Hi, Now the problem with RPA package is fixed. However, PREBS fails to build on Windows server because of a problem with GenomicRanges. GenomicRanges fails to build on WindowsServer itself. Here is the error:
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/GenomicRanges_1.23.27.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicRanges.buildbin-libdir --merge-multiarch GenomicRanges_1.23.27.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.23.27.zip && rm GenomicRanges_1.23.27.tar.gz GenomicRanges_1.23.27.zip ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'GenomicRanges' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o C:/Rtools/mingw_32/bin/gcc -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o C:/Rtools/mingw_32/bin/gcc -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o C:/Rtools/mingw_32/bin/gcc -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"c:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c transcript_utils.c -o transcript_utils.o transcript_utils.c: In function 'tlocs2rlocs': transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized] return on_minus_strand ? end - tloc : start + tloc; ^ transcript_utils.c:120:24: note: 'end' was declared here int nexons, j, start, end, width; ^ transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized] return on_minus_strand ? end - tloc : start + tloc; ^ transcript_utils.c:120:17: note: 'start' was declared here int nexons, j, start, end, width; ^ C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR installing to E:/biocbld/bbs-3.3-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386 ** R ** inst ** preparing package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'zlibbioc' ERROR: lazy loading failed for package 'GenomicRanges' * removing 'E:/biocbld/bbs-3.3-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges' Warning: running command 'E:/biocbld/bbs-3.3-bioc/R/bin/i386/Rcmd.exe INSTALL --library=GenomicRanges.buildbin-libdir GenomicRanges_1.23.27.tar.gz --no-multiarch' had status 1 On Thu, Apr 21, 2016 at 5:40 PM, Karolis Uziela < karolis.uzi...@scilifelab.se> wrote: > Regarding 2) I cant evalute more chunks, because they depend on packages > that are not in Bioconductor (Custom CDF). Regarding 1) I will fix it > On Apr 21, 2016 5:37 PM, "Karolis Uziela" <karolis.uzi...@scilifelab.se> > wrote: > >> The problem is that Leo Lahti has accidentally changed the output format >> of his RPA package. I have already informed Leo regarding this and he >> promised to fix it. >> On Apr 21, 2016 5:16 PM, "Obenchain, Valerie" < >> valerie.obench...@roswellpark.org> wrote: >> >>> Karolis, >>> >>> prebs is failing on all platforms in devel: >>> >>> http://www.bioconductor.org/checkResults/devel/bioc-LATEST/ >>> >>> I see there haven't been any recent commits so the problem may be with a >>> dependency or change in R devel. I took a closer look at this pacakge >>> and found these problems: >>> >>> 1) need to add library(prebsdata) to vignette >>> >>> 2) need to evaluation more vignette chunks >>> Of 15 chunks only 4 are evaluated. >>> >>> 3) The vignette throws this error: >>> >>> > prebs_values <- calc_prebs(bam_files, manufacturer_cdf_mapping) >>> Inferred name for CDF package: HGU133Plus2_mapping.txt -> hgu133plus2cdf >>> >>> [1] "Finished: input1.bam" >>> [1] "Finished: input2.bam" >>> Note: Some probe IDs contain duplicates. If you are using manufacturer's >>> CDF then you can ignore this message. >>> >>> Estimated values for Bayesian prior: >>> >>> Alpha=1e-04 >>> >>> Beta=0.0136640101662362 >>> >>> Calculating Expression >>> Error in (function (classes, fdef, mtable) : >>> unable to find an inherited method for function ‘exprs’ for signature >>> ‘"list"’ >>> In addition: Warning message: >>> In rpa(abatch, bg.method = "none", cdf = CDF_NAME) : >>> RPA is a multi-array preprocessing method. The input affybatch has at >>> most a single array, however. Returning expressionSet with no background >>> correction or normalization. >>> > >>> >>> Please have a look and check in a fix asap. We are freezing devel builds >>> next week for the May 4 release. If the package isn't fixed by next >>> Tuesday (26) we will start End of Life: >>> >>> http://www.bioconductor.org/developers/package-end-of-life/ >>> >>> Let us know if you have questions. >>> >>> Valerie >>> >>> >>> >>> >>> >>> >>> >>> This email message may contain legally privileged and/or confidential >>> information. If you are not the intended recipient(s), or the employee or >>> agent responsible for the delivery of this message to the intended >>> recipient(s), you are hereby notified that any disclosure, copying, >>> distribution, or use of this email message is prohibited. If you have >>> received this message in error, please notify the sender immediately by >>> e-mail and delete this email message from your computer. Thank you. >>> >> -- Karolis Uziela PhD student Science for Life Laboratory Box 1031 17121 Solna, Sweden Mob. +46 729 120 395 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel