Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

2017-08-15 Thread Neumann, Steffen 
Indeed, is magically fixed today. 
Thanks for the clarification.
Yours,
Steffen

On Fri, 2017-08-11 at 11:38 -0400, Martin Morgan wrote:
> On 08/10/2017 04:14 PM, Neumann, Steffen wrote:
> > Hi BioC,
> > 
> > since that build error we have updated xcms to 2.99.6,
> > and have started to convert the xcmsDirect vignette to Rmd.
> > Now, we have the same kind of build error on the xcmsMsn vignette,
> > http://bioconductor.org/checkResults/devel/bioc-LATEST/xcms/tokay1-
> > buildsrc.html
> > 
> > I think that just converting the vignettes will fix the symptoms,
> > but we should really fix the cause of the error, for that
> > we need some more diagnostics, we weren't yet able to reproduce.
> > 
> > Any ideas ?
> 
> This generally looks like a transient problem we see, maybe related
> to 
> disk latency associated with large files (e.g., plots) produced
> during 
> the vignette processing, but we really don't have a clear handle on
> this.
> 
> Martin
> 
> > 
> > Yours,
> > Steffen
> > 
> > 
> > On Sun, 2017-07-30 at 19:42 +, Neumann, Steffen wrote:
> > > Hi,
> > > 
> > > Hi,
> > > 
> > > any suggestions or better diagnostics that could help us
> > > fixing this, in case it really is something in xcms ?
> > > 
> > > There were a few earlier reports with similar messages,
> > > 
> > > back in 2013, slightly hinting at virus scanners:
> > > http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-
> > > outp
> > > ut-file-quot-td4664111.html
> > > 
> > > Back in 2015, but both referring to SPB:
> > > https://github.com/Bioconductor/packagebuilder/issues/2
> > > https://github.com/Bioconductor/packagebuilder/issues/26
> > > 
> > > And from 2016 without any resolution:
> > > https://github.com/r-hub/rhub/issues/58
> > > 
> > > Yours,
> > > Steffen
> > > 
> > > 
> > > 
> > > On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:
> > > > Dear all,
> > > > 
> > > > one of the xcms vignettes fails to build on tokay1 recently
> > > > with
> > > > the
> > > > error message:
> > > > 
> > > > Warning: running command
> > > > '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --
> > > > pdf
> > > > "xcmsDirect.tex" --max-iterations=20 -I
> > > > "C:/Users/biocbuild/bbs-
> > > > 3.6-
> > > > bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> > > > bioc/R/share/texmf/bibtex/bst"' had status 1
> > > > Error in find_vignette_product(name, by = "texi2pdf", engine =
> > > > engine) :
> > > >    Failed to locate the 'texi2pdf' output file (by engine
> > > > 'utils::Sweave') for vignette with name 'xcmsDirect'. The
> > > > following
> > > > files exist in directory '.': 'FlowChart.graffle',
> > > > 'FlowChart.pdf',
> > > > 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> > > > 'new_functionality.R', 'new_functionality.Rmd',
> > > > 'new_functionality.html', 'new_functionality.org',
> > > > 'references.bib',
> > > > 'xcms.bib', 'xcms.org', 'xcmsDirect-005.pdf',
> > > > 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw',
> > > > 'xcmsMSn.Rnw',
> > > > 'xcmsPreprocess.Rnw-notrun'
> > > > Calls:  -> find_vignette_product
> > > > Execution halted
> > > > 
> > > > is this some problem with tokay1 or is it related to the
> > > > vignette
> > > > (I
> > > > have no problems building this vignette in my Windows build
> > > > machine)?
> > > > 
> > > > thanks, jo
> > > > 
> > > > 
> > > > [[alternative HTML version deleted]]
> > > > 
> > > > ___
> > > > Bioc-devel@r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > 
> > > -- 
> > > 
> > > IPB HalleAG Massenspektrometrie &
> > > Bioinformatik
> > > Dr. Steffen Neumann  http://www.IPB-Halle.DE
> > > Weinberg 3   http://msbi.bic-gh.de
> > > 06120 Halle  Tel. +49 (0) 345 5582 - 1470
> > >    +49 (0) 345 5582 - 0
> > > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
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-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE 

Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

2017-08-11 Thread Martin Morgan 

On 08/10/2017 04:14 PM, Neumann, Steffen wrote:

Hi BioC,

since that build error we have updated xcms to 2.99.6,
and have started to convert the xcmsDirect vignette to Rmd.
Now, we have the same kind of build error on the xcmsMsn vignette,
http://bioconductor.org/checkResults/devel/bioc-LATEST/xcms/tokay1-buildsrc.html

I think that just converting the vignettes will fix the symptoms,
but we should really fix the cause of the error, for that
we need some more diagnostics, we weren't yet able to reproduce.

Any ideas ?


This generally looks like a transient problem we see, maybe related to 
disk latency associated with large files (e.g., plots) produced during 
the vignette processing, but we really don't have a clear handle on this.


Martin



Yours,
Steffen


On Sun, 2017-07-30 at 19:42 +, Neumann, Steffen wrote:

Hi,

Hi,

any suggestions or better diagnostics that could help us
fixing this, in case it really is something in xcms ?

There were a few earlier reports with similar messages,

back in 2013, slightly hinting at virus scanners:
http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-outp
ut-file-quot-td4664111.html

Back in 2015, but both referring to SPB:
https://github.com/Bioconductor/packagebuilder/issues/2
https://github.com/Bioconductor/packagebuilder/issues/26

And from 2016 without any resolution:
https://github.com/r-hub/rhub/issues/58

Yours,
Steffen



On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:

Dear all,

one of the xcms vignettes fails to build on tokay1 recently with
the
error message:

Warning: running command
'"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf
"xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-
3.6-
bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
bioc/R/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine =
engine) :
   Failed to locate the 'texi2pdf' output file (by engine
'utils::Sweave') for vignette with name 'xcmsDirect'. The following
files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf',
'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
'new_functionality.R', 'new_functionality.Rmd',
'new_functionality.html', 'new_functionality.org',
'references.bib',
'xcms.bib', 'xcms.org', 'xcmsDirect-005.pdf',
'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw',
'xcmsMSn.Rnw',
'xcmsPreprocess.Rnw-notrun'
Calls:  -> find_vignette_product
Execution halted

is this some problem with tokay1 or is it related to the vignette
(I
have no problems building this vignette in my Windows build
machine)?

thanks, jo


[[alternative HTML version deleted]]

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IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

2017-08-10 Thread Neumann, Steffen 
Hi BioC, 

since that build error we have updated xcms to 2.99.6,
and have started to convert the xcmsDirect vignette to Rmd.
Now, we have the same kind of build error on the xcmsMsn vignette,
http://bioconductor.org/checkResults/devel/bioc-LATEST/xcms/tokay1-buildsrc.html

I think that just converting the vignettes will fix the symptoms, 
but we should really fix the cause of the error, for that 
we need some more diagnostics, we weren't yet able to reproduce.

Any ideas ?

Yours,
Steffen


On Sun, 2017-07-30 at 19:42 +, Neumann, Steffen wrote:
> Hi, 
> 
> Hi,
> 
> any suggestions or better diagnostics that could help us 
> fixing this, in case it really is something in xcms ? 
> 
> There were a few earlier reports with similar messages, 
> 
> back in 2013, slightly hinting at virus scanners: 
> http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-outp
> ut-file-quot-td4664111.html
> 
> Back in 2015, but both referring to SPB:
> https://github.com/Bioconductor/packagebuilder/issues/2
> https://github.com/Bioconductor/packagebuilder/issues/26
> 
> And from 2016 without any resolution:
> https://github.com/r-hub/rhub/issues/58
> 
> Yours,
> Steffen
> 
> 
> 
> On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:
> > Dear all,
> > 
> > one of the xcms vignettes fails to build on tokay1 recently with
> > the
> > error message:
> > 
> > Warning: running command
> > '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf
> > "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-
> > 3.6-
> > bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> > bioc/R/share/texmf/bibtex/bst"' had status 1
> > Error in find_vignette_product(name, by = "texi2pdf", engine =
> > engine) :
> >   Failed to locate the 'texi2pdf' output file (by engine
> > 'utils::Sweave') for vignette with name 'xcmsDirect'. The following
> > files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf',
> > 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> > 'new_functionality.R', 'new_functionality.Rmd',
> > 'new_functionality.html', 'new_functionality.org',
> > 'references.bib',
> > 'xcms.bib', 'xcms.org', 'xcmsDirect-005.pdf',
> > 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw',
> > 'xcmsMSn.Rnw',
> > 'xcmsPreprocess.Rnw-notrun'
> > Calls:  -> find_vignette_product
> > Execution halted
> > 
> > is this some problem with tokay1 or is it related to the vignette
> > (I
> > have no problems building this vignette in my Windows build
> > machine)?
> > 
> > thanks, jo
> > 
> > 
> > [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> -- 
> 
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   http://msbi.bic-gh.de
> 06120 Halle  Tel. +49 (0) 345 5582 - 1470
>   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] Vignette for xcms fails to build on tokay1

2017-07-30 Thread Neumann, Steffen 
Hi, 

Hi,

any suggestions or better diagnostics that could help us 
fixing this, in case it really is something in xcms ? 

There were a few earlier reports with similar messages, 

back in 2013, slightly hinting at virus scanners: 
http://r.789695.n4.nabble.com/quot-Failed-to-locate-the-texi2pdf-output-file-quot-td4664111.html

Back in 2015, but both referring to SPB:
https://github.com/Bioconductor/packagebuilder/issues/2
https://github.com/Bioconductor/packagebuilder/issues/26

And from 2016 without any resolution:
https://github.com/r-hub/rhub/issues/58

Yours,
Steffen



On Thu, 2017-07-27 at 10:23 +, Rainer Johannes wrote:
> Dear all,
> 
> one of the xcms vignettes fails to build on tokay1 recently with the
> error message:
> 
> Warning: running command
> '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf
> "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.6-
> bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.6-
> bioc/R/share/texmf/bibtex/bst"' had status 1
> Error in find_vignette_product(name, by = "texi2pdf", engine =
> engine) :
>   Failed to locate the 'texi2pdf' output file (by engine
> 'utils::Sweave') for vignette with name 'xcmsDirect'. The following
> files exist in directory '.': 'FlowChart.graffle', 'FlowChart.pdf',
> 'benchmarking.Rmd-notrun', 'biomed-central.csl', 'example.tsv',
> 'new_functionality.R', 'new_functionality.Rmd',
> 'new_functionality.html', 'new_functionality.org', 'references.bib',
> 'xcms.bib', 'xcms.org', 'xcmsDirect-005.pdf',
> 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw', 'xcmsMSn.Rnw',
> 'xcmsPreprocess.Rnw-notrun'
> Calls:  -> find_vignette_product
> Execution halted
> 
> is this some problem with tokay1 or is it related to the vignette (I
> have no problems building this vignette in my Windows build machine)?
> 
> thanks, jo
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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[Bioc-devel] Vignette for xcms fails to build on tokay1

2017-07-27 Thread Rainer Johannes 
Dear all,

one of the xcms vignettes fails to build on tokay1 recently with the error 
message:

Warning: running command '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" 
--quiet --pdf "xcmsDirect.tex" --max-iterations=20 -I 
"C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/tex/latex" -I 
"C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for 
vignette with name 'xcmsDirect'. The following files exist in directory '.': 
'FlowChart.graffle', 'FlowChart.pdf', 'benchmarking.Rmd-notrun', 
'biomed-central.csl', 'example.tsv', 'new_functionality.R', 
'new_functionality.Rmd', 'new_functionality.html', 'new_functionality.org', 
'references.bib', 'xcms.bib', 'xcms.org', 
'xcmsDirect-005.pdf', 'xcmsDirect.Rnw', 'xcmsDirect.tex', 'xcmsInstall.Rnw', 
'xcmsMSn.Rnw', 'xcmsPreprocess.Rnw-notrun'
Calls:  -> find_vignette_product
Execution halted

is this some problem with tokay1 or is it related to the vignette (I have no 
problems building this vignette in my Windows build machine)?

thanks, jo


[[alternative HTML version deleted]]

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