[BioC] [devteam-bioc] R2.15.2 Rsamtools icc compiler bam_md.c(315) et al

Martin Morgan mtmorgan at fhcrc.org
Fri Nov 2 01:57:17 CET 2012


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
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>


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