Re: [Bioc-devel] prebs failing in devel
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" > To: "Valerie Obenchain" , "bioc-devel" > > Cc: "Dan Tenenbaum" > 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" >> 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/d
Re: [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.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" > 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 -> hgu1
