[Bioc-devel] prebs failing in devel
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.uziela at 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.uziela at 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.Obenchain at 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]]