Hi Everyone, When I uploaded my package to Bioconductor it passed all tests for the Linux OS, but failed on the Windows Server. The error is below. Warning: running command '"c:\MikTex2.9\miktex\bin\texify.exe" --quiet --pdf "pathVar.tex" --max-iterations=20 -I "E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I "E:/biocbld/bbs-3.3-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 'pathVar'. The following files exist in directory '.': 'outline_fig_2.pdf', 'pathVar-2SamDisc_1.pdf', 'pathVar-dens_1.pdf', 'pathVar-diagnostics.pdf', 'pathVar-hist_1.pdf', 'pathVar.Rnw', 'pathVar.tex' Calls: <Anonymous> -> find_vignette_product Execution halted Also, here is a link to the build report. Does anyone know why this is happening? When I build it locally on my mac, the vignette is made and building the package is completed without any errors. http://bioconductor.org/checkResults/3.3/bioc-LATEST/pathVar/moscato2-buildsrc.html Best, Sam
[Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008
4 messages · Dan Tenenbaum, Samuel E Zimmerman
----- Original Message -----
From: "Samuel E Zimmerman" <sezimmer at einstein.yu.edu> To: "bioc-devel" <bioc-devel at r-project.org> Sent: Wednesday, January 27, 2016 8:35:24 AM Subject: [Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008
Hi Everyone, When I uploaded my package to Bioconductor it passed all tests for the Linux OS, but failed on the Windows Server. The error is below. Warning: running command '"c:\MikTex2.9\miktex\bin\texify.exe" --quiet --pdf "pathVar.tex" --max-iterations=20 -I "E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I "E:/biocbld/bbs-3.3-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 'pathVar'. The following files exist in directory '.': 'outline_fig_2.pdf', 'pathVar-2SamDisc_1.pdf', 'pathVar-dens_1.pdf', 'pathVar-diagnostics.pdf', 'pathVar-hist_1.pdf', 'pathVar.Rnw', 'pathVar.tex' Calls: <Anonymous> -> find_vignette_product Execution halted Also, here is a link to the build report. Does anyone know why this is happening? When I build it locally on my mac, the vignette is made and building the package is completed without any errors. http://bioconductor.org/checkResults/3.3/bioc-LATEST/pathVar/moscato2-buildsrc.html
This is a known issue that has been reported to R-devel. It is also very difficult to reproduce because it only happens once in a while. I just built your package successfully on moscato2, and in fact in the build report that is coming out later today it also built successfully. So all you have to do is wait. ;) Dan
Best, Sam [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Great. Thank you for the quick reply and solution! Sam
From: Dan Tenenbaum [dtenenba at fredhutch.org]
Sent: Wednesday, January 27, 2016 11:43 AM
To: Samuel E Zimmerman
Cc: bioc-devel
Subject: Re: [Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008
Sent: Wednesday, January 27, 2016 11:43 AM
To: Samuel E Zimmerman
Cc: bioc-devel
Subject: Re: [Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008
----- Original Message ----- > From: "Samuel E Zimmerman" <sezimmer at einstein.yu.edu> > To: "bioc-devel" <bioc-devel at r-project.org> > Sent: Wednesday, January 27, 2016 8:35:24 AM > Subject: [Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008 > Hi Everyone, > > When I uploaded my package to Bioconductor it passed all tests for the Linux OS, > but failed on the Windows Server. The error is below. > > > Warning: running command '"c:\MikTex2.9\miktex\bin\texify.exe" --quiet --pdf > "pathVar.tex" --max-iterations=20 -I > "E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I > "E:/biocbld/bbs-3.3-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 'pathVar'. The following files exist in directory '.': > 'outline_fig_2.pdf', 'pathVar-2SamDisc_1.pdf', 'pathVar-dens_1.pdf', > 'pathVar-diagnostics.pdf', 'pathVar-hist_1.pdf', 'pathVar.Rnw', 'pathVar.tex' > Calls: <Anonymous> -> find_vignette_product > Execution halted > > Also, here is a link to the build report. Does anyone know why this is > happening? When I build it locally on my mac, the vignette is made and building > the package is completed without any errors. > > http://bioconductor.org/checkResults/3.3/bioc-LATEST/pathVar/moscato2-buildsrc.html > This is a known issue that has been reported to R-devel. It is also very difficult to reproduce because it only happens once in a while. I just built your package successfully on moscato2, and in fact in the build report that is coming out later today it also built successfully. So all you have to do is wait. ;) Dan > Best, > Sam > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel
So it turns out there is not going to be a build report for windows in devel today, for an unrelated reason. But it should be ok in tomorrow's build. Dan ----- Original Message -----
From: "Samuel E Zimmerman" <sezimmer at einstein.yu.edu> To: "Dan Tenenbaum" <dtenenba at fredhutch.org> Cc: "bioc-devel" <bioc-devel at r-project.org> Sent: Wednesday, January 27, 2016 10:14:55 AM Subject: RE: [Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008
Great. Thank you for the quick reply and solution! Sam
________________________________________ From: Dan Tenenbaum [dtenenba at fredhutch.org] Sent: Wednesday, January 27, 2016 11:43 AM To: Samuel E Zimmerman Cc: bioc-devel Subject: Re: [Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008 ----- Original Message ----- From: "Samuel E Zimmerman" <sezimmer at einstein.yu.edu> To: "bioc-devel" <bioc-devel at r-project.org> Sent: Wednesday, January 27, 2016 8:35:24 AM Subject: [Bioc-devel] package passes R CMD BUILD on Linux (Ubuntu) but not Windows Server 2008 Hi Everyone, When I uploaded my package to Bioconductor it passed all tests for the Linux OS, but failed on the Windows Server. The error is below. Warning: running command '"c:\MikTex2.9\miktex\bin\texify.exe" --quiet --pdf "pathVar.tex" --max-iterations=20 -I "E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I "E:/biocbld/bbs-3.3-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 'pathVar'. The following files exist in directory '.': 'outline_fig_2.pdf', 'pathVar-2SamDisc_1.pdf', 'pathVar-dens_1.pdf', 'pathVar-diagnostics.pdf', 'pathVar-hist_1.pdf', 'pathVar.Rnw', 'pathVar.tex' Calls: <Anonymous> -> find_vignette_product Execution halted Also, here is a link to the build report. Does anyone know why this is happening? When I build it locally on my mac, the vignette is made and building the package is completed without any errors. http://bioconductor.org/checkResults/3.3/bioc-LATEST/pathVar/moscato2-buildsrc.html This is a known issue that has been reported to R-devel. It is also very difficult to reproduce because it only happens once in a while. I just built your package successfully on moscato2, and in fact in the build report that is coming out later today it also built successfully. So all you have to do is wait. ;) Dan Best, Sam [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel