Re: [R-pkg-devel] Installing "Additional" Packages During Tests

2019-03-18 Thread Uwe Ligges 
Simply resubmit such a package, we will lookninto the details and the 
team will decide.


Best,
Uwe  Ligges

On 18.03.2019 17:28, brodie gaslam wrote:
I believe your first point makes the alternate workflow below illegal, 
but the subsequent ones add just enough ambiguity that I'd like to makes 
sure.  How about:


0. Only during the running of tests
1. Create a temporary directory tmplib using tempfile()/dircreate().
2. Install dummy package to that temporary directory using `lib=tmplib`: 
install.packages(srcdir, type='src', repos=NULL, lib=tmplib).

3. In the tests, use library(testpkg, lib.loc=tmplib)
4. unload / remove / unlink temp directory on.exit

This is only in the test running.  None of the code in the package 
proper that the user would invoke in normal use installs packages.  It 
only happens if the user installs and runs the tests, and with the above 
modification, it would only be into a temporary library directory.


Thank you for your patience and attention.

Best,

Brodie.


On Monday, March 18, 2019, 11:56:55 AM EDT, Uwe Ligges 
 wrote:



1. You should never install packages without asking the user.

2. a package should never write to the user file space or default
libraries unless the user akss for it explicitly.
In tests, use tempdir().

3. You cannot expect that the library is writeable. It is not in many
network installations.

Best,
Uwe Ligges



On 18.03.2019 16:48, brodie gaslam via R-package-devel wrote:
 >
 > Subject:
 > Installing "Additional" Packages During Tests
 > From:
 > brodie gaslam mailto:brodie.gas...@yahoo.com>>
 > Date:
 > 18.03.2019, 16:48
 > To:
 > List R-package-devel >

 >
 > To:
 > List R-package-devel >

 >
 >
 > Sorry, previous e-mail got pre-maturely sent due to fat finger...
 > My package unitizer[1] has recently gained the following type of error:
 >   Warning in install.packages(pkg, repos = NULL, type = "src") 
: 'lib = 
"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages"' is not 
writable

 >   Error in install.packages(pkg, repos = NULL, type = "src") :
 >   unable to install packages
 >
 > While I did recently update the package to resolve the RNGversion 
issue, this problem seems unrelated as some of the CRAN machines produce 
it, and some don't, on the same package version.
 > The tests install some dummy packages with `install.packages`, and 
this has worked for a long time, but no longer, presumably due to 
changes in permissions of the test running daemon.  The packages are 
removed on.exit.  The packages are used for integration tests as 
unitizer is a package-testing-package and it is useful to be able to 
test functionality that includes use on actual packages that change.

 >
 > Should I expect this to be the new normal, where I will be henceforth 
disallowed from installing packages temporarily?  Will there be an 
acceptable workaround (e.g. setting up a temporary library in a tempdir 
and try to `install.packages` into that; I admit I have no familiarity 
with this other than the vague awareness maybe this could be done)?
 > FWIW, perhaps an indication that this is something I shouldn't be 
doing came up earlier in the year when I had to resort to temporarily 
unsetting "R_TESTS" as per [2].

 > Thanks in advance for any input.
 > Best,
 > Brodie.
 >
 >
 > [1]: 
https://cran.r-project.org/web/checks/check_results_unitizer.html[2]: 
https://github.com/r-lib/testthat/issues/144

 >     [[alternative HTML version deleted]]
 >
 >
 > __
 > R-package-devel@r-project.org  
mailing list

 > https://stat.ethz.ch/mailman/listinfo/r-package-devel
 >


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Re: [R-pkg-devel] Installing "Additional" Packages During Tests

2019-03-18 Thread Uwe Ligges 




On 18.03.2019 17:28, brodie gaslam wrote:
I believe your first point makes the alternate workflow below illegal, 
but the subsequent ones add just enough ambiguity that I'd like to makes 
sure.  How about:


0. Only during the running of tests
1. Create a temporary directory tmplib using tempfile()/dircreate().
2. Install dummy package to that temporary directory using `lib=tmplib`: 
install.packages(srcdir, type='src', repos=NULL, lib=tmplib).

3. In the tests, use library(testpkg, lib.loc=tmplib)
4. unload / remove / unlink temp directory on.exit

This is only in the test running.  None of the code in the package 
proper that the user would invoke in normal use installs packages.  It 
only happens if the user installs and runs the tests, and with the above 
modification, it would only be into a temporary library directory.


Thank you for your patience and attention.


Please submit following these suggestions and the CRAN team will look 
into the details and decide.


Best,
Uwe




Best,

Brodie.


On Monday, March 18, 2019, 11:56:55 AM EDT, Uwe Ligges 
 wrote:



1. You should never install packages without asking the user.

2. a package should never write to the user file space or default
libraries unless the user akss for it explicitly.
In tests, use tempdir().

3. You cannot expect that the library is writeable. It is not in many
network installations.

Best,
Uwe Ligges



On 18.03.2019 16:48, brodie gaslam via R-package-devel wrote:
 >
 > Subject:
 > Installing "Additional" Packages During Tests
 > From:
 > brodie gaslam mailto:brodie.gas...@yahoo.com>>
 > Date:
 > 18.03.2019, 16:48
 > To:
 > List R-package-devel >

 >
 > To:
 > List R-package-devel >

 >
 >
 > Sorry, previous e-mail got pre-maturely sent due to fat finger...
 > My package unitizer[1] has recently gained the following type of error:
 >   Warning in install.packages(pkg, repos = NULL, type = "src") 
: 'lib = 
"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages"' is not 
writable

 >   Error in install.packages(pkg, repos = NULL, type = "src") :
 >   unable to install packages
 >
 > While I did recently update the package to resolve the RNGversion 
issue, this problem seems unrelated as some of the CRAN machines produce 
it, and some don't, on the same package version.
 > The tests install some dummy packages with `install.packages`, and 
this has worked for a long time, but no longer, presumably due to 
changes in permissions of the test running daemon.  The packages are 
removed on.exit.  The packages are used for integration tests as 
unitizer is a package-testing-package and it is useful to be able to 
test functionality that includes use on actual packages that change.

 >
 > Should I expect this to be the new normal, where I will be henceforth 
disallowed from installing packages temporarily?  Will there be an 
acceptable workaround (e.g. setting up a temporary library in a tempdir 
and try to `install.packages` into that; I admit I have no familiarity 
with this other than the vague awareness maybe this could be done)?
 > FWIW, perhaps an indication that this is something I shouldn't be 
doing came up earlier in the year when I had to resort to temporarily 
unsetting "R_TESTS" as per [2].

 > Thanks in advance for any input.
 > Best,
 > Brodie.
 >
 >
 > [1]: 
https://cran.r-project.org/web/checks/check_results_unitizer.html[2]: 
https://github.com/r-lib/testthat/issues/144

 >     [[alternative HTML version deleted]]
 >
 >
 > __
 > R-package-devel@r-project.org  
mailing list

 > https://stat.ethz.ch/mailman/listinfo/r-package-devel
 >


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Re: [R-pkg-devel] Installing "Additional" Packages During Tests

2019-03-18 Thread brodie gaslam via R-package-devel 
--- Begin Message ---
 I believe your first point makes the alternate workflow below illegal, but the 
subsequent ones add just enough ambiguity that I'd like to makes sure.  How 
about:
0. Only during the running of tests
1. Create a temporary directory tmplib using tempfile()/dircreate().
2. Install dummy package to that temporary directory using `lib=tmplib`: 
install.packages(srcdir, type='src', repos=NULL, lib=tmplib).
3. In the tests, use library(testpkg, lib.loc=tmplib)4. unload / remove / 
unlink temp directory on.exit
This is only in the test running.  None of the code in the package proper that 
the user would invoke in normal use installs packages.  It only happens if the 
user installs and runs the tests, and with the above modification, it would 
only be into a temporary library directory.
Thank you for your patience and attention.
Best,
Brodie.


On Monday, March 18, 2019, 11:56:55 AM EDT, Uwe Ligges 
 wrote:  
 
 1. You should never install packages without asking the user.

2. a package should never write to the user file space or default 
libraries unless the user akss for it explicitly.
In tests, use tempdir().

3. You cannot expect that the library is writeable. It is not in many 
network installations.

Best,
Uwe Ligges



On 18.03.2019 16:48, brodie gaslam via R-package-devel wrote:
> 
> Subject:
> Installing "Additional" Packages During Tests
> From:
> brodie gaslam 
> Date:
> 18.03.2019, 16:48
> To:
> List R-package-devel 
> 
> To:
> List R-package-devel 
> 
> 
> Sorry, previous e-mail got pre-maturely sent due to fat finger...
> My package unitizer[1] has recently gained the following type of error:
>   Warning in install.packages(pkg, repos = NULL, type = "src") : 'lib 
>= "/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages"' is not writable
>   Error in install.packages(pkg, repos = NULL, type = "src") :
>   unable to install packages
> 
> While I did recently update the package to resolve the RNGversion issue, this 
> problem seems unrelated as some of the CRAN machines produce it, and some 
> don't, on the same package version.
> The tests install some dummy packages with `install.packages`, and this has 
> worked for a long time, but no longer, presumably due to changes in 
> permissions of the test running daemon.  The packages are removed on.exit.  
> The packages are used for integration tests as unitizer is a 
> package-testing-package and it is useful to be able to test functionality 
> that includes use on actual packages that change.
> 
> Should I expect this to be the new normal, where I will be henceforth 
> disallowed from installing packages temporarily?  Will there be an acceptable 
> workaround (e.g. setting up a temporary library in a tempdir and try to 
> `install.packages` into that; I admit I have no familiarity with this other 
> than the vague awareness maybe this could be done)?
> FWIW, perhaps an indication that this is something I shouldn't be doing came 
> up earlier in the year when I had to resort to temporarily unsetting 
> "R_TESTS" as per [2].
> Thanks in advance for any input.
> Best,
> Brodie.
> 
> 
> [1]: https://cran.r-project.org/web/checks/check_results_unitizer.html[2]: 
> https://github.com/r-lib/testthat/issues/144
>     [[alternative HTML version deleted]]
> 
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
  
[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Installing "Additional" Packages During Tests

2019-03-18 Thread Uwe Ligges 

1. You should never install packages without asking the user.

2. a package should never write to the user file space or default 
libraries unless the user akss for it explicitly.

In tests, use tempdir().

3. You cannot expect that the library is writeable. It is not in many 
network installations.


Best,
Uwe Ligges



On 18.03.2019 16:48, brodie gaslam via R-package-devel wrote:


Subject:
Installing "Additional" Packages During Tests
From:
brodie gaslam 
Date:
18.03.2019, 16:48
To:
List R-package-devel 

To:
List R-package-devel 


Sorry, previous e-mail got pre-maturely sent due to fat finger...
My package unitizer[1] has recently gained the following type of error:
  Warning in install.packages(pkg, repos = NULL, type = "src") : 'lib = 
"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages"' is not writable
  Error in install.packages(pkg, repos = NULL, type = "src") :
  unable to install packages

While I did recently update the package to resolve the RNGversion issue, this 
problem seems unrelated as some of the CRAN machines produce it, and some 
don't, on the same package version.
The tests install some dummy packages with `install.packages`, and this has 
worked for a long time, but no longer, presumably due to changes in permissions 
of the test running daemon.  The packages are removed on.exit.  The packages 
are used for integration tests as unitizer is a package-testing-package and it 
is useful to be able to test functionality that includes use on actual packages 
that change.

Should I expect this to be the new normal, where I will be henceforth 
disallowed from installing packages temporarily?  Will there be an acceptable 
workaround (e.g. setting up a temporary library in a tempdir and try to 
`install.packages` into that; I admit I have no familiarity with this other 
than the vague awareness maybe this could be done)?
FWIW, perhaps an indication that this is something I shouldn't be doing came up earlier 
in the year when I had to resort to temporarily unsetting "R_TESTS" as per [2].
Thanks in advance for any input.
Best,
Brodie.


[1]: https://cran.r-project.org/web/checks/check_results_unitizer.html[2]: 
https://github.com/r-lib/testthat/issues/144
[[alternative HTML version deleted]]


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[R-pkg-devel] Installing "Additional" Packages During Tests

2019-03-18 Thread brodie gaslam via R-package-devel 
--- Begin Message ---
Sorry, previous e-mail got pre-maturely sent due to fat finger...
My package unitizer[1] has recently gained the following type of error:
 Warning in install.packages(pkg, repos = NULL, type = "src") : 'lib = 
"/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages"' is not writable
 Error in install.packages(pkg, repos = NULL, type = "src") : 
 unable to install packages

While I did recently update the package to resolve the RNGversion issue, this 
problem seems unrelated as some of the CRAN machines produce it, and some 
don't, on the same package version.
The tests install some dummy packages with `install.packages`, and this has 
worked for a long time, but no longer, presumably due to changes in permissions 
of the test running daemon.  The packages are removed on.exit.  The packages 
are used for integration tests as unitizer is a package-testing-package and it 
is useful to be able to test functionality that includes use on actual packages 
that change.

Should I expect this to be the new normal, where I will be henceforth 
disallowed from installing packages temporarily?  Will there be an acceptable 
workaround (e.g. setting up a temporary library in a tempdir and try to 
`install.packages` into that; I admit I have no familiarity with this other 
than the vague awareness maybe this could be done)?
FWIW, perhaps an indication that this is something I shouldn't be doing came up 
earlier in the year when I had to resort to temporarily unsetting "R_TESTS" as 
per [2].
Thanks in advance for any input.
Best,
Brodie.


[1]: https://cran.r-project.org/web/checks/check_results_unitizer.html[2]: 
https://github.com/r-lib/testthat/issues/144
[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Meaning and consequences of action pending in the submission pipeline

2019-03-18 Thread Uwe Ligges 
pending means a team member has to do a closer inspection and needs more 
time while waiting means user reactions, this is a recent change since 
we wrote the publication you cited.


Best,
Uwe Ligges



On 15.03.2019 18:51, Staudacher, Jochen, Prof. Dr. wrote:

Dear colleagues,

I submitted a new package on Saturday, 9 March 2019.

Approx. 48 hours ago, i.e. on Wednesday, 13 March 2019, my package was moved to the 
subfolder "pending".

I am worried, because I did not receive any email from CRAN concerning why my package was 
"pending" and what I needed to do.

According to

https://journal.r-project.org/archive/2018-1/cran.pdf

the action "pending" in the submission pipeline means that a decision is 
pending a response from the package maintainer and implies the action includes an 
informative email message to the package maintainer.

Do I misunderstand the meaning and consequences of the action "pending"?

Any advice will be gratefully received.

Cheers,

Jochen


Prof. Dr. Jochen Staudacher
Fakult�t Informatik
Hochschule Kempten
Bahnhofstr. 61
87435 Kempten
Tel.: +49 (0)831 2523-513
Email: jochen.staudac...@hs-kempten.de

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[R-pkg-devel] Installing Additional "Packages" During Tests

2019-03-18 Thread brodie gaslam via R-package-devel 
--- Begin Message ---
My package unitizer has recently gained a new set of errors that look like:

[[alternative HTML version deleted]]

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