Problem with creating default NAMESPACE on FreeBSD

[Rainer Hurling]

After building and installing R-devel from 21/07/2011 on FreeBSD
9.0-CURRENT (amd64), starting R gives the following warning:

[..snip..]
Beim Start - Warnmeldung:
package 'datasets' in options("defaultPackages") was not found

This happens with all versions after 14/07/2011. I think it is related to

NEWS Sat, 16 Jul 2011
CHANGES IN R-devel PACKAGE INSTALLATION
Packages without explicit ‘NAMESPACE’ files will have a default one
created at build or INSTALL time, so all packages will have namespaces.
A consequence of this is that ‘.First.lib’ functions need to be renamed,
usually as ‘.onLoad’ but sometimes as ‘.onAttach’.


Package 'datasets' seems to be installed correctly under
/usr/local/lib/R/library/:

ls -l datasets/
total 18
-rw-r--r--  1 root  wheel  -  289 22 Jul 08:12:04 2011 DESCRIPTION
-rw-r--r--  1 root  wheel  - 5547 22 Jul 08:12:04 2011 INDEX
drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 Meta
drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 R
drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 data
drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 help
drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 html


Calling options("defaultPackages") shows all relevant packages:

$defaultPackages
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"


But trying to load library 'datasets' fails with the following message:

library(datasets)
Fehler in library(datasets) :
   package 'datasets' does not have a NAMESPACE and should be re-installed


Googling around for some days now it looks like this does not happen to
anyone else (at least there are no infos). Does anybody knows what is
going on here?

Any help would be appreciated,
Rainer Hurling



sessionInfo()
R Under development (unstable) (2011-07-21 r56467)
Platform: amd64-portbld-freebsd9.0 (64-bit)

locale:
[1]
de_DE.ISO8859-15/de_DE.ISO8859-15/de_DE.ISO8859-15/C/de_DE.ISO8859-15/de_DE.ISO8859-15

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

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[Prof Brian Ripley]

It does not seem to happen to anyone else, including me on FreeBSD.
Is this a completely clean install?  src/library/datasets/Makefile
definitely installs a NAMESPACE file as part of the mkR1 target, so I
would check that you have a src/library/datasets/NAMESPACE file in
your sources.

(There was a short window on the 16th when it happened as a commit for
src/library/datasets/NAMESPACE was missed at first.)


On Fri, 22 Jul 2011, Rainer Hurling wrote:

> After building and installing R-devel from 21/07/2011 on FreeBSD 9.0-CURRENT
> (amd64), starting R gives the following warning:
>
> [..snip..]
> Beim Start - Warnmeldung:
> package 'datasets' in options("defaultPackages") was not found
>
> This happens with all versions after 14/07/2011. I think it is related to
>
> NEWS Sat, 16 Jul 2011
> CHANGES IN R-devel PACKAGE INSTALLATION
> Packages without explicit ‘NAMESPACE’ files will have a default one created
> at build or INSTALL time, so all packages will have namespaces. A consequence
> of this is that ‘.First.lib’ functions need to be renamed, usually as
> ‘.onLoad’ but sometimes as ‘.onAttach’.
>
>
> Package 'datasets' seems to be installed correctly under
> /usr/local/lib/R/library/:
>
> ls -l datasets/
> total 18
> -rw-r--r--  1 root  wheel  -  289 22 Jul 08:12:04 2011 DESCRIPTION
> -rw-r--r--  1 root  wheel  - 5547 22 Jul 08:12:04 2011 INDEX
> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 Meta
> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 R
> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 data
> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 help
> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 html
>
>
> Calling options("defaultPackages") shows all relevant packages:
>
> $defaultPackages
> [1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"
>
>
> But trying to load library 'datasets' fails with the following message:
>
> library(datasets)
> Fehler in library(datasets) :
>  package 'datasets' does not have a NAMESPACE and should be re-installed
>
>
> Googling around for some days now it looks like this does not happen to
> anyone else (at least there are no infos). Does anybody knows what is going
> on here?
>
> Any help would be appreciated,
> Rainer Hurling
>
>
>
> sessionInfo()
> R Under development (unstable) (2011-07-21 r56467)
> Platform: amd64-portbld-freebsd9.0 (64-bit)
>
> locale:
> [1]
> de_DE.ISO8859-15/de_DE.ISO8859-15/de_DE.ISO8859-15/C/de_DE.ISO8859-15/de_DE.ISO8859-15
>
> attached base packages:
> [1] stats     graphics  grDevices utils     methods   base
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  [phone] (self)
1 South Parks Road,                     [phone] (PA)
Oxford OX1 3TG, UK                Fax:  [phone]
______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Prof Brian Ripley]

One possibility is that you are building from a tarball snapshot
without mentioning it, and the (unspecified) tarball is incomplete.

For R-devel using tarballs is not a wise idea: they are really only
checked carefully in pre-release periods.  (One of the checks is that
AFAIR CRAN builds from the tarballs, but CRAN is not manned at
present.)

But as far as I can the 'make dist' procedure does work now and did
at some point in the last week.

On Fri, 22 Jul 2011, Prof Brian Ripley wrote:

> It does not seem to happen to anyone else, including me on FreeBSD. Is this a
> completely clean install?  src/library/datasets/Makefile definitely installs
> a NAMESPACE file as part of the mkR1 target, so I would check that you have a
> src/library/datasets/NAMESPACE file in your sources.
>
> (There was a short window on the 16th when it happened as a commit for
> src/library/datasets/NAMESPACE was missed at first.)
>
>
> On Fri, 22 Jul 2011, Rainer Hurling wrote:
>
>> After building and installing R-devel from 21/07/2011 on FreeBSD
>> 9.0-CURRENT (amd64), starting R gives the following warning:
>>
>> [..snip..]
>> Beim Start - Warnmeldung:
>> package 'datasets' in options("defaultPackages") was not found
>>
>> This happens with all versions after 14/07/2011. I think it is related to
>>
>> NEWS Sat, 16 Jul 2011
>> CHANGES IN R-devel PACKAGE INSTALLATION
>> Packages without explicit ‘NAMESPACE’ files will have a default one created
>> at build or INSTALL time, so all packages will have namespaces. A
>> consequence of this is that ‘.First.lib’ functions need to be renamed,
>> usually as ‘.onLoad’ but sometimes as ‘.onAttach’.
>>
>>
>> Package 'datasets' seems to be installed correctly under
>> /usr/local/lib/R/library/:
>>
>> ls -l datasets/
>> total 18
>> -rw-r--r--  1 root  wheel  -  289 22 Jul 08:12:04 2011 DESCRIPTION
>> -rw-r--r--  1 root  wheel  - 5547 22 Jul 08:12:04 2011 INDEX
>> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 Meta
>> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 R
>> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 data
>> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 help
>> drwxr-xr-x  2 root  wheel  -  512 22 Jul 08:12:04 2011 html
>>
>>
>> Calling options("defaultPackages") shows all relevant packages:
>>
>> $defaultPackages
>> [1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"
>>
>>
>> But trying to load library 'datasets' fails with the following message:
>>
>> library(datasets)
>> Fehler in library(datasets) :
>>  package 'datasets' does not have a NAMESPACE and should be re-installed
>>
>>
>> Googling around for some days now it looks like this does not happen to
>> anyone else (at least there are no infos). Does anybody knows what is going
>> on here?
>>
>> Any help would be appreciated,
>> Rainer Hurling
>>
>>
>>
>> sessionInfo()
>> R Under development (unstable) (2011-07-21 r56467)
>> Platform: amd64-portbld-freebsd9.0 (64-bit)
>>
>> locale:
>> [1]
>> de_DE.ISO8859-15/de_DE.ISO8859-15/de_DE.ISO8859-15/C/de_DE.ISO8859-15/de_DE.ISO8859-15
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     methods   base
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> --
> Brian D. Ripley,                  [hidden email]
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  [phone] (self)
> 1 South Parks Road,                     [phone] (PA)
> Oxford OX1 3TG, UK                Fax:  [phone]

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  [phone] (self)
1 South Parks Road,                     [phone] (PA)
Oxford OX1 3TG, UK                Fax:  [phone]
______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Rainer Hurling]

On 22.07.2011 14:50 (UTC+1), Prof Brian Ripley wrote:

> One possibility is that you are building from a tarball snapshot without
> mentioning it, and the (unspecified) tarball is incomplete.
>
> For R-devel using tarballs is not a wise idea: they are really only
> checked carefully in pre-release periods. (One of the checks is that
> AFAIR CRAN builds from the tarballs, but CRAN is not manned at present.)
>
> But as far as I can the 'make dist' procedure does work now and did at
> some point in the last week.
>
> On Fri, 22 Jul 2011, Prof Brian Ripley wrote:
>
>> It does not seem to happen to anyone else, including me on FreeBSD. Is
>> this a completely clean install? src/library/datasets/Makefile
>> definitely installs a NAMESPACE file as part of the mkR1 target, so I
>> would check that you have a src/library/datasets/NAMESPACE file in
>> your sources.
>>
>> (There was a short window on the 16th when it happened as a commit for
>> src/library/datasets/NAMESPACE was missed at first.)

Many thanks for answering and sorry for the late reaction. We had some
trouble in business yesterday.

It was not a totally clean installation before. I only deinstalled the
old R version before installing the new one in the same place (make
deinstall / make reinstall with a selfmade port math/R-devel for testing
purposes). Other packages etc. had not been deleted before.

I forgot to mention that there were warnings in the build for several
packages, like that:

installing to /usr/ports/math/R-devel/work/R-devel/library/mgcv/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
During startup - Warning message:
package 'datasets' in options("defaultPackages") was not found

BUT:
Today I tried again with newest version r56478 and surprisingly, all
that problems disappeared. Even no more warnings at build time.

For sureness I checked again older versions (between 15.07. and 21.07)
but the build warnings there exist, with version r56478 they went away.

Rainer Hurling


P.S.: Thanks for the hint with the problems of the tarball. I had not
been aware of it. In this case here it (mostly) also works with the
tarball version.

>> On Fri, 22 Jul 2011, Rainer Hurling wrote:
>>
>>> After building and installing R-devel from 21/07/2011 on FreeBSD
>>> 9.0-CURRENT (amd64), starting R gives the following warning:
>>>
>>> [..snip..]
>>> Beim Start - Warnmeldung:
>>> package 'datasets' in options("defaultPackages") was not found
>>>
>>> This happens with all versions after 14/07/2011. I think it is
>>> related to
>>>
>>> NEWS Sat, 16 Jul 2011
>>> CHANGES IN R-devel PACKAGE INSTALLATION
>>> Packages without explicit ‘NAMESPACE’ files will have a default one
>>> created at build or INSTALL time, so all packages will have
>>> namespaces. A consequence of this is that ‘.First.lib’ functions need
>>> to be renamed, usually as ‘.onLoad’ but sometimes as ‘.onAttach’.
>>>
>>>
>>> Package 'datasets' seems to be installed correctly under
>>> /usr/local/lib/R/library/:
>>>
>>> ls -l datasets/
>>> total 18
>>> -rw-r--r-- 1 root wheel - 289 22 Jul 08:12:04 2011 DESCRIPTION
>>> -rw-r--r-- 1 root wheel - 5547 22 Jul 08:12:04 2011 INDEX
>>> drwxr-xr-x 2 root wheel - 512 22 Jul 08:12:04 2011 Meta
>>> drwxr-xr-x 2 root wheel - 512 22 Jul 08:12:04 2011 R
>>> drwxr-xr-x 2 root wheel - 512 22 Jul 08:12:04 2011 data
>>> drwxr-xr-x 2 root wheel - 512 22 Jul 08:12:04 2011 help
>>> drwxr-xr-x 2 root wheel - 512 22 Jul 08:12:04 2011 html
>>>
>>>
>>> Calling options("defaultPackages") shows all relevant packages:
>>>
>>> $defaultPackages
>>> [1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
>>>
>>>
>>> But trying to load library 'datasets' fails with the following message:
>>>
>>> library(datasets)
>>> Fehler in library(datasets) :
>>> package 'datasets' does not have a NAMESPACE and should be re-installed
>>>
>>>
>>> Googling around for some days now it looks like this does not happen
>>> to anyone else (at least there are no infos). Does anybody knows what
>>> is going on here?
>>>
>>> Any help would be appreciated,
>>> Rainer Hurling
>>>
>>>
>>>
>>> sessionInfo()
>>> R Under development (unstable) (2011-07-21 r56467)
>>> Platform: amd64-portbld-freebsd9.0 (64-bit)
>>>
>>> locale:
>>> [1]
>>> de_DE.ISO8859-15/de_DE.ISO8859-15/de_DE.ISO8859-15/C/de_DE.ISO8859-15/de_DE.ISO8859-15
>>>
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils methods base

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