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.ha...@novartis.com
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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