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

Starr Hazard [guest] guest at bioconductor.org
Thu Nov 1 18:31:16 CET 2012


>  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
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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)
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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
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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)
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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)
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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)
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* 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


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