[Bioc-devel] GenomicRanges broken in the devel branch

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 ?GenomicRanges? ...
** 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 ?int? in declaration of
?cachedCharSeq?
transcript_utils.c:146: error: expected ?;?, ?,? or ?)? before ?*? token
transcript_utils.c:167: warning: type defaults to ?int? in declaration of
?cachedCharSeq?
transcript_utils.c:167: error: expected ?;?, ?,? or ?)? before ?*? token
transcript_utils.c: In function ?extract_transcripts?:
transcript_utils.c:260: error: ?cachedCharSeq? 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 ?;? before ?X?
transcript_utils.c:262: error: ?cachedXVectorList? undeclared (first use
in this function)
transcript_utils.c:262: error: expected ?;? before ?cached_ans?
transcript_utils.c:266: error: ?X? undeclared (first use in this function)
transcript_utils.c:266: warning: implicit declaration of function
?cache_XRaw?
transcript_utils.c:271: warning: implicit declaration of function
?alloc_XRawList?
transcript_utils.c:271: warning: assignment makes pointer from integer
without a cast
transcript_utils.c:273: error: ?cached_ans? undeclared (first use in this
function)
transcript_utils.c:273: warning: implicit declaration of function
?cache_XVectorList?
transcript_utils.c:274: warning: implicit declaration of function
?get_cachedXVectorList_length?
transcript_utils.c:285: error: ?Y? undeclared (first use in this function)
transcript_utils.c:285: warning: implicit declaration of function
?get_cachedXRawList_elt?
transcript_utils.c:288: warning: implicit declaration of function
?copy_transcript?
make: *** [transcript_utils.o] Error 1
ERROR: compilation failed for package ?GenomicRanges?
* removing ?/Users/hahnefl1/R/source/R-release/localPackages/GenomicRanges?



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