[Bioc-devel] GenomicRanges broken in the devel branch

[Hervé Pagès]

Hi Florian,

Many packages broke because of the split between IRanges and XVector.
I tried to fix most of them during the week-end but somehow managed to
forget to fix GenomicRanges. Should be fixed now. You can get it thru
svn now or wait until tomorrow to get it thru biocLite().

Sorry for the inconvenience,
H.

On 05/13/2013 04:51 AM, Hahne, Florian wrote:
> You've probably already spotted this, but GenomicRanges seems to be
> broken, and because I just upgraded to the latest R I now can't build most
> of the Bioconductor packages that depend on it.
>
>> biocLite("GenomicRanges")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.11.1), R version 3.0.1.
> Installing package(s) 'GenomicRanges'
> trying URL
> 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GenomicRanges_1.13.
> 9.tar.gz'
> Content type 'application/x-gzip' length 2578455 bytes (2.5 Mb)
> opened URL
> ==================================================
> downloaded 2.5 Mb
>
> Bioconductor version 2.13 (BiocInstaller 1.11.1), ?biocLite for help
> * installing *source* package ŒGenomicRanges¹ ...
> ** libs
> *** arch - i386
> gcc -arch i386 -std=gnu99
> -I/Users/hahnefl1/R/source/R-release/build/include
> -I/Users/hahnefl1/R/source/R-release/build/include/i386 -DNDEBUG
> -I/usr/local/include
> -I"/Users/hahnefl1/R/source/R-release/localPackages/IRanges/include"
> -fPIC  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
> gcc -arch i386 -std=gnu99
> -I/Users/hahnefl1/R/source/R-release/build/include
> -I/Users/hahnefl1/R/source/R-release/build/include/i386 -DNDEBUG
> -I/usr/local/include
> -I"/Users/hahnefl1/R/source/R-release/localPackages/IRanges/include"
> -fPIC  -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
> gcc -arch i386 -std=gnu99
> -I/Users/hahnefl1/R/source/R-release/build/include
> -I/Users/hahnefl1/R/source/R-release/build/include/i386 -DNDEBUG
> -I/usr/local/include
> -I"/Users/hahnefl1/R/source/R-release/localPackages/IRanges/include"
> -fPIC  -g -O2  -c cigar_utils.c -o cigar_utils.o
> gcc -arch i386 -std=gnu99
> -I/Users/hahnefl1/R/source/R-release/build/include
> -I/Users/hahnefl1/R/source/R-release/build/include/i386 -DNDEBUG
> -I/usr/local/include
> -I"/Users/hahnefl1/R/source/R-release/localPackages/IRanges/include"
> -fPIC  -g -O2  -c transcript_utils.c -o transcript_utils.o
> transcript_utils.c:146: warning: type defaults to Œint¹ in declaration of
> ŒcachedCharSeq¹
> transcript_utils.c:146: error: expected Œ;¹, Œ,¹ or Œ)¹ before Œ*¹ token
> transcript_utils.c:167: warning: type defaults to Œint¹ in declaration of
> ŒcachedCharSeq¹
> transcript_utils.c:167: error: expected Œ;¹, Œ,¹ or Œ)¹ before Œ*¹ token
> transcript_utils.c: In function Œextract_transcripts¹:
> transcript_utils.c:260: error: ŒcachedCharSeq¹ undeclared (first use in
> this function)
> transcript_utils.c:260: error: (Each undeclared identifier is reported
> only once
> transcript_utils.c:260: error: for each function it appears in.)
> transcript_utils.c:260: error: expected Œ;¹ before ŒX¹
> transcript_utils.c:262: error: ŒcachedXVectorList¹ undeclared (first use
> in this function)
> transcript_utils.c:262: error: expected Œ;¹ before Œcached_ans¹
> transcript_utils.c:266: error: ŒX¹ undeclared (first use in this function)
> transcript_utils.c:266: warning: implicit declaration of function
> Œcache_XRaw¹
> transcript_utils.c:271: warning: implicit declaration of function
> Œalloc_XRawList¹
> transcript_utils.c:271: warning: assignment makes pointer from integer
> without a cast
> transcript_utils.c:273: error: Œcached_ans¹ undeclared (first use in this
> function)
> transcript_utils.c:273: warning: implicit declaration of function
> Œcache_XVectorList¹
> transcript_utils.c:274: warning: implicit declaration of function
> Œget_cachedXVectorList_length¹
> transcript_utils.c:285: error: ŒY¹ undeclared (first use in this function)
> transcript_utils.c:285: warning: implicit declaration of function
> Œget_cachedXRawList_elt¹
> transcript_utils.c:288: warning: implicit declaration of function
> Œcopy_transcript¹
> make: *** [transcript_utils.o] Error 1
> ERROR: compilation failed for package ŒGenomicRanges¹
> * removing Œ/Users/hahnefl1/R/source/R-release/localPackages/GenomicRanges¹
>
>
>
> Strangely enough this is the same error I see on the developer build page,
> and I am wondering how the broken package made it into biocLite. Guess is
> an R version issue
> Would be great if somebody could take a look.
>
> Florian
>
>
>> sessionInfo()
> R version 3.0.1 RC (2013-05-12 r62736)
> Platform: i386-apple-darwin12.3.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.11.1
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.1
>
>
>
>
>
>
>
> Florian Hahne
> Novartis Institute For Biomedical Research
> Translational Sciences / Preclinical Safety / PCS Informatics
> Expert Data Integration and Modeling Bioinformatics
> CHBS, WKL-135.2.26
> Novartis Institute For Biomedical Research, Werk Klybeck
> Klybeckstrasse 141
> CH-4057 Basel
> Switzerland
> Phone: +41 61 6967127
> Email : florian.hahne at novartis.com
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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