     [hidden email] <mailto:[hidden email]> mailing list --
>>>     To UNSUBSCRIBE and more, see
>>>     https://stat.ethz.ch/mailman/listinfo/r-help
>>>     <https://stat.ethz.ch/mailman/listinfo/r-help>
>>>     PLEASE do read the posting guide
>>>     http://www.R-project.org/posting-guide.html
>>>     <http://www.R-project.org/posting-guide.html>
>>>     and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>>
>>>
>>> --
>>> Dimitri Liakhovitski
>>>
>>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posti
> ng-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: Error with installed.packages with R 3.4.0 on Windows

Patrick Connolly-4
In reply to this post by Peter Dalgaard-2
On Fri, 28-Apr-2017 at 07:04PM +0200, peter dalgaard wrote:

|>
|> > On 28 Apr 2017, at 12:08 , Duncan Murdoch <[hidden email]> wrote:
|> >
|> > On 28/04/2017 4:45 AM, Thierry Onkelinx wrote:
|> >> Dear Peter,
|> >>
|> >> It actually breaks install.packages(). So it is not that innocent.
|> >
|> > I don't think he meant that it is harmless, he meant that the fix is easy, and is in place in R-patched and R-devel.  You should use R-patched and you won't have the problem.
|>
|> Read more carefully: I said that the _fix_ is harmless for this case, but might not be so in general.
|>
|> -pd


Apparently it isn't harmless.  

> install.packages("withr")
Error in readRDS(dest) : error reading from connection
>

>
> sessionInfo()
R version 3.4.0 Patched (2017-05-19 r72713)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/hrapgc/local/R-patched/lib/libRblas.so
LAPACK: /home/hrapgc/local/R-patched/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
 [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8  
 [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] grDevices utils     stats     graphics  methods   base    

other attached packages:
[1] lattice_0.20-35

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0    grid_3.4.0    
>

Has anyone a workaround?

--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.  
   ___    Patrick Connolly  
 {~._.~}                   Great minds discuss ideas    
 _( Y )_           Average minds discuss events
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)                        ..... Eleanor Roosevelt
         
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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Re: Error with installed.packages with R 3.4.0 on Windows

Martin Morgan-3
On 05/22/2017 05:10 AM, Patrick Connolly wrote:

> On Fri, 28-Apr-2017 at 07:04PM +0200, peter dalgaard wrote:
>
> |>
> |> > On 28 Apr 2017, at 12:08 , Duncan Murdoch <[hidden email]> wrote:
> |> >
> |> > On 28/04/2017 4:45 AM, Thierry Onkelinx wrote:
> |> >> Dear Peter,
> |> >>
> |> >> It actually breaks install.packages(). So it is not that innocent.
> |> >
> |> > I don't think he meant that it is harmless, he meant that the fix is easy, and is in place in R-patched and R-devel.  You should use R-patched and you won't have the problem.
> |>
> |> Read more carefully: I said that the _fix_ is harmless for this case, but might not be so in general.
> |>
> |> -pd
>
>
> Apparently it isn't harmless.
>
>> install.packages("withr")
> Error in readRDS(dest) : error reading from connection

that seems like a plain-old network connectivity issue, or perhaps an
issue with the CRAN mirror you're using. Can you debug on your end, e.g,.

   options(error=recover)
   install.packages("withr")
   ...

then select the 'frame' where the error occurs, look around

   ls()

find the value of 'dest', and e.g., try to open dest in your  browser.

Martin Morgan

>>
>
>>
>> sessionInfo()
> R version 3.4.0 Patched (2017-05-19 r72713)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.5 LTS
>
> Matrix products: default
> BLAS: /home/hrapgc/local/R-patched/lib/libRblas.so
> LAPACK: /home/hrapgc/local/R-patched/lib/libRlapack.so
>
> locale:
>  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8
>  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8
>  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grDevices utils     stats     graphics  methods   base
>
> other attached packages:
> [1] lattice_0.20-35
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0 tools_3.4.0    grid_3.4.0
>>
>
> Has anyone a workaround?
>


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Error in readRDS(dest) (was Re: Error with installed.packages with R 3.4.0 on Windows)

Patrick Connolly-4
On Mon, 22-May-2017 at 05:43AM -0400, Martin Morgan wrote:

|> On 05/22/2017 05:10 AM, Patrick Connolly wrote:

|> >Apparently it isn't harmless.
|> >
|> >>install.packages("withr")
|> >Error in readRDS(dest) : error reading from connection
|>
|> that seems like a plain-old network connectivity issue, or perhaps
|> an issue with the CRAN mirror you're using. Can you debug on your
|> end, e.g,.
|>
|>   options(error=recover)
|>   install.packages("withr")
|>   ...
|>
|> then select the 'frame' where the error occurs, look around
|>
|>   ls()
|>
|> find the value of 'dest', and e.g., try to open dest in your  browser.

This is what I get

>   options(error=recover)
>   install.packages("withr")
^C

Enter a frame number, or 0 to exit  

1: install.packages("withr")
2: available.packages(contriburl = contriburl, method = method)
3: tryCatch({
    download.file(url = paste0(repos, "/PACKAGES.rds"), destfile
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatchOne(expr, names, parentenv, handlers[[1]])
6: doTryCatch(return(expr), name, parentenv, handler)
7: download.file(url = paste0(repos, "/PACKAGES.rds"), destfile = dest, method

Selection: 7
Called from: eval(substitute(browser(skipCalls = skip), list(skip = 7 - which)),
    envir = sys.frame(which))
Browse[1]> dest
Error during wrapup: object 'dest' not found

That indicates to me that the problem is further back but I have no
idea how make use of that information.


Browse[1]> ls()
[1] "cacheOK"  "destfile" "extra"    "method"   "mode"     "quiet"    "url"    
Browse[1]> url
[1] "http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES.rds"
Browse[1]> destfile
[1] "/tmp/RtmpplJSrB/repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds"
Browse[1]>

The destfile above is zero-length and I suppose is where dest is
intended to end up.

Where else should I be looking?  Earlier installations never had this
issue so I don't have anything to compare.

TIA
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.  
   ___    Patrick Connolly  
 {~._.~}                   Great minds discuss ideas    
 _( Y )_           Average minds discuss events
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)                        ..... Eleanor Roosevelt
         
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

______________________________________________
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Error in readRDS(dest) (was Re: Error with installed.packages with R 3.4.0 on Windows)

Martin Maechler
>>>>> Patrick Connolly <[hidden email]>
>>>>>     on Tue, 23 May 2017 20:47:22 +1200 writes:

    > On Mon, 22-May-2017 at 05:43AM -0400, Martin Morgan wrote:
    > |> On 05/22/2017 05:10 AM, Patrick Connolly wrote:

    > |> >Apparently it isn't harmless.
    > |> >
    > |> >>install.packages("withr")
    > |> >Error in readRDS(dest) : error reading from connection
    > |>
    > |> that seems like a plain-old network connectivity issue, or perhaps
    > |> an issue with the CRAN mirror you're using. Can you debug on your
    > |> end, e.g,.
    > |>
    > |>   options(error=recover)
    > |>   install.packages("withr")
    > |>   ...
    > |>
    > |> then select the 'frame' where the error occurs, look around
    > |>
    > |>   ls()
    > |>
    > |> find the value of 'dest', and e.g., try to open dest in your  browser.

    > This is what I get

    >> options(error=recover)
    >> install.packages("withr")
    > ^C

    > Enter a frame number, or 0 to exit  

    > 1: install.packages("withr")
    > 2: available.packages(contriburl = contriburl, method = method)
    > 3: tryCatch({
    > download.file(url = paste0(repos, "/PACKAGES.rds"), destfile
    > 4: tryCatchList(expr, classes, parentenv, handlers)
    > 5: tryCatchOne(expr, names, parentenv, handlers[[1]])
    > 6: doTryCatch(return(expr), name, parentenv, handler)
    > 7: download.file(url = paste0(repos, "/PACKAGES.rds"), destfile = dest, method

    > Selection: 7

'7'  was the wrong choice:  'dest' exists in the frame that
     *calls* download.file, in this case, it is frame 2, i.e.,
     inside available.packages(.)  where the  tryCatch() call to
     download.file() happens.

Given the above stack trace.
It may be easier to just do

    debugonce(available.packages)
    install.packages("withr")

and then inside available.packages, (using 'n') step to the
point _before_ the tryCatch(...) call happens; there, e.g. use

      ls.str()

which gives an str() of all your local objects, notably 'dest'
and 'method'.
but you can also try other things once inside
available.packages().

Martin


    > Called from: eval(substitute(browser(skipCalls = skip), list(skip = 7 - which)),
    > envir = sys.frame(which))
    > Browse[1]> dest
    > Error during wrapup: object 'dest' not found

    > That indicates to me that the problem is further back but I have no
    > idea how make use of that information.


    > Browse[1]> ls()
    > [1] "cacheOK"  "destfile" "extra"    "method"   "mode"     "quiet"    "url"    
    > Browse[1]> url
    > [1] "http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES.rds"
    > Browse[1]> destfile
    > [1] "/tmp/RtmpplJSrB/repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds"
    > Browse[1]>

    > The destfile above is zero-length and I suppose is where dest is
    > intended to end up.

    > Where else should I be looking?  Earlier installations never had this
    > issue so I don't have anything to compare.

    > TIA
    > --

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Re: Error in readRDS(dest) (was Re: Error with installed.packages with R 3.4.0 on Windows)

Patrick Connolly-4
On Tue, 23-May-2017 at 12:20PM +0200, Martin Maechler wrote:

[...]

|>
|> Given the above stack trace.
|> It may be easier to just do
|>
|>     debugonce(available.packages)
|>     install.packages("withr")
|>
|> and then inside available.packages, (using 'n') step to the
|> point _before_ the tryCatch(...) call happens; there, e.g. use
|>
|>       ls.str()

I got:

contriburl :  chr [1:2] "http://cran.stat.auckland.ac.nz/src/contrib" ...
dest :  chr "/tmp/Rtmp6D0KNY/repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds"
fields :  chr [1:16] "Package" "Version" "Priority" "Depends" "Imports" "LinkingTo" ...
filters :  NULL
localcran :  logi FALSE
method : <missing>
repos :  chr "http://cran.stat.auckland.ac.nz/src/contrib"
requiredFields :  chr [1:16] "Package" "Version" "Priority" "Depends" "Imports" "LinkingTo" ...
res :  chr[0 , 1:17]
type :  chr "source"


So I thought the missing method was the problem.  However, it's
exactly the same with R-3.3.3.  So still no answwer.

Then I tried:

debugonce(readRDS)
install.packages("withr")

Browse[2]> con
A connection with    
description "/tmp/RtmpqzKzzK/repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds"
class       "gzfile"              
mode        "rb"                  
text        "binary"              
opened      "opened"              
can read    "yes"                  
can write   "no"

## With R-3.3.3

Browse[2]> con      
                                                description
"/home/hrapgc/local/R-3.3.3/library/abind/Meta/package.rds"
                                                      class
                                                   "gzfile"
                                                       mode
                                                       "rb"
                                                       text
                                                   "binary"
                                                     opened
                                                   "opened"
                                                   can read
                                                      "yes"
                                                  can write
                                                       "no"

So, in 3.4.0, con refers to a repo and is zero length whereas 3.3.3
refers to a library.  To me that would appear to be a major
difference.  That must have something to do with it.  But what?

Since the latter works and the former doesn't, it seems as though the
problem is with 3.4.0's readRDS().  But others seem not to have the
same problem.  I'm no closer to understanding what's happenning.


--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.  
   ___    Patrick Connolly  
 {~._.~}                   Great minds discuss ideas    
 _( Y )_           Average minds discuss events
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)                        ..... Eleanor Roosevelt
         
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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Re: Error in readRDS(dest) (was Re: Error with installed.packages with R 3.4.0 on Windows)

Patrick Connolly-4
In reply to this post by Martin Maechler
On Tue, 23-May-2017 at 12:20PM +0200, Martin Maechler wrote:

[...]

|>
|> Given the above stack trace.
|> It may be easier to just do
|>
|>     debugonce(available.packages)
|>     install.packages("withr")
|>
|> and then inside available.packages, (using 'n') step to the
|> point _before_ the tryCatch(...) call happens; there, e.g. use
|>
|>       ls.str()
|>
|> which gives an str() of all your local objects, notably 'dest'
|> and 'method'.
|> but you can also try other things once inside
|> available.packages().

I couldn't see any differences between R-3.3.3 (which works) and
R-3.4.0 (which doesn't) until I got to here, a few lines before the
download.file line:

Browse[2]>
debug: dest <- file.path(tempdir(), paste0("repos_", URLencode(repos,
    TRUE), ".rds"))
Browse[2]>

When I check out those directories in a terminal, there's a big diffrence:

With R-3.4.0
~ > ll /tmp/RtmpFUhtpY
total 4
drwxr-xr-x 2 hrapgc hrapgc 4096 May 31 10:45 downloaded_packages/
-rw-r--r-- 1 hrapgc hrapgc    0 May 31 10:56 repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds


With R-3.3.3
~ > ll /tmp/RtmpkPgL3A
total 380
drwxr-xr-x 2 hrapgc hrapgc   4096 May 31 11:01 downloaded_packages/
-rw-r--r-- 1 hrapgc hrapgc   8214 May 31 11:01 libloc_185_3165c7f52d5fdf96.rds
-rw-r--r-- 1 hrapgc hrapgc 372263 May 31 11:01 repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds

So, if I could figure out what makes *that* difference I could get
somewhere.  I see there's considerably extra code in the newer of the
two versions of available.packages() but being a bear with a small
brain, I can't figure out what differences should be expected.  I have
no idea what populates those 'dest' directories.

TIA
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.  
   ___    Patrick Connolly  
 {~._.~}                   Great minds discuss ideas    
 _( Y )_           Average minds discuss events
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)                        ..... Eleanor Roosevelt
         
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

______________________________________________
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Re: Error in readRDS(dest) (was Re: Error with installed.packages with R 3.4.0 on Windows)

Martin Morgan-3
On 05/31/2017 04:38 AM, Patrick Connolly wrote:

> On Tue, 23-May-2017 at 12:20PM +0200, Martin Maechler wrote:
>
> [...]
>
> |>
> |> Given the above stack trace.
> |> It may be easier to just do
> |>
> |>     debugonce(available.packages)
> |>     install.packages("withr")
> |>
> |> and then inside available.packages, (using 'n') step to the
> |> point _before_ the tryCatch(...) call happens; there, e.g. use
> |>
> |>       ls.str()
> |>
> |> which gives an str() of all your local objects, notably 'dest'
> |> and 'method'.
> |> but you can also try other things once inside
> |> available.packages().
>
> I couldn't see any differences between R-3.3.3 (which works) and
> R-3.4.0 (which doesn't) until I got to here, a few lines before the
> download.file line:
>
> Browse[2]>
> debug: dest <- file.path(tempdir(), paste0("repos_", URLencode(repos,
>      TRUE), ".rds"))
> Browse[2]>
>
> When I check out those directories in a terminal, there's a big diffrence:
>
> With R-3.4.0
> ~ > ll /tmp/RtmpFUhtpY
> total 4
> drwxr-xr-x 2 hrapgc hrapgc 4096 May 31 10:45 downloaded_packages/
> -rw-r--r-- 1 hrapgc hrapgc    0 May 31 10:56 repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds
>
>

The file repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds
was likely created earlier in your R session. Likely the download a few
lines down

                     download.file(url = paste0(repos, "/PACKAGES.rds"),
                                   destfile = dest, method = method,
                                   cacheOK = FALSE, quiet = TRUE, mode =
"wb")

'succeeded' but created a zero-length file.

You could try to troubleshoot this with something like the following,
downloading to a temporary location

   dest = tempfile()
   url = "http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES.rds"
   download.file(url, dest)
   file.size(dest)

If this succeeds (it should download a file of several hundred KB), then
try adding the options method, cacheOK, quiet, mode to the
download.file() call. 'method' can be determined when you are in
available.packages while debugging; if R says that it is missing, then
it will be assigned, in download.file, to either
getOption("download.file.method") or (if the option is NULL or "auto")
"libcurl".

If the download 'succeeds' but the temporary file created is 0 bytes,
then it would be good to share the problematic command with us.

Martin Morgan

> With R-3.3.3
> ~ > ll /tmp/RtmpkPgL3A
> total 380
> drwxr-xr-x 2 hrapgc hrapgc   4096 May 31 11:01 downloaded_packages/
> -rw-r--r-- 1 hrapgc hrapgc   8214 May 31 11:01 libloc_185_3165c7f52d5fdf96.rds
> -rw-r--r-- 1 hrapgc hrapgc 372263 May 31 11:01 repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds
>
> So, if I could figure out what makes *that* difference I could get
> somewhere.  I see there's considerably extra code in the newer of the
> two versions of available.packages() but being a bear with a small
> brain, I can't figure out what differences should be expected.  I have
> no idea what populates those 'dest' directories.
>
> TIA
>


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Re: Error in readRDS(dest) SOLVED

Patrick Connolly-4
On Wed, 31-May-2017 at 10:05AM -0400, Martin Morgan wrote:

|> On 05/31/2017 04:38 AM, Patrick Connolly wrote:

|> >When I check out those directories in a terminal, there's a big diffrence:
|> >
|> >With R-3.4.0
|> >~ > ll /tmp/RtmpFUhtpY
|> >total 4
|> >drwxr-xr-x 2 hrapgc hrapgc 4096 May 31 10:45 downloaded_packages/
|> >-rw-r--r-- 1 hrapgc hrapgc    0 May 31 10:56 repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds
|> >
|> >
|>
|> The file
|> repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds was
|> likely created earlier in your R session. Likely the download a few
|> lines down
|>
|>                     download.file(url = paste0(repos, "/PACKAGES.rds"),
|>                                   destfile = dest, method = method,
|>                                   cacheOK = FALSE, quiet = TRUE,
|> mode = "wb")
|>
|> 'succeeded' but created a zero-length file.
|>
|> You could try to troubleshoot this with something like the
|> following, downloading to a temporary location
|>
|>   dest = tempfile()
|>   url = "http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES.rds"
|>   download.file(url, dest)
|>   file.size(dest)

That works fine using R-3.3.3 but with R-3.4.0, this happens:

>  download.file(url, dest)
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES.rds'
Error in download.file(url, dest) :
  cannot open URL 'http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES.rds'
In addition: Warning message:
In download.file(url, dest) :
  URL 'http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES.rds': status was 'Couldn't connect to server'
>

Which seems to indicate that something else is preventing connexion to
the server.  Is there something that's changed with the way proxy
servers are used? was the question that led me to check out the
changes in R 3.4.0 which mentions visible changes to download.file().
So I tried method = "internal" which worked!

So making the same setting to the call to install.packages() fixed my
problem.


Thanks for all the suggestions which led me to the solution.  I just
wonder if there could be a more informative error message.

--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.  
   ___    Patrick Connolly  
 {~._.~}                   Great minds discuss ideas    
 _( Y )_           Average minds discuss events
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)                        ..... Eleanor Roosevelt
         
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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