search for: biocbld

...checked? For some packages, it only installs for the default arch ('i386'). Then testing the package for 'x64' fails. For example, Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz: ----------------------------------------------------------- * using log directory 'D:/biocbld/bbs-2.9-bioc/meat/fabia.Rcheck' * using R version 2.14.0 Under development (unstable) (2011-05-30 r56020) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'fabia/DESCRIPTION' ... OK * this is packag...

...nd R-2.12 (2010-08-26 r52817) on both machines: >>> On 64-bit Windows: R\bin\R.exe CMD build ACME --> produces no output at all and returns code 0. >>> On 32-bit Windows: R\bin\R.exe CMD check --no-vignettes --timings affypdnn_1.23.0.tar.gz * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/affypdnn.Rcheck' * using R version 2.12.0 Under development (unstable) (2010-08-26 r52817) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'affypdnn/DESCRIPTION' ... OK * this is...

Hi, The R-based version of R CMD build doesn't work for me on Windows: E:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\Biobase * checking for file 'meat\Biobase/DESCRIPTION' ... OK * preparing 'Biobase': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes Warning in shell(sprintf("%...

Hi, 'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder on Windows: D:\biocbld\bbs-2.7-bioc>ls meat/BUS/src BUS.cpp BUS.h D:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\BUS * checking for file 'meat\BUS/DESCRIPTION' ... OK * preparing 'BUS': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to r...

...re package ( https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xmapcore/username/password: readonly) has this: R=${R_HOME}/bin/R SUITE=../cookbook/delia.R [...] ${R} --vanilla --verbose < ${SUITE} the output of trying to build this package includes: * creating vignettes ... ERROR E:\biocbld\BBS-2~1.8-B\R/bin/R --vanilla --verbose < ../cookbook/delia.R E:biocbldBBS-2~1.8-BR/bin/R: not found make: *** [pdf] Error 127 Error in tools::buildVignettes(dir = ".") : running 'make' failed Execution halted It seems R_HOME is not getting resolved to a valid path. That's...

Hi, Every day a few Bioconductor packages (different ones each day) fail to build, on Windows only, with an error like this: D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OrganismDbi [...] Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for...

...inary package building. It seems, however, that write access to $R_HOME is required as part of the install step even when -l is used to specify an alternate package library. here's an example of what we're seeing: C:\rlibdir\hpages>set R_LIBS=c:\rlibdir\hpages C:\rlibdir\hpages>d:\biocbld\R-devel\bin\R CMD INSTALL -l=%R_LIBS% --build Biobase_1.6.7.tar.gz Using auto-selected zip options 'Biobase-ZIPDATA=zip Biobase-HELP=ziponly' ---------- Making package Biobase ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... ......

Hi, So in an interactive R session, R.home() returns the following: > R.home() [1] "D:/biocbld/bbs-3.2-bioc/R" However, if I call it from system2(), I get different results: > system2("R", "-q -e R.home()") > R.home() [1] "D:/biocbld/BBS-3~1.2-B/R" Similarly: > system2("R", "-q -e Sys.getenv('R_HOME')") > Sys.gete...

Hi, On Windows, with last R-devel tarball (r40647) from ftp://ftp.stat.math.ethz.ch/Software/R/R-devel_2007-02-04.tar.gz I get the following build error: E:\biocbld\bbs-2.0-bioc\R\src\gnuwin32> make ... ... ---------- Making package utils ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata installing R files Error in namespaceExport(ns, exports) : undefined exports :?, CRAN.packages, Rprof, Rprofmem, RShowDo c, RSiteS...

...r) package graph. Unfortunately, the current stable release of graphviz for Windows http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.22.2.msi contains a graph.dll in its bin directory. The situation is that Rgraphviz needs to link to the graph.dll from graphviz, E:\paboyoun>..\biocbld\bbs-2.4-bioc\R\bin\R CMD build Rgraphviz [...omitting output...] ** libs making DLL ... [...omitting output...] gcc -shared -s -o Rgraphviz.dll tmp.def LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwr ite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init....

...on windows only ( it builds successfully on Mac and Linux) when trying to build bumphunter http://bioconductor.org/packages/2.12/bioc/html/bumphunter.html Warning: running command '"C:\PROGRA?2\MIKTEX?1.9\miktex\bin\texi2dvi.exe" --quiet --pdf "bumphunter.tex" -I "E:/biocbld/bbs-2.12-bioc/R/share/texmf/tex/latex" -I "E:/biocbld/bbs-2.12-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')...

...> >> On Fri, Apr 12, 2013 at 5:34 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote: >> >>> Hi, >>> Every day a few Bioconductor packages (different ones each day) fail >>> to build, on Windows only, with an error like this: >>> >>> D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD >>> build --keep-empty-dirs --no-resave-data OrganismDbi >>> [...] >>> Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : >>> Failed to locate the 'texi2pdf'...

...trying URL 'http://cran.fhcrc.org/src/contrib/multtest_2.6.0.tar.gz' Content type 'application/x-gzip' length 1457444 bytes (1.4 Mb) opened URL downloaded 1.4 Mb ERROR: dependency 'Biobase' is not available for package 'multtest' * removing 'D:/biocbld/bbs-2.7-bioc/R/library/multtest' The downloaded packages are in 'C:\Users\biocbuild2\AppData\Local\Temp\2\RtmpPzRqzb\downloaded_packages' Warning message: In install.packages("multtest", type = "source") : installation of package 'multtest' h...

..."Sys.getenv('TEXINPUTS')" | R --slave TEXINPUTS "" But on Windows: E:\tmp>echo %TEXINPUTS% %TEXINPUTS% E:\tmp>echo Sys.getenv("TEXINPUTS") | R\bin\R.exe --slave TEXINPUTS ".;;E:/biocbld/bbs-2.7-bioc/R/share/texmf/tex/latex;" So on Linux if I cd to the inst/doc folder of a package source tree that has a Makefile and run echo "tools:::buildVignettes('pkgname', '.')" | R --slave it fails with error: ! LaTeX Error: File `Sweave.sty' not fou...

...hat we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty: E:\biocbld\bbs-2.7-bioc\R\library>ls -al DLBCL total 1 drwxr-xr-x+ 1 biocbuild2 root 0 2010-11-08 14:11 . drwxr-xr-x+ 1 biocbuild2 root 0 2010-11-10 00:14 .. -rwxr-xr-x+ 1 biocbuild2 root 0 2010-11-08 14:11 DESCRIPTION -rwxr-xr-x+ 1 biocbuild2 root 357 2010-11-08 14:11 INDEX drwxr-x...

...xing the DESCRIPTION file for EBImage. FYI, the Windows > >> version does not build: > >> > >> * creating vignettes ... ERROR > >> Error in inDL(x, as.logical(local), as.logical(now), ...) : > >> unable to load shared library > >> > 'D:/biocbld/bbs-2.3-bioc/tmpdir/Rinst415629052/EBImage/libs/EBImage.dll': > >> LoadLibrary failure: The specified procedure could not be found. > >> > >> Error: processing vignette 'AnalysisWithEBImage.Rnw' failed with > >> diagnostics: > >> chunk 1 (...

In the process of updating R to R 2.7 alpha or R 2.7 beta for the BioConductor 2.2 builds on Windows, I have hit a snag because the BioC build system has long path names (e.g. D:\biocbld\bbs-2.2-bioc\R) and these path names are not resolving properly by MiKTeX 2.7 during vignette construction. Take, for example, the attached vignette from Biobase, Bioconductor.Rnw. I have built R from source at E:\paboyoun\bbs-2.2-bioc\R and the session information for this R is === BEGIN R B...