For some reason zlibbioc was unavailable on windows yesterday, but GenomicRanges is ok in the build report that will come out later today.
Dan ----- Original Message ----- > From: "Karolis Uziela" <karolis.uzi...@scilifelab.se> > To: "Valerie Obenchain" <valerie.obench...@roswellpark.org>, "bioc-devel" > <bioc-devel@r-project.org> > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org> > Sent: Monday, April 25, 2016 1:02:02 AM > Subject: Re: 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.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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
