[BioC] [devteam-bioc] R2.15.2 Rsamtools icc compiler bam_md.c(315) et al
Martin Morgan
mtmorgan at fhcrc.org
Mon Nov 5 21:25:58 CET 2012
Rsamtools 1.11.6, available via biocLite when using R-devel, might address these
issues; I don't have access to icc so am not sure.
In the end the issue is (mostly) the -std=c99 flag, and I addressed this by
revising code (in Rsamtools) to be c99 conformant (for me, avoiding strdup) and
adding directives at the head of samtools files deviating from the standard. I'm
not sure that these directives are supported across compilers.
- #define _POSIX_C_SOURCE 200112L /* Rsamtools: c99 fileno, fdopen, etc */
- #define _SVID_SOURCE /* Rsamtools: c99 strdup, drand48 */
- #define _BSD_SOURCE /* Rsamtools: c99 M_SQRT2 */
On 11/01/2012 05:57 PM, Maintainer wrote:
> I've started to look in to this. There seem to be at least three issues in the
> warnings and error below associated with use of the icc compiler.
>
> 1. getopt
>
> this is used in samtools code that is not relevant to Rsamtools, and can be
> addressed easily.
>
> 2. strdup
>
> this would appear to be a POSIX function that the icc does not support; this can
> be worked around with a little effort. It is used in Rsamtools source code.
>
> 3. fdopen
>
> This also appears to be a POSIX function not supported by icc. It is in samtools
> source code. I'm not exactly sure how to work around this; maybe _fdopen is a
> replacement but I haven't found definitive information about this.
>
> I wonder whether there are not other similar issues with using Bioconductor
> packages with C source code on icc compilers, and whether a less frustrating
> solution would be to compile R with gcc?
>
> Input from other developers welcome.
>
> Martin
>
>
> On 11/01/2012 10:31 AM, Maintainer wrote:
>>
>>> biocLite("cummeRbund")
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>> Installing package(s) 'cummeRbund'
>> also installing the dependencies 'Rsamtools', 'GenomicFeatures', 'biovizBase', 'rtracklayer', 'Gviz'
>>
>> trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Rsamtools_1.10.1.tar.gz'
>> Content type 'application/x-gzip' length 2111065 bytes (2.0 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.0 Mb
>>
>> trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/GenomicFeatures_1.10.0.tar.gz'
>> Content type 'application/x-gzip' length 742114 bytes (724 Kb)
>> opened URL
>> ==================================================
>> downloaded 724 Kb
>>
>> trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/biovizBase_1.6.0.tar.gz'
>> Content type 'application/x-gzip' length 1025033 bytes (1001 Kb)
>> opened URL
>> ==================================================
>> downloaded 1001 Kb
>>
>> trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/rtracklayer_1.18.0.tar.gz'
>> Content type 'application/x-gzip' length 1307339 bytes (1.2 Mb)
>> opened URL
>> ==================================================
>> downloaded 1.2 Mb
>>
>> trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Gviz_1.2.0.tar.gz'
>> Content type 'application/x-gzip' length 1391602 bytes (1.3 Mb)
>> opened URL
>> ==================================================
>> downloaded 1.3 Mb
>>
>> trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/cummeRbund_2.0.0.tar.gz'
>> Content type 'application/x-gzip' length 2327551 bytes (2.2 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.2 Mb
>>
>> * installing *source* package 'Rsamtools' ...
>> ** libs
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c Biostrings_stubs.c -o Biostrings_stubs.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c IRanges_stubs.c -o IRanges_stubs.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c as_bam.c -o as_bam.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c bamfile.c -o bamfile.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> bamfile.c(90): warning #188: enumerated type mixed with another type
>> R_RegisterCFinalizerEx(ext, _bamfile_finalizer, TRUE);
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c bcffile.c -o bcffile.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> bcffile.c(107): warning #188: enumerated type mixed with another type
>> _bcf_close(bfile->file, FALSE);
>> ^
>>
>> bcffile.c(114): warning #188: enumerated type mixed with another type
>> R_RegisterCFinalizerEx(ext, _bcffile_finalizer, TRUE);
>> ^
>>
>> bcffile.c(496): warning #188: enumerated type mixed with another type
>> _bcf_close(fin, FALSE);
>> ^
>>
>> bcffile.c(497): warning #188: enumerated type mixed with another type
>> _bcf_close(fout, FALSE);
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c encode.c -o encode.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c fafile.c -o fafile.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> fafile.c(58): warning #188: enumerated type mixed with another type
>> R_RegisterCFinalizerEx(ext, _fafile_finalizer, TRUE);
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c io_sam.c -o io_sam.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> io_sam.c(100): warning #188: enumerated type mixed with another type
>> bd->parse_status = 0;
>> ^
>>
>> io_sam.c(371): warning #266: function "strdup" declared implicitly
>> k = kh_put(str, h, strdup(s), &ret);
>> ^
>>
>> io_sam.c(371): warning #2330: argument of type "const char *" is incompatible with parameter of type "void *" (dropping qualifiers)
>> k = kh_put(str, h, strdup(s), &ret);
>> ^
>>
>> io_sam.c(551): warning #188: enumerated type mixed with another type
>> return FALSE;
>> ^
>>
>> io_sam.c(558): warning #188: enumerated type mixed with another type
>> return FALSE;
>> ^
>>
>> io_sam.c(560): warning #188: enumerated type mixed with another type
>> return TRUE;
>> ^
>>
>> io_sam.c(655): warning #266: function "strdup" declared implicitly
>> sbd->qname[idx] = strdup(bam1_qname(bam));
>> ^
>>
>> io_sam.c(687): warning #188: enumerated type mixed with another type
>> bd->parse_status |= CIGAR_BUFFER_OVERFLOW_ERROR;
>> ^
>>
>> io_sam.c(937): warning #188: enumerated type mixed with another type
>> LOGICAL(reverseComplement)[0],
>> ^
>>
>> io_sam.c(980): warning #188: enumerated type mixed with another type
>> _init_BAM_DATA(bfile, space, keepFlags, isSimpleCigar, FALSE,
>> ^
>>
>> io_sam.c(1030): warning #188: enumerated type mixed with another type
>> _init_BAM_DATA(bfile, space, keepFlags, isSimpleCigar, FALSE,
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c pileupbam.c -o pileupbam.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> pileupbam.c(690): warning #188: enumerated type mixed with another type
>> p.what = 0;
>> ^
>>
>> pileupbam.c(692): warning #188: enumerated type mixed with another type
>> p.what |= WHAT_SEQ;
>> ^
>>
>> pileupbam.c(694): warning #188: enumerated type mixed with another type
>> p.what |= WHAT_QUAL;
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools_patch.c -o samtools_patch.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c tabixfile.c -o tabixfile.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> tabixfile.c(52): warning #188: enumerated type mixed with another type
>> R_RegisterCFinalizerEx(ext, _tabixfile_finalizer, TRUE);
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c utilities.c -o utilities.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c zip_compression.c -o zip_compression.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/bgzf.c -o samtools/bgzf.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> samtools/bgzf.c(179): warning #266: function "fdopen" declared implicitly
>> FILE* file = fdopen(fd, "w");
>> ^
>>
>> samtools/bgzf.c(358): warning #1338: arithmetic on pointer to void or function type
>> fp->uncompressed_block + input_length,
>> ^
>>
>> samtools/bgzf.c(375): warning #1338: arithmetic on pointer to void or function type
>> zs.next_in = fp->compressed_block + 18;
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/kstring.c -o samtools/kstring.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/bam_aux.c -o samtools/bam_aux.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/bam.c -o samtools/bam.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/bam_import.c -o samtools/bam_import.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> samtools/bam_import.c(76): warning #266: function "fileno" declared implicitly
>> gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
>> ^
>>
>> samtools/bam_import.c(126): warning #266: function "fileno" declared implicitly
>> fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
>> ^
>>
>> samtools/bam_import.c(132): warning #266: function "strdup" declared implicitly
>> char *s = strdup(str->s);
>> ^
>>
>> samtools/bam_import.c(206): warning #266: function "strdup" declared implicitly
>> h->target_name[i] = strdup(tmp[i]);
>> ^
>>
>> samtools/bam_import.c(472): warning #266: function "fileno" declared implicitly
>> gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/sam.c -o samtools/sam.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> samtools/sam.c(22): warning #266: function "strdup" declared implicitly
>> h->target_name[i] = strdup(h0->target_name[i]);
>> ^
>>
>> samtools/sam.c(47): warning #266: function "fileno" declared implicitly
>> fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
>> ^
>>
>> samtools/sam.c(76): warning #266: function "fileno" declared implicitly
>> fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/bam_index.c -o samtools/bam_index.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> samtools/bam_index.c(52): warning #266: function "drand48" declared implicitly
>> KSORT_INIT(off, pair64_t, pair64_lt)
>> ^
>>
>> samtools/bam_index.c(399): warning #266: function "strdup" declared implicitly
>> fn = strdup(p + 1);
>> ^
>>
>> samtools/bam_index.c(399): warning #2330: argument of type "const char *" is incompatible with parameter of type "void *" (dropping qualifiers)
>> fn = strdup(p + 1);
>> ^
>>
>> samtools/bam_index.c(400): warning #266: function "strdup" declared implicitly
>> } else fn = strdup(_fn);
>> ^
>>
>> samtools/bam_index.c(400): warning #2330: argument of type "const char *" is incompatible with parameter of type "void *" (dropping qualifiers)
>> } else fn = strdup(_fn);
>> ^
>>
>> samtools/bam_index.c(492): warning #266: function "strdup" declared implicitly
>> } else fnidx = strdup(_fnidx);
>> ^
>>
>> samtools/bam_index.c(492): warning #2330: argument of type "const char *" is incompatible with parameter of type "void *" (dropping qualifiers)
>> } else fnidx = strdup(_fnidx);
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> samtools/bam_lpileup.c(15): warning #266: function "drand48" declared implicitly
>> KSORT_INIT(node, freenode_p, freenode_lt)
>> ^
>>
>> icc -std=gnu99 -I/shared/app/R-2.15.2-mpich2i12/lib64/R/include -DNDEBUG -I/usr/local/include -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Biostrings/include" -I"/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -std=c99 -c samtools/bam_md.c -o samtools/bam_md.o
>> icc: command line warning #10121: overriding '-stdgnu99' with '-stdc99'
>> samtools/bam_md.c(315): warning #266: function "getopt" declared implicitly
>> while ((c = getopt(argc, argv, "EqreuNhbSC:n:Ad")) >= 0) {
>> ^
>>
>> samtools/bam_md.c(326): error: identifier "optarg" is undefined
>> case 'n': max_nm = atoi(optarg); break;
>> ^
>>
>> samtools/bam_md.c(337): error: identifier "optind" is undefined
>> if (optind + 1 >= argc) {
>> ^
>>
>> samtools/bam_md.c(349): error: identifier "optind" is undefined
>> fp = samopen(argv[optind], mode_r, 0);
>> ^
>>
>> compilation aborted for samtools/bam_md.c (code 2)
>> make: *** [samtools/bam_md.o] Error 2
>> ERROR: compilation failed for package 'Rsamtools'
>> * removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Rsamtools'
>> ERROR: dependency 'Rsamtools' is not available for package 'rtracklayer'
>> * removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/rtracklayer'
>> ERROR: dependency 'rtracklayer' is not available for package 'GenomicFeatures'
>> * removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/GenomicFeatures'
>> ERROR: dependencies 'Rsamtools', 'GenomicFeatures' are not available for package 'biovizBase'
>> * removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/biovizBase'
>> ERROR: dependencies 'rtracklayer', 'GenomicFeatures', 'biovizBase' are not available for package 'Gviz'
>> * removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/Gviz'
>> ERROR: dependencies 'rtracklayer', 'Gviz' are not available for package 'cummeRbund'
>> * removing '/depot/shared/app/R-2.15.2-mpich2i12/lib64/R/library/cummeRbund'
>>
>> The downloaded source packages are in
>> '/tmp/RtmpCNWPrS/downloaded_packages'
>> Warning messages:
>> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>> installation of package 'Rsamtools' had non-zero exit status
>> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>> installation of package 'rtracklayer' had non-zero exit status
>> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>> installation of package 'GenomicFeatures' had non-zero exit status
>> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>> installation of package 'biovizBase' had non-zero exit status
>> 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>> installation of package 'Gviz' had non-zero exit status
>> 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>> installation of package 'cummeRbund' had non-zero exit status
>>>
>>
>>
>> -- output of sessionInfo():
>>
>>> sessionInfo()
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
>> [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
>> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] BiocInstaller_1.8.3
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.15.2
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>> ________________________________________________________________________
>> devteam-bioc mailing list
>> To unsubscribe from this mailing list send a blank email to
>> devteam-bioc-leave at lists.fhcrc.org
>> You can also unsubscribe or change your personal options at
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>>
>
>
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