Re: [Rd] Test suite failures in R-devel_2017-02-25_r72256

[Prof Brian Ripley]

On 27/02/2017 09:30, Peter Simons wrote:

Hi,

I tried compiling the latest pre-release for R 3.3.3 for the NixOS Linux
distribution [1], but the build fails during the "make check" phase
because of the following 2 issues:


Hmm, R-devel (your subject line) is not a pre-release of R 3.3.3: it is 
'R Under development' for what is planned as R 3.4.0.  Pre-release 
tarballs for 3.3.3 are things like R-rc_2017-02-26_r72260.tar.gz (and 
were previously labelled R-beta).


Your first point only occurs in R-devel, and was something already 
reported and under investigation.  Note that test does not actually 
depend on network access: it depends on having an accessible CRAN 
mirror.  The latter could be local (and is on the CRAN check farm, for 
example).  So we have been working on a more sophisticated condition to 
run that test.


There are lots of possible check environments: it is very time-consuming 
to check them all and reasonable coverage is only attempted once a 
pre-release reaches 'alpha' status -- 3.4.0 has not done so but is 
planned to be in late March.


I have just re-checked on Linux, and R 3.3.3 RC passed its checks 
without Internet access (which is checked for where needed).


I also re-checked 3.3.3 RC without recommended packages and got the 
expected messages about incomplete testing but no failures except in 
'make check-recommended' (expected!).


Our posting guide does ask you to include the output of sessionInfo(): 
that would have avoided the version confusion (and might even have 
alerted you to it).




1) The "tools" test in "tests/Examples" requires network access, which
   it doesn't have in our build environment. Therefore, it fails as
   follows according to "tools-Ex.Rout.fail":

   | [...]
   | > set.seed(11)
   | > ## End(Don't show)
   | > pdb <- CRAN_package_db()
   | Warning in url(sprintf("%s/%s", cran, path), open = "rb") :
   |   URL 'http://CRAN.R-project.org/web/packages/packages.rds': status was 
'Couldn't resolve host name'
   | Error in url(sprintf("%s/%s", cran, path), open = "rb") :
   |   cannot open the connection to 
'http://CRAN.R-project.org/web/packages/packages.rds'
   | Calls: CRAN_package_db -> as.data.frame -> read_CRAN_object -> gzcon -> url
   | Execution halted

   I'm wondering whether it would be possible to extend the test suite
   with a configure-time flag that disable tests which depend on network
   access? My experience is that most modern Linux distributions run
   their builds in a restricted environment and therefore will run into
   trouble if the suite assumes that it can access the Internet.

2) When R is compiled with the --without-recommended-packages flag
   (which is our preferred configuration), the "base" test in
   "tests/Examples" fails, apparently because it depends on MASS. I'm
   citing from "base-Ex.Rout.fail":

   | >  ## The string "foo" and the symbol 'foo' can be used interchangably 
here:
   | >  stopifnot( identical(isNamespaceLoaded(  "foo"   ), FALSE),
   | + identical(isNamespaceLoaded(quote(foo)), FALSE),
   | + identical(isNamespaceLoaded(quote(stats)), statL))
   | >
   | > hasM <- isNamespaceLoaded("MASS") # (to restore if needed)
   | > Mns <- asNamespace("MASS") # loads it if not already
   | Error in loadNamespace(name) : there is no package called 'MASS'
   | Calls: asNamespace ... tryCatch -> tryCatchList -> tryCatchOne -> 

   | Execution halted

I hope this helps!

Best regards,
Peter



[1] http://nixos.org/

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Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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Re: [R-pkg-devel] .bib file in vignette not found during R CMD check

[Henrik Bengtsson]

On Tue, Feb 28, 2017 at 2:47 PM, Duncan Murdoch
 wrote:
> On 28/02/2017 5:17 PM, Patrick Schratz wrote:
>>
>> Thanks Duncan, that was the problem! Although the Rbuildignore entry
>> pointed to the main dir
>
>
> No, it contains patterns, not paths, and is matched "case-insensitively
> against the file and directory names relative to the top-level package
> source directory".  Put ^ at the beginning if you want to refer to the main
> dir.
>
> Hadley, reporting what gets omitted might be a good suggestion, but it might
> report too much in a package with compiled code (the .o files will generally
> be omitted; rgl has 51 of those in src...).

I like this idea.  It could be done such that R CMD build lists the
files omitted based solely on the content of .Rbuildignore, which I
assume is also what Hadley meant.  This way *.o files wouldn't be
listed since they're omitted by the built-in rules of R CMD build
itself.

/Henrik

>
> Duncan Murdoch
>
> and my .bib file was lying under vignettes/...
>>
>> That Rbuildignore entry was a leftover when my .bib file was initially
>> lying in the top directory and hence was throwing notes during R CMD
>> check.
>>
>> Afterwards I used full paths in the vignette to specify the .bib
>> location. This approach works fine until you submit to CRAN which of
>> course cannot deal with full paths (and you forget about that you used a
>> full path when releasing).
>>
>> @hadley
>> Could be useful as most often you do not think of possible leftover
>> entries in Rbuildignore...
>>
>> 2017-02-28 18:57 GMT+01:00 Duncan Murdoch > >:
>>
>> On 28/02/2017 10:44 AM, Patrick Schratz wrote:
>>
>> When building the vignette using R CMD Build or
>> `devtools::build_vignette()` everything works fine.
>>
>> However, during R CMD check I get the following
>>
>> ** checking running R code from vignettes ...*
>> *   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
>> * NONE*
>> ** checking re-building of vignette outputs ... WARNING*
>> *Error in re-building vignettes:*
>> *  ...*
>> *pandoc-citeproc: Could not find Biblio.bib*
>> *CallStack (from HasCallStack):*
>> *  error, called at src/Text/CSL/Pandoc.hs:224:39 in
>> pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
>> *pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
>> *Filter returned error status 1*
>> *Error: processing vignette 'sperrorest-vignette.Rmd' failed with
>> diagnostics:*
>> *pandoc document conversion failed with error 83*
>> *Execution halted*
>>
>> The .bib file is lying in `/vignettes`. There is a similar
>> question on SO
>>
>> >
>> >
>> but
>> the answer does not address the problem.
>> When using full paths everything is fine. However, I cannot use
>> full paths
>> when submitting to CRAN.
>>
>> If you want to check on your own, please use the `dev` branch;
>> https://github.com/pat-s/sperrorest/tree/dev
>> 
>>
>> pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
>> pandoc: stable 1.19.2.1 (bottled), HEAD
>>
>>
>> Your .Rbuildignore file says not to include Biblio.bib.  Don't do
>> that.
>>
>> Duncan Murdoch
>>
>>
>
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Re: [R-pkg-devel] .bib file in vignette not found during R CMD check

[Duncan Murdoch]

On 28/02/2017 5:17 PM, Patrick Schratz wrote:

Thanks Duncan, that was the problem! Although the Rbuildignore entry
pointed to the main dir


No, it contains patterns, not paths, and is matched "case-insensitively 
against the file and directory names relative to the top-level package 
source directory".  Put ^ at the beginning if you want to refer to the 
main dir.


Hadley, reporting what gets omitted might be a good suggestion, but it 
might report too much in a package with compiled code (the .o files will 
generally be omitted; rgl has 51 of those in src...).


Duncan Murdoch

and my .bib file was lying under vignettes/...

That Rbuildignore entry was a leftover when my .bib file was initially
lying in the top directory and hence was throwing notes during R CMD check.

Afterwards I used full paths in the vignette to specify the .bib
location. This approach works fine until you submit to CRAN which of
course cannot deal with full paths (and you forget about that you used a
full path when releasing).

@hadley
Could be useful as most often you do not think of possible leftover
entries in Rbuildignore...

2017-02-28 18:57 GMT+01:00 Duncan Murdoch >:

On 28/02/2017 10:44 AM, Patrick Schratz wrote:

When building the vignette using R CMD Build or
`devtools::build_vignette()` everything works fine.

However, during R CMD check I get the following

** checking running R code from vignettes ...*
*   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
* NONE*
** checking re-building of vignette outputs ... WARNING*
*Error in re-building vignettes:*
*  ...*
*pandoc-citeproc: Could not find Biblio.bib*
*CallStack (from HasCallStack):*
*  error, called at src/Text/CSL/Pandoc.hs:224:39 in
pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
*pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
*Filter returned error status 1*
*Error: processing vignette 'sperrorest-vignette.Rmd' failed with
diagnostics:*
*pandoc document conversion failed with error 83*
*Execution halted*

The .bib file is lying in `/vignettes`. There is a similar
question on SO

>
but
the answer does not address the problem.
When using full paths everything is fine. However, I cannot use
full paths
when submitting to CRAN.

If you want to check on your own, please use the `dev` branch;
https://github.com/pat-s/sperrorest/tree/dev


pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
pandoc: stable 1.19.2.1 (bottled), HEAD


Your .Rbuildignore file says not to include Biblio.bib.  Don't do that.

Duncan Murdoch




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Re: [R-pkg-devel] .bib file in vignette not found during R CMD check

[Hadley Wickham]

I wonder if it would be useful for R CMD build to list the files it
ignores? A misspecified .Rbuildignore seems to be reasonable for a
high proportion of weird errors where you have no idea what's going
wrong.

Hadley

On Tue, Feb 28, 2017 at 11:57 AM, Duncan Murdoch
 wrote:
> On 28/02/2017 10:44 AM, Patrick Schratz wrote:
>>
>> When building the vignette using R CMD Build or
>> `devtools::build_vignette()` everything works fine.
>>
>> However, during R CMD check I get the following
>>
>> ** checking running R code from vignettes ...*
>> *   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
>> * NONE*
>> ** checking re-building of vignette outputs ... WARNING*
>> *Error in re-building vignettes:*
>> *  ...*
>> *pandoc-citeproc: Could not find Biblio.bib*
>> *CallStack (from HasCallStack):*
>> *  error, called at src/Text/CSL/Pandoc.hs:224:39 in
>> pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
>> *pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
>> *Filter returned error status 1*
>> *Error: processing vignette 'sperrorest-vignette.Rmd' failed with
>> diagnostics:*
>> *pandoc document conversion failed with error 83*
>> *Execution halted*
>>
>> The .bib file is lying in `/vignettes`. There is a similar question on SO
>>
>> 
>> but
>> the answer does not address the problem.
>> When using full paths everything is fine. However, I cannot use full paths
>> when submitting to CRAN.
>>
>> If you want to check on your own, please use the `dev` branch;
>> https://github.com/pat-s/sperrorest/tree/dev
>>
>> pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
>> pandoc: stable 1.19.2.1 (bottled), HEAD
>
>
> Your .Rbuildignore file says not to include Biblio.bib.  Don't do that.
>
> Duncan Murdoch
>
>
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Re: [R-pkg-devel] .bib file in vignette not found during R CMD check

[Duncan Murdoch]

On 28/02/2017 10:44 AM, Patrick Schratz wrote:

When building the vignette using R CMD Build or
`devtools::build_vignette()` everything works fine.

However, during R CMD check I get the following

** checking running R code from vignettes ...*
*   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
* NONE*
** checking re-building of vignette outputs ... WARNING*
*Error in re-building vignettes:*
*  ...*
*pandoc-citeproc: Could not find Biblio.bib*
*CallStack (from HasCallStack):*
*  error, called at src/Text/CSL/Pandoc.hs:224:39 in
pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
*pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
*Filter returned error status 1*
*Error: processing vignette 'sperrorest-vignette.Rmd' failed with
diagnostics:*
*pandoc document conversion failed with error 83*
*Execution halted*

The .bib file is lying in `/vignettes`. There is a similar question on SO

but
the answer does not address the problem.
When using full paths everything is fine. However, I cannot use full paths
when submitting to CRAN.

If you want to check on your own, please use the `dev` branch;
https://github.com/pat-s/sperrorest/tree/dev

pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
pandoc: stable 1.19.2.1 (bottled), HEAD


Your .Rbuildignore file says not to include Biblio.bib.  Don't do that.

Duncan Murdoch

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Re: [Rd] Test suite failures in R-devel_2017-02-25_r72256

[Martin Maechler]

> Martin Maechler 
> on Mon, 27 Feb 2017 16:08:40 +0100 writes:

> Peter Simons 
> on Mon, 27 Feb 2017 10:30:39 +0100 writes:

>> Hi, I tried compiling the latest pre-release for R 3.3.3
>> for the NixOS Linux distribution [1], but the build fails
>> during the "make check" phase because of the following 2
>> issues:

>> 1) The "tools" test in "tests/Examples" requires network
>> access, which it doesn't have in our build
>> environment. 

> One may argue that the 'make check' (or even 'make check-all')
> tests could / should be allowed more resources than the pure
> build environment.

>> Therefore, it fails as follows according to
>> "tools-Ex.Rout.fail":

>> | [...]
>> | > set.seed(11)
>> | > ## End(Don't show)
>> | > pdb <- CRAN_package_db()
>> | Warning in url(sprintf("%s/%s", cran, path), open = "rb") :
>> |   URL 'http://CRAN.R-project.org/web/packages/packages.rds': status 
was 'Couldn't resolve host name'
>> | Error in url(sprintf("%s/%s", cran, path), open = "rb") :
>> |   cannot open the connection to 
'http://CRAN.R-project.org/web/packages/packages.rds'
>> | Calls: CRAN_package_db -> as.data.frame -> read_CRAN_object -> gzcon 
-> url
>> | Execution halted

>> I'm wondering whether it would be possible to extend the test suite
>> with a configure-time flag that disable tests which depend on network
>> access? My experience is that most modern Linux distributions run
>> their builds in a restricted environment and therefore will run into
>> trouble if the suite assumes that it can access the Internet.

> [see above] Is it necessary to also run the 'make check' part in
> that restricted environment?  Or could that ('checking") not get
> more priviledges?

> Note that you can only run  "make check" if you don't install
> recommended packages, whereas more thorough testing would
> include
>  make check-devel
> or even
>  make check-all
>
> but these do have quite a bit more requirements including
> recommended packages being present.

I have to correct myself:  The above paragraph may be misleading:

Much, if not all of
  make check-devel
and   make check-all
have worked well since R version 3.1.0  which had in its NEWS an entry

 • More of 'make check' will work if recommended packages are not
   installed: but recommended packages remain needed for thorough
   checking of an R build.

Further, the 'R-admin' manual (on 'make check-all' etc) contains

 |  Note that these checks are only run completely 
 |  if the recommended packages are installed.

so their presence is not required  but much recommended for
thorough testing.

Martin

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[R-pkg-devel] .bib file in vignette not found during R CMD check

[Patrick Schratz]

When building the vignette using R CMD Build or
`devtools::build_vignette()` everything works fine.

However, during R CMD check I get the following

** checking running R code from vignettes ...*
*   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
* NONE*
** checking re-building of vignette outputs ... WARNING*
*Error in re-building vignettes:*
*  ...*
*pandoc-citeproc: Could not find Biblio.bib*
*CallStack (from HasCallStack):*
*  error, called at src/Text/CSL/Pandoc.hs:224:39 in
pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
*pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
*Filter returned error status 1*
*Error: processing vignette 'sperrorest-vignette.Rmd' failed with
diagnostics:*
*pandoc document conversion failed with error 83*
*Execution halted*

The .bib file is lying in `/vignettes`. There is a similar question on SO

but
the answer does not address the problem.
When using full paths everything is fine. However, I cannot use full paths
when submitting to CRAN.

If you want to check on your own, please use the `dev` branch;
https://github.com/pat-s/sperrorest/tree/dev

pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
pandoc: stable 1.19.2.1 (bottled), HEAD

Best, Patrick

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