Re: [R-pkg-devel] R CMD Check: Tests running infinite

[Patrick Schratz]

Dear Uwe,

thanks for the hint. My cluster is closed after the `foreach`call using
`stopCluster()`.

Before, I´ll do the following to init the cluster:

*cl <- makeCluster(par.args$par.units, outfile = out.progress)*
*registerDoParallel(cl, cores = par.args$par.units)*

*foreach()*

*stopCluster(cl)*

Do you know of any other package which is using foreach in combination with
tests and is hosted on Github? So I could compare settings.

Best, Patrick

2017-02-02 0:01 GMT+01:00 Uwe Ligges :

> Check whether the parallel cluster is closed. Can it be that the cluster
> is still open and the check process waits for them to complete?
>
> Best,
> Uwe Ligges
>
>
>
> On 31.01.2017 13:45, Patrick Schratz wrote:
>
>> Hello,
>>
>> when running R CMD check / devtools::check, section "running tests..." is
>> not finishing (40 min+).
>>
>> *Checking tests only works:*
>>
>> *==> Sourcing R files in 'tests' directory*
>>
>> *testthat results
>> *
>> *OK: 7 SKIPPED: 0 FAILED: 0*
>>
>> *Tests complete*
>>
>>
>> As well as running tests line-by-line.
>>
>> How can I debug my tests to discover the problem during R CMD check?
>>
>> *Tests are using parallelization (foreach + doParallel)*
>>
>> Best, Patrick
>>
>> [[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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[R-pkg-devel] While using R CMD check: LaTex error: File `inconsolata.sty' not found

[Cathy Lee Gierke]

I cannot find any recent solution to this problem, and older ones do not
seem to work.

I just installed the small version of MacTeX called BasicTeX, to allow my
package to build PDFs.   http://tug.org/mactex/morepackages.html

Everything worked, except I get the error  "LaTex error: File
`inconsolata.sty' not found".  I tried to install inconsolata.sty as
suggested here,
https://stat.ethz.ch/pipermail/r-help//2013-July/356743.html but
get an error saying zi4 is not there when following the Read.Me install
instructions:

Mac OS X: Method A (recommended): type

>sudo mkdir -p /usr/local/texlive/texmf-local/web2c
>sudo cp -Rfp * /usr/local/texlive/texmf-local
>sudo echo Map zi4.map >> /usr/local/texlive/texmf-local/web2c/updmap.cfg
>sudo mktexlsr
..

kpsewhich zi4.sty returns nothing

kpsewhich inconsolata.sty returns nothing

So they must not be installed.  Any idea how to fix this?

Thanks much,
Cathy Lee Gierke


*“Darkness cannot drive out darkness: only light can do that. Hate cannot
drive out hate: only love can do that.” *
*“The arc of the moral universe is long, but it bends towards justice.”*
*“Nothing in the world is more dangerous than sincere ignorance and
conscientious stupidity.” *
*“Never forget that everything Hitler did in Germany was legal.”   *
*“Forgiveness is not an occasional act, it is a constant attitude.” *
*“Injustice anywhere is a threat to justice everywhere.”  *

― Martin Luther King Jr.



[[alternative HTML version deleted]]

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Re: [R-pkg-devel] R CMD Check: Tests running infinite

[Henrik Bengtsson]

Use

  registerDoParallel(cl)

The number of parallel workers is already contained in the 'cl'
object, so don't
specify 'cores'!  (If you do that, I suspect you create yet another cluster
(a multicore one) which is used but never closed)

registerDoParallel() should ideally give an error in your case. Author
BCC:ed.

Henrik

On Feb 5, 2017 03:56, "Patrick Schratz"  wrote:

> Dear Uwe,
>
> thanks for the hint. My cluster is closed after the `foreach`call using
> `stopCluster()`.
>
> Before, I´ll do the following to init the cluster:
>
> *cl <- makeCluster(par.args$par.units, outfile = out.progress)*
> *registerDoParallel(cl, cores = par.args$par.units)*
>
> *foreach()*
>
> *stopCluster(cl)*
>
> Do you know of any other package which is using foreach in combination with
> tests and is hosted on Github? So I could compare settings.
>
> Best, Patrick
>
> 2017-02-02 0:01 GMT+01:00 Uwe Ligges :
>
> > Check whether the parallel cluster is closed. Can it be that the cluster
> > is still open and the check process waits for them to complete?
> >
> > Best,
> > Uwe Ligges
> >
> >
> >
> > On 31.01.2017 13:45, Patrick Schratz wrote:
> >
> >> Hello,
> >>
> >> when running R CMD check / devtools::check, section "running tests..."
> is
> >> not finishing (40 min+).
> >>
> >> *Checking tests only works:*
> >>
> >> *==> Sourcing R files in 'tests' directory*
> >>
> >> *testthat results
> >> *
> >> *OK: 7 SKIPPED: 0 FAILED: 0*
> >>
> >> *Tests complete*
> >>
> >>
> >> As well as running tests line-by-line.
> >>
> >> How can I debug my tests to discover the problem during R CMD check?
> >>
> >> *Tests are using parallelization (foreach + doParallel)*
> >>
> >> Best, Patrick
> >>
> >> [[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]]
>
> __
> 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] R CMD Check: Tests running infinite

[Patrick Schratz]

Thanks for the hint, Hendrik!
However, this change did not make a difference :/

I tried to use all cluster closing functions I came across but tests are
still running infinite..

*cl <- makeCluster(par.args$par.units, outfile = out.progress)*

*registerDoParallel(cl)*

*foreach()*

*parallel::stopCluster(cl)*
*doParallel::registerDoSEQ()*
*doParallel::stopImplicitCluster()*

2017-02-05 15:04 GMT+01:00 Henrik Bengtsson :

> Use
>
>   registerDoParallel(cl)
>
> The number of parallel workers is already contained in the 'cl' object, so
> don't specify 'cores'!  (If you do that, I suspect you create yet another
> cluster (a multicore one) which is used but never closed)
>
> registerDoParallel() should ideally give an error in your case. Author
> BCC:ed.
>
> Henrik
>
> On Feb 5, 2017 03:56, "Patrick Schratz"  wrote:
>
>> Dear Uwe,
>>
>> thanks for the hint. My cluster is closed after the `foreach`call using
>> `stopCluster()`.
>>
>> Before, I´ll do the following to init the cluster:
>>
>> *cl <- makeCluster(par.args$par.units, outfile = out.progress)*
>> *registerDoParallel(cl, cores = par.args$par.units)*
>>
>> *foreach()*
>>
>> *stopCluster(cl)*
>>
>>
>> Do you know of any other package which is using foreach in combination
>> with
>> tests and is hosted on Github? So I could compare settings.
>>
>> Best, Patrick
>>
>> 2017-02-02 0:01 GMT+01:00 Uwe Ligges :
>>
>> > Check whether the parallel cluster is closed. Can it be that the cluster
>> > is still open and the check process waits for them to complete?
>> >
>> > Best,
>> > Uwe Ligges
>> >
>> >
>> >
>> > On 31.01.2017 13:45, Patrick Schratz wrote:
>> >
>> >> Hello,
>> >>
>> >> when running R CMD check / devtools::check, section "running tests..."
>> is
>> >> not finishing (40 min+).
>> >>
>> >> *Checking tests only works:*
>> >>
>> >> *==> Sourcing R files in 'tests' directory*
>> >>
>> >> *testthat results
>> >> *
>> >> *OK: 7 SKIPPED: 0 FAILED: 0*
>> >>
>> >> *Tests complete*
>> >>
>> >>
>> >> As well as running tests line-by-line.
>> >>
>> >> How can I debug my tests to discover the problem during R CMD check?
>> >>
>> >> *Tests are using parallelization (foreach + doParallel)*
>> >>
>> >> Best, Patrick
>> >>
>> >> [[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]]
>>
>> __
>> 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] While using R CMD check: LaTex error: File `inconsolata.sty' not found

[Kasper Daniel Hansen]

If you installed MacTex basic, you should have the command line utility
  tlmgr
available. On my system it is in
  /Library/TeX/texbin/tlmgr
and you may need to add this to your path. Using this, it is simple to
install additional packages, by
  tlmgr install inconsolata
You probably need to add a sudo to this, so the full command becomes
  sudo tlmgr install inconsolata

(depending on how old MacTex is compared to recent releases, you _may_ need
to update tlmgr itself first.  I think it will be something like
  tlmgr update --self
but the program will tell you about this when you run it)

Best,
Kasper

On Sun, Feb 5, 2017 at 8:20 AM, Cathy Lee Gierke  wrote:

> I cannot find any recent solution to this problem, and older ones do not
> seem to work.
>
> I just installed the small version of MacTeX called BasicTeX, to allow my
> package to build PDFs.   http://tug.org/mactex/morepackages.html
>
> Everything worked, except I get the error  "LaTex error: File
> `inconsolata.sty' not found".  I tried to install inconsolata.sty as
> suggested here,
> https://stat.ethz.ch/pipermail/r-help//2013-July/356743.html but
> get an error saying zi4 is not there when following the Read.Me install
> instructions:
>
> Mac OS X: Method A (recommended): type
>
> >sudo mkdir -p /usr/local/texlive/texmf-local/web2c
> >sudo cp -Rfp * /usr/local/texlive/texmf-local
> >sudo echo Map zi4.map >> /usr/local/texlive/texmf-local/web2c/updmap.cfg
> >sudo mktexlsr
> ..
>
> kpsewhich zi4.sty returns nothing
>
> kpsewhich inconsolata.sty returns nothing
>
> So they must not be installed.  Any idea how to fix this?
>
> Thanks much,
> Cathy Lee Gierke
>
>
> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
> drive out hate: only love can do that.” *
> *“The arc of the moral universe is long, but it bends towards justice.”*
> *“Nothing in the world is more dangerous than sincere ignorance and
> conscientious stupidity.” *
> *“Never forget that everything Hitler did in Germany was legal.”   *
> *“Forgiveness is not an occasional act, it is a constant attitude.” *
> *“Injustice anywhere is a threat to justice everywhere.”  *
>
> ― Martin Luther King Jr.
>
> 
>
> [[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] R CMD Check: Tests running infinite

[Patrick Schratz]

@gaborcsardi solved it :) See here:
https://github.com/hadley/testthat/issues/567#issuecomment-277536577


2017-02-05 16:07 GMT+01:00 Patrick Schratz :

> Thanks for the hint, Hendrik!
> However, this change did not make a difference :/
>
> I tried to use all cluster closing functions I came across but tests are
> still running infinite..
>
> *cl <- makeCluster(par.args$par.units, outfile = out.progress)*
>
> *registerDoParallel(cl)*
>
> *foreach()*
>
> *parallel::stopCluster(cl)*
> *doParallel::registerDoSEQ()*
> *doParallel::stopImplicitCluster()*
>
> 2017-02-05 15:04 GMT+01:00 Henrik Bengtsson :
>
>> Use
>>
>>   registerDoParallel(cl)
>>
>> The number of parallel workers is already contained in the 'cl' object,
>> so don't specify 'cores'!  (If you do that, I suspect you create yet
>> another cluster (a multicore one) which is used but never closed)
>>
>> registerDoParallel() should ideally give an error in your case. Author
>> BCC:ed.
>>
>> Henrik
>>
>> On Feb 5, 2017 03:56, "Patrick Schratz" 
>> wrote:
>>
>>> Dear Uwe,
>>>
>>> thanks for the hint. My cluster is closed after the `foreach`call using
>>> `stopCluster()`.
>>>
>>> Before, I´ll do the following to init the cluster:
>>>
>>> *cl <- makeCluster(par.args$par.units, outfile = out.progress)*
>>> *registerDoParallel(cl, cores = par.args$par.units)*
>>>
>>> *foreach()*
>>>
>>> *stopCluster(cl)*
>>>
>>>
>>> Do you know of any other package which is using foreach in combination
>>> with
>>> tests and is hosted on Github? So I could compare settings.
>>>
>>> Best, Patrick
>>>
>>> 2017-02-02 0:01 GMT+01:00 Uwe Ligges :
>>>
>>> > Check whether the parallel cluster is closed. Can it be that the
>>> cluster
>>> > is still open and the check process waits for them to complete?
>>> >
>>> > Best,
>>> > Uwe Ligges
>>> >
>>> >
>>> >
>>> > On 31.01.2017 13:45, Patrick Schratz wrote:
>>> >
>>> >> Hello,
>>> >>
>>> >> when running R CMD check / devtools::check, section "running
>>> tests..." is
>>> >> not finishing (40 min+).
>>> >>
>>> >> *Checking tests only works:*
>>> >>
>>> >> *==> Sourcing R files in 'tests' directory*
>>> >>
>>> >> *testthat results
>>> >> *
>>> >> *OK: 7 SKIPPED: 0 FAILED: 0*
>>> >>
>>> >> *Tests complete*
>>> >>
>>> >>
>>> >> As well as running tests line-by-line.
>>> >>
>>> >> How can I debug my tests to discover the problem during R CMD check?
>>> >>
>>> >> *Tests are using parallelization (foreach + doParallel)*
>>> >>
>>> >> Best, Patrick
>>> >>
>>> >> [[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]]
>>>
>>> __
>>> R-package-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>
>

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[R-pkg-devel] Delaporte: Test Errors on Sun Sparc

[Avraham Adler]

I recently changed the back-end compiled code for the Delaporte
package from C++ to Fortran/C, and after some birthing pains (and a
lot of patience shown by CRAN), it's fully functional _except_ on
sparc-sun-solaris2.10 [1]. There, 10 of the 44 tests return errors.
I've done enough research to know that there may be endian issues
involved, but I do not know how to address them.

Interestingly, some of the errors look as if they are caused by
returning the "ones-complement" (if that is a word, meaning returning
1 - x instead of x) in some cases. See tests 3, 4, 6, and 7 for
examples. In the next version (which won't be posted to CRAN for at
least a month 8-) ), I've expanded the number of tests from 44 to (at
least) 86 to try to more cleanly isolate possible failures, but I
don't have access to a sparc-based Sun server, nor is there one on
Rhub and win-builder, so I cannot test it.

Has anyone seen anything similar or does this ring any bells?

Thank you,

Avi

[1] 


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Re: [R-pkg-devel] While using R CMD check: LaTex error: File `inconsolata.sty' not found

[Cathy Lee Gierke]

Hey, it worked!!  Thanks!

I had tried sudo tlmgr install collection-fontsrecommended earlier, but it
didn't install what I needed

― Martin Luther King Jr.



On Sun, Feb 5, 2017 at 12:27 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> If you installed MacTex basic, you should have the command line utility
>   tlmgr
> available. On my system it is in
>   /Library/TeX/texbin/tlmgr
> and you may need to add this to your path. Using this, it is simple to
> install additional packages, by
>   tlmgr install inconsolata
> You probably need to add a sudo to this, so the full command becomes
>   sudo tlmgr install inconsolata
>
> (depending on how old MacTex is compared to recent releases, you _may_
> need to update tlmgr itself first.  I think it will be something like
>   tlmgr update --self
> but the program will tell you about this when you run it)
>
> Best,
> Kasper
>
> On Sun, Feb 5, 2017 at 8:20 AM, Cathy Lee Gierke  wrote:
>
>> I cannot find any recent solution to this problem, and older ones do not
>> seem to work.
>>
>> I just installed the small version of MacTeX called BasicTeX, to allow my
>> package to build PDFs.   http://tug.org/mactex/morepackages.html
>>
>> Everything worked, except I get the error  "LaTex error: File
>> `inconsolata.sty' not found".  I tried to install inconsolata.sty as
>> suggested here,
>> https://stat.ethz.ch/pipermail/r-help//2013-July/356743.html but
>> get an error saying zi4 is not there when following the Read.Me install
>> instructions:
>>
>> Mac OS X: Method A (recommended): type
>>
>> >sudo mkdir -p /usr/local/texlive/texmf-local/web2c
>> >sudo cp -Rfp * /usr/local/texlive/texmf-local
>> >sudo echo Map zi4.map >> /usr/local/texlive/texmf-local/web2c/updmap.cfg
>> >sudo mktexlsr
>> ..
>>
>> kpsewhich zi4.sty returns nothing
>>
>> kpsewhich inconsolata.sty returns nothing
>>
>> So they must not be installed.  Any idea how to fix this?
>>
>> Thanks much,
>> Cathy Lee Gierke
>>
>>
>> *“Darkness cannot drive out darkness: only light can do that. Hate cannot
>> drive out hate: only love can do that.” *
>> *“The arc of the moral universe is long, but it bends towards justice.”*
>> *“Nothing in the world is more dangerous than sincere ignorance and
>> conscientious stupidity.” *
>> *“Never forget that everything Hitler did in Germany was legal.”   *
>> *“Forgiveness is not an occasional act, it is a constant attitude.” *
>> *“Injustice anywhere is a threat to justice everywhere.”  *
>>
>> ― Martin Luther King Jr.
>>
>> 
>>
>> [[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] Delaporte: Test Errors on Sun Sparc

[Mark van der Loo]

Avraham,

I can't help you out directly but Jeroen Ooms has a VM image with Solaris &
R available: https://github.com/jeroenooms/solarisvm

best,
Mark



Op zo 5 feb. 2017 om 21:27 schreef Avraham Adler :

> I recently changed the back-end compiled code for the Delaporte
> package from C++ to Fortran/C, and after some birthing pains (and a
> lot of patience shown by CRAN), it's fully functional _except_ on
> sparc-sun-solaris2.10 [1]. There, 10 of the 44 tests return errors.
> I've done enough research to know that there may be endian issues
> involved, but I do not know how to address them.
>
> Interestingly, some of the errors look as if they are caused by
> returning the "ones-complement" (if that is a word, meaning returning
> 1 - x instead of x) in some cases. See tests 3, 4, 6, and 7 for
> examples. In the next version (which won't be posted to CRAN for at
> least a month 8-) ), I've expanded the number of tests from 44 to (at
> least) 86 to try to more cleanly isolate possible failures, but I
> don't have access to a sparc-based Sun server, nor is there one on
> Rhub and win-builder, so I cannot test it.
>
> Has anyone seen anything similar or does this ring any bells?
>
> Thank you,
>
> Avi
>
> [1] <
> https://www.r-project.org/nosvn/R.check/r-patched-solaris-sparc/Delaporte-00check.html
> >
>
> __
> 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] R CMD Check: Tests running infinite

[Henrik Bengtsson]

In case someone else bumps into this later and finds this thread; can
you confirm that this was a problem specific to using the testthat
package for running the tests?

/Henrik

On Sun, Feb 5, 2017 at 11:28 AM, Patrick Schratz
 wrote:
> @gaborcsardi solved it :) See here:
> https://github.com/hadley/testthat/issues/567#issuecomment-277536577
>
>
> 2017-02-05 16:07 GMT+01:00 Patrick Schratz :
>>
>> Thanks for the hint, Hendrik!
>> However, this change did not make a difference :/
>>
>> I tried to use all cluster closing functions I came across but tests are
>> still running infinite..
>>
>> cl <- makeCluster(par.args$par.units, outfile = out.progress)
>> registerDoParallel(cl)
>>
>> foreach()
>>
>> parallel::stopCluster(cl)
>> doParallel::registerDoSEQ()
>> doParallel::stopImplicitCluster()
>>
>> 2017-02-05 15:04 GMT+01:00 Henrik Bengtsson :
>>>
>>> Use
>>>
>>>   registerDoParallel(cl)
>>>
>>> The number of parallel workers is already contained in the 'cl' object,
>>> so don't specify 'cores'!  (If you do that, I suspect you create yet another
>>> cluster (a multicore one) which is used but never closed)
>>>
>>> registerDoParallel() should ideally give an error in your case. Author
>>> BCC:ed.
>>>
>>> Henrik
>>>
>>> On Feb 5, 2017 03:56, "Patrick Schratz" 
>>> wrote:

 Dear Uwe,

 thanks for the hint. My cluster is closed after the `foreach`call using
 `stopCluster()`.

 Before, I´ll do the following to init the cluster:

 *cl <- makeCluster(par.args$par.units, outfile = out.progress)*
 *registerDoParallel(cl, cores = par.args$par.units)*

 *foreach()*

 *stopCluster(cl)*


 Do you know of any other package which is using foreach in combination
 with
 tests and is hosted on Github? So I could compare settings.

 Best, Patrick

 2017-02-02 0:01 GMT+01:00 Uwe Ligges :

 > Check whether the parallel cluster is closed. Can it be that the
 > cluster
 > is still open and the check process waits for them to complete?
 >
 > Best,
 > Uwe Ligges
 >
 >
 >
 > On 31.01.2017 13:45, Patrick Schratz wrote:
 >
 >> Hello,
 >>
 >> when running R CMD check / devtools::check, section "running
 >> tests..." is
 >> not finishing (40 min+).
 >>
 >> *Checking tests only works:*
 >>
 >> *==> Sourcing R files in 'tests' directory*
 >>
 >> *testthat results
 >> *
 >> *OK: 7 SKIPPED: 0 FAILED: 0*
 >>
 >> *Tests complete*
 >>
 >>
 >> As well as running tests line-by-line.
 >>
 >> How can I debug my tests to discover the problem during R CMD check?
 >>
 >> *Tests are using parallelization (foreach + doParallel)*
 >>
 >> Best, Patrick
 >>
 >> [[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]]

 __
 R-package-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>>
>

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