[Bioc-devel] prebs failing in devel
Dan Tenenbaum
dtenenba at fredhutch.org
Mon Apr 25 17:18:24 CEST 2016
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.uziela at scilifelab.se>
> To: "Valerie Obenchain" <Valerie.Obenchain at roswellpark.org>, "bioc-devel" <bioc-devel at r-project.org>
> Cc: "Dan Tenenbaum" <dtenenba at 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.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
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>>>>
>>>
>
>
> --
>
> Karolis Uziela
>
> PhD student
> Science for Life Laboratory
> Box 1031
> 17121 Solna, Sweden
> Mob. +46 729 120 395
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