Hi everyone, I'm trying to install Rsamtools and I'm getting a compilation error. Please see the transcript below for the error (at the very bottom) and the sessionInfo() output. Thank you in advance. > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). > biocLite("Rsamtools") Using R version 2.13.1, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "Rsamtools" Please wait... Installing package(s) into ‘/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13’ (as ‘lib’ is unspecified) trying URL ' http://bioconductor.org/packages/2.8/bioc/src/contrib/Rsamtools_1.4.3. tar.gz ' Content type 'application/x-gzip' length 2074383 bytes (2.0 Mb) opened URL ================================================== downloaded 2.0 Mb * installing *source* package ‘Rsamtools’ ... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gzeof in -lz... yes checking for bzero... yes checking for memset... yes checking for pow... no checking for sqrt... no checking for strcasecmp... yes checking for strdup... yes checking for strstr... yes checking for strtol... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for _LARGEFILE_SOURCE value needed for large files... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for off_t... yes checking for size_t... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/Rsamtools.mk ** libs gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c R_init_Rsamtools.c -o R_init_Rsamtools.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c as_bam.c -o as_bam.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bamfile.c -o bamfile.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bcffile.c -o bcffile.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c encode.c -o encode.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c fafile.c -o fafile.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c io_sam.c -o io_sam.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools_patch.c -o samtools_patch.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c utilities.c -o utilities.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bgzf.c -o samtools/bgzf.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/kstring.c -o samtools/kstring.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam_aux.c -o samtools/bam_aux.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam.c -o samtools/bam.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam_import.c -o samtools/bam_import.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/sam.c -o samtools/sam.o samtools/sam.c: In function ‘samopen’: samtools/sam.c:96: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam_index.c -o samtools/bam_index.o samtools/bam_index.c: In function ‘bam_index_save’: samtools/bam_index.c:258: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:261: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:262: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:270: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:271: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:277: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:278: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:283: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:289: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:290: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:291: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:298: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:299: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:304: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:307: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c:312: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bam_index.c: In function ‘bam_index_load_core’: samtools/bam_index.c:326: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result samtools/bam_index.c:333: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result samtools/bam_index.c:346: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result samtools/bam_index.c:349: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result samtools/bam_index.c:353: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result samtools/bam_index.c:357: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result samtools/bam_index.c:367: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result samtools/bam_index.c:371: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result samtools/bam_index.c: In function ‘download_from_remote’: samtools/bam_index.c:437: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam_pileup.c -o samtools/bam_pileup.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam_md.c -o samtools/bam_md.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/glf.c -o samtools/glf.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/razf.c -o samtools/razf.o samtools/razf.c: In function ‘save_zindex’: samtools/razf.c:96: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c:99: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c:106: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c:107: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c: In function ‘_razf_write’: samtools/razf.c:201: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c: In function ‘razf_flush’: samtools/razf.c:221: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c:234: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c: In function ‘razf_end_flush’: samtools/razf.c:258: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c: In function ‘razf_close’: samtools/razf.c:807: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c:808: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c:811: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/razf.c:813: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/faidx.c -o samtools/faidx.o samtools/faidx.c: In function ‘download_and_open’: samtools/faidx.c:252: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/knetfile.c -o samtools/knetfile.o samtools/knetfile.c: In function ‘kftp_send_cmd’: samtools/knetfile.c:236: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result samtools/knetfile.c: In function ‘khttp_connect_file’: samtools/knetfile.c:415: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam_sort.c -o samtools/bam_sort.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/sam_header.c -o samtools/sam_header.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bam_reheader.c -o samtools/bam_reheader.o samtools/bam_reheader.c: In function ‘bam_reheader’: samtools/bam_reheader.c:25: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/kprobaln.c -o samtools/kprobaln.o ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/glf.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o samtools/bcftools/vcf.c: In function ‘vcf_hdr_write’: samtools/bcftools/vcf.c:128: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result samtools/bcftools/vcf.c: In function ‘vcf_write’: samtools/bcftools/vcf.c:144: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/ld.c -o samtools/bcftools/ld.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/index.c -o samtools/bcftools/index.o samtools/bcftools/index.c: In function ‘download_from_remote’: samtools/bcftools/index.c:195: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/ld.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o mkdir -p /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/usretc cp Rsamtools.mk /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/usretc mkdir -p /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/include/samtools/bcftools cp samtools/*.h /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/include/samtools/ cp samtools/bcftools/*h /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/include/samtools/bcftools/ mkdir -p /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/usrlib cp libbam.a libbcf.a /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/usrlib gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o samtools_patch.o utilities.o -L. -lbam -lbcf -lz -L/usr/lib64/R/lib -lR /usr/bin/ld: /usr/local/lib64/libbam.a(bgzf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib64/libbam.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [Rsamtools.so] Error 1 ERROR: compilation failed for package ‘Rsamtools’ * removing ‘/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools’ The downloaded packages are in ‘/tmp/Rtmpc9YtaR/downloaded_packages’ Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'Rsamtools' had non-zero exit status > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.1 Thank you very much for your help, Kathryn -- Kathryn Iverson, MS Bioinformatics kiverson@umich.edu www.kathryniverson.com University of Michigan | Department of Microbiology and Immunology University of Michigan | Center for Computational Medicine and Biology [[alternative HTML version deleted]]

Hi Martin, I was able to successfully install Rsamtools with "R CMD INSTALL Rsamtools" after changing Makevars.common. I was also able to install the ShortRead package (dependent on Rsamtools) so everything seems to be in order. Thanks again everyone for all your help and patience. Best, Kathryn On Thu, Sep 22, 2011 at 1:02 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 09/22/2011 09:51 AM, Kathryn Iverson wrote: > >> Hi Martin, >> I don't seem to have >> >> PKG_LIBS += \ >> $(SHLIB_OPENMP_CFLAGS) \ >> -L. -lbam -lbcf -ltabix >> >> >> in any of the Makevars files. The copy of Rsamtools I grabbed is from >> bioconductor here [0]. See below for the contents of Makevars* >> >> [0] http://www.bioconductor.org/**packages/devel/bioc/html/** >> Rsamtools.html<http: www.bioconductor.org="" packages="" devel="" bioc="" html="" rsamtools.html=""> >> > > Hi Kathryn > > Several confusions, some on my part. You're using the release version of R, > so you need the release version of Rsamtools > > http://www.bioconductor.org/**packages/release/bioc/html/**Rsamtools .html<http: www.bioconductor.org="" packages="" release="" bioc="" html="" rsamtools="" .html=""> > > then in that file there is a Makevars.common, but the change required is > > PKG_LIBS += ./libbam.a ./libbcf.a > > instead of > > PKG_LIBS += -L. -lbam -lbcf > > Please let me know if this is on the right track. > > Martin > > Thanks, >> Kathryn >> >> [kiverson@axiom src]$ more Makevars.common >> PKG_OBJECTS = \ >> io_sam.o utilities.o encode.o \ >> Biostrings_stubs.o IRanges_stubs.o \ >> R_init_Rsamtools.o >> SAMTOOLS_OBJECTS = \ >> bam.o bam_import.o bam_index.o kstring.o bam_aux.o \ >> sam_header.o \ >> bgzf.o razf.o \ >> knetfile.o \ >> sam.o bam_pileup.o faidx.o >> # these flags are for SAMTOOLS; -Dinline="" turns off inlining, which >> # is leads to undefined symbols for gcc -O0 >> DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> PKG_CFLAGS += $(DFLAGS) >> >> >> [kiverson@axiom src]$ more Makevars.in >> PKG_LIBS+=@LIBS@ >> include Makevars.common >> OBJECTS = $(PKG_OBJECTS) $(SAMTOOLS_OBJECTS:%=samtools/**%) >> >> all: $(SHLIB) >> >> clean: >> rm -f $(OBJECTS) >> >> >> [kiverson@axiom src]$ more Makevars.win >> PKG_LIBS+=$(ZLIB_LIBS) -lws2_32 >> include Makevars.common >> OBJECTS = $(PKG_OBJECTS) $(SAMTOOLS_OBJECTS:%=samtools/**%) >> >> all: $(SHLIB) >> >> clean: >> rm -f $(OBJECTS) >> >> >> [kiverson@axiom src]$ more Makevars >> PKG_LIBS+=-lz >> include Makevars.common >> OBJECTS = $(PKG_OBJECTS) $(SAMTOOLS_OBJECTS:%=samtools/**%) >> >> all: $(SHLIB) >> >> clean: >> rm -f $(OBJECTS) >> [kiverson@axiom src]$ >> >> Martin >> >> >> Thanks again, >> Kathryn >> >> On Thu, Sep 22, 2011 at 11:52 AM, Gordon Brown >> <gordon.brown@cancer.org.uk>> <mailto:gordon.brown@cancer.**org.uk <gordon.brown@cancer.org.uk=""> >> >>__wrote: >> >> >> Hi, Kathryn, >> >> Your copy of libbam (libbam.a) is a static library, not a >> shared library >> (and you can't, in general, link to a static library when >> trying to make a >> shared library). If you compile the shared version of >> libbam ("make dylib" >> in the samtools package will create "libbam.so.1"), and put >> it in >> /usr/local/lib64, Rsamtools should find that instead and use >> it. >> >> Hope this helps. >> >> Cheers, >> >> - Gord >> >> >> On 2011/09/22 16:36, "Kathryn Iverson"<kiverson@umich.edu>> <mailto:kiverson@umich.edu>> wrote: >> >> >> Hi everyone, >> I'm trying to install Rsamtools and I'm getting a >> compilation error. >> >> Please >> >> see the transcript below for the error (at the very >> bottom) and the >> sessionInfo() output. Thank you in advance. >> >> >> source("http://bioconductor.__**org/biocLite.R >> <http: bioconductor.org="" **bioclite.r<http:="" bio="" conductor.org="" bioclite.r=""> >> >") >> >> BioC_mirror = http://bioconductor.org >> Change using chooseBioCmirror(). >> >> biocLite("Rsamtools") >> >> Using R version 2.13.1, biocinstall version 2.8.4. >> Installing Bioconductor version 2.8 packages: >> [1] "Rsamtools" >> Please wait... >> >> Installing package(s) into >> Œ/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13¹ >> (as Œlib¹ is unspecified) >> trying URL ' >> >> http://bioconductor.org/__**packages/2.8/bioc/src/contrib/** >> __Rsamtools_1.4.3.tar.gz<http: bioconductor.org="" __packages="" 2.8="" bio="" c="" src="" contrib="" __rsamtools_1.4.3.tar.gz=""> >> <http: bioconductor.org="" **packages="" 2.8="" bioc="" src="" contrib="" **="">> Rsamtools_1.4.3.tar.gz<http: bioconductor.org="" packages="" 2.8="" bioc="" sr="" c="" contrib="" rsamtools_1.4.3.tar.gz=""> >> > >> >> ' >> Content type 'application/x-gzip' length 2074383 bytes >> (2.0 Mb) >> opened URL >> ==============================**__==================== >> downloaded 2.0 Mb >> >> * installing *source* package ŒRsamtools¹ ... >> checking for gcc... gcc >> checking whether the C compiler works... yes >> checking for C compiler default output file name... a.out >> checking for suffix of executables... >> checking whether we are cross compiling... no >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ISO C89... none needed >> checking for gzeof in -lz... yes >> checking for bzero... yes >> checking for memset... yes >> checking for pow... no >> checking for sqrt... no >> checking for strcasecmp... yes >> checking for strdup... yes >> checking for strstr... yes >> checking for strtol... yes >> checking how to run the C preprocessor... gcc -E >> checking for grep that handles long lines and -e... >> /bin/grep >> checking for egrep... /bin/grep -E >> checking for ANSI C header files... yes >> checking for sys/types.h... yes >> checking for sys/stat.h... yes >> checking for stdlib.h... yes >> checking for string.h... yes >> checking for memory.h... yes >> checking for strings.h... yes >> checking for inttypes.h... yes >> checking for stdint.h... yes >> checking for unistd.h... yes >> checking zlib.h usability... yes >> checking zlib.h presence... yes >> checking for zlib.h... yes >> checking fcntl.h usability... yes >> checking fcntl.h presence... yes >> checking for fcntl.h... yes >> checking malloc.h usability... yes >> checking malloc.h presence... yes >> checking for malloc.h... yes >> checking stddef.h usability... yes >> checking stddef.h presence... yes >> checking for stddef.h... yes >> checking for ptrdiff_t... yes >> checking for an ANSI C-conforming const... yes >> checking for inline... inline >> checking for _LARGEFILE_SOURCE value needed for large >> files... no >> checking for stdlib.h... (cached) yes >> checking for GNU libc compatible malloc... yes >> checking for working memcmp... yes >> checking for stdlib.h... (cached) yes >> checking for GNU libc compatible realloc... yes >> checking for stdbool.h that conforms to C99... yes >> checking for _Bool... yes >> checking for off_t... yes >> checking for size_t... yes >> configure: creating ./config.status >> config.status: creating src/Makevars >> config.status: creating src/Rsamtools.mk >> ** libs >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c Biostrings_stubs.c -o Biostrings_stubs.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c IRanges_stubs.c -o IRanges_stubs.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c R_init_Rsamtools.c -o R_init_Rsamtools.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c as_bam.c -o as_bam.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c bamfile.c -o bamfile.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c bcffile.c -o bcffile.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c encode.c -o encode.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c fafile.c -o fafile.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c io_sam.c -o io_sam.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools_patch.c -o samtools_patch.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c utilities.c -o utilities.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bgzf.c -o samtools/bgzf.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/kstring.c -o samtools/kstring.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam_aux.c -o samtools/bam_aux.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam.c -o samtools/bam.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam_import.c -o samtools/bam_import.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/sam.c -o samtools/sam.o >> samtools/sam.c: In function Œsamopen¹: >> samtools/sam.c:96: warning: ignoring return value of >> Œfwrite¹, declared >> >> with >> >> attribute warn_unused_result >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam_index.c -o samtools/bam_index.o >> samtools/bam_index.c: In function Œbam_index_save¹: >> samtools/bam_index.c:258: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:261: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:262: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:270: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:271: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:277: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:278: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:283: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:289: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:290: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:291: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:298: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:299: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:304: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:307: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:312: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c: In function Œbam_index_load_core¹: >> samtools/bam_index.c:326: warning: ignoring return value >> of Œfread¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:333: warning: ignoring return value >> of Œfread¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:346: warning: ignoring return value >> of Œfread¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:349: warning: ignoring return value >> of Œfread¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:353: warning: ignoring return value >> of Œfread¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:357: warning: ignoring return value >> of Œfread¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:367: warning: ignoring return value >> of Œfread¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c:371: warning: ignoring return value >> of Œfread¹, >> declared with attribute warn_unused_result >> samtools/bam_index.c: In function Œdownload_from_remote¹: >> samtools/bam_index.c:437: warning: ignoring return value >> of Œfwrite¹, >> declared with attribute warn_unused_result >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam_pileup.c -o samtools/bam_pileup.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam_md.c -o samtools/bam_md.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/glf.c -o samtools/glf.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/razf.c -o samtools/razf.o >> samtools/razf.c: In function Œsave_zindex¹: >> samtools/razf.c:96: warning: ignoring return value of >> Œwrite¹, declared >> >> with >> >> attribute warn_unused_result >> samtools/razf.c:99: warning: ignoring return value of >> Œwrite¹, declared >> >> with >> >> attribute warn_unused_result >> samtools/razf.c:106: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c:107: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c: In function Œ_razf_write¹: >> samtools/razf.c:201: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c: In function Œrazf_flush¹: >> samtools/razf.c:221: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c:234: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c: In function Œrazf_end_flush¹: >> samtools/razf.c:258: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c: In function Œrazf_close¹: >> samtools/razf.c:807: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c:808: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c:811: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> samtools/razf.c:813: warning: ignoring return value of >> Œwrite¹, declared >> with attribute warn_unused_result >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/faidx.c -o samtools/faidx.o >> samtools/faidx.c: In function Œdownload_and_open¹: >> samtools/faidx.c:252: warning: ignoring return value of >> Œfwrite¹, >> >> declared >> >> with attribute warn_unused_result >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/knetfile.c -o samtools/knetfile.o >> samtools/knetfile.c: In function Œkftp_send_cmd¹: >> samtools/knetfile.c:236: warning: ignoring return value >> of Œwrite¹, >> >> declared >> >> with attribute warn_unused_result >> samtools/knetfile.c: In function Œkhttp_connect_file¹: >> samtools/knetfile.c:415: warning: ignoring return value >> of Œwrite¹, >> >> declared >> >> with attribute warn_unused_result >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam_sort.c -o samtools/bam_sort.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/sam_header.c -o samtools/sam_header.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bam_reheader.c -o samtools/bam_reheader.o >> samtools/bam_reheader.c: In function Œbam_reheader¹: >> samtools/bam_reheader.c:25: warning: ignoring return >> value of Œfwrite¹, >> declared with attribute warn_unused_result >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/kprobaln.c -o samtools/kprobaln.o >> ar -crus libbam.a samtools/bgzf.o samtools/kstring.o >> samtools/bam_aux.o >> samtools/bam.o samtools/bam_import.o samtools/sam.o >> samtools/bam_index.o >> samtools/bam_pileup.o samtools/bam_lpileup.o >> samtools/bam_md.o >> samtools/glf.o samtools/razf.o samtools/faidx.o >> samtools/knetfile.o >> samtools/bam_sort.o samtools/sam_header.o >> samtools/bam_reheader.o >> samtools/kprobaln.o samtools_patch.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o >> samtools/bcftools/vcf.c: In function Œvcf_hdr_write¹: >> samtools/bcftools/vcf.c:128: warning: ignoring return >> value of Œfwrite¹, >> declared with attribute warn_unused_result >> samtools/bcftools/vcf.c: In function Œvcf_write¹: >> samtools/bcftools/vcf.c:144: warning: ignoring return >> value of Œfwrite¹, >> declared with attribute warn_unused_result >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/bcfutils.c -o >> samtools/bcftools/bcfutils.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/ld.c -o samtools/bcftools/ld.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/index.c -o samtools/bcftools/index.o >> samtools/bcftools/index.c: In function >> Œdownload_from_remote¹: >> samtools/bcftools/index.c:195: warning: ignoring return >> value of >> >> Œfwrite¹, >> >> declared with attribute warn_unused_result >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o >> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include >> >> -I"/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/* >> *__Biostrings/include" >> >> -I"/home/kiverson/R/x86_64-__** >> redhat-linux-gnu-library/2.13/**__IRanges/include" >> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 >> -Dfprintf=_samtools_fprintf >> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools >> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 >> -fexceptions -fstack-protector --param=ssp-buffer- size=4 >> -m64 >> >> -mtune=generic >> >> -c samtools/bcftools/bcf2qcall.c -o >> samtools/bcftools/bcf2qcall.o >> ar -crus libbcf.a samtools/bcftools/bcf.o >> samtools/bcftools/vcf.o >> samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o >> samtools/bcftools/ld.o samtools/bcftools/kfunc.o >> >> samtools/bcftools/index.o >> >> samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o >> samtools_patch.o >> mkdir -p >> /home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/ >> **__Rsamtools/usretc >> cp Rsamtools.mk >> /home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/ >> **__Rsamtools/usretc >> mkdir -p >> >> /home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/** >> __Rsamtools/include/samtoo >> >> ls/bcftools >> cp samtools/*.h >> >> /home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/** >> __Rsamtools/include/samtoo >> >> ls/ >> cp samtools/bcftools/*h >> >> /home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/** >> __Rsamtools/include/samtoo >> >> ls/bcftools/ >> mkdir -p >> /home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/ >> **__Rsamtools/usrlib >> cp libbam.a libbcf.a >> /home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/ >> **__Rsamtools/usrlib >> gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o >> Rsamtools.so >> Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o >> as_bam.o bamfile.o >> bcffile.o encode.o fafile.o io_sam.o samtools_patch.o >> utilities.o -L. >> >> -lbam >> >> -lbcf -lz -L/usr/lib64/R/lib -lR >> /usr/bin/ld: /usr/local/lib64/libbam.a(__**bgzf.o): >> relocation R_X86_64_32 >> against `a local symbol' can not be used when making a >> shared object; >> recompile with -fPIC >> /usr/local/lib64/libbam.a: could not read symbols: Bad >> value >> collect2: ld returned 1 exit status >> make: *** [Rsamtools.so] Error 1 >> ERROR: compilation failed for package ŒRsamtools¹ >> * removing >> >> Œ/home/kiverson/R/x86_64-__**redhat-linux-gnu- library/2.13/** >> __Rsamtools¹ >> >> >> The downloaded packages are in >> Œ/tmp/Rtmpc9YtaR/downloaded___**packages¹ >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, ...) : >> installation of package 'Rsamtools' had non-zero exit >> status >> >> >> sessionInfo() >> >> R version 2.13.1 (2011-07-08) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets >> methods base >> >> loaded via a namespace (and not attached): >> [1] tools_2.13.1 >> >> >> >> Thank you very much for your help, >> Kathryn >> >> -- >> Kathryn Iverson, MS Bioinformatics >> kiverson@umich.edu <mailto:kiverson@umich.edu> >> www.kathryniverson.com <http: www.kathryniverson.com**=""> >> >> University of Michigan | Department of Microbiology and >> Immunology >> University of Michigan | Center for Computational >> Medicine and Biology >> >> [[alternative HTML version deleted]] >> >> >> >> NOTICE AND DISCLAIMER >> This e-mail (including any attachments) is intended >> fo...{{dropped:29}} >> >> >> >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<https :="" stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> > >> Search the archives: >> http://news.gmane.org/gmane.__**science.biology.informatics.__** >> conductor<http: news.gmane.org="" gmane.__science.biology.informatics="" .__conductor=""> >> <http: news.gmane.org="" gmane.**science.biology.informatics.**="">> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> > >> >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 <tel:206%20667-2793> >> >> >> >> >> -- >> Kathryn Iverson, MS Bioinformatics >> kiverson@umich.edu <mailto:kiverson@umich.edu> >> www.kathryniverson.com <http: www.kathryniverson.**com="" <http:="" www.kathryniverson.com=""/> >> > >> >> University of Michigan | Department of Microbiology and Immunology >> University of Michigan | Center for Computational Medicine and Biology >> >> > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > -- Kathryn Iverson, MS Bioinformatics kiverson@umich.edu www.kathryniverson.com University of Michigan | Department of Microbiology and Immunology University of Michigan | Center for Computational Medicine and Biology [[alternative HTML version deleted]]

Hi, Kathryn, Your copy of libbam (libbam.a) is a static library, not a shared library (and you can't, in general, link to a static library when trying to make a shared library). If you compile the shared version of libbam ("make dylib" in the samtools package will create "libbam.so.1"), and put it in /usr/local/lib64, Rsamtools should find that instead and use it. Hope this helps. Cheers, - Gord On 2011/09/22 16:36, "Kathryn Iverson" <kiverson at="" umich.edu=""> wrote: > Hi everyone, > I'm trying to install Rsamtools and I'm getting a compilation error. Please > see the transcript below for the error (at the very bottom) and the > sessionInfo() output. Thank you in advance. > > >> source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). >> biocLite("Rsamtools") > Using R version 2.13.1, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "Rsamtools" > Please wait... > > Installing package(s) into > ?/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13? > (as ?lib? is unspecified) > trying URL ' > http://bioconductor.org/packages/2.8/bioc/src/contrib/Rsamtools_1.4. 3.tar.gz > ' > Content type 'application/x-gzip' length 2074383 bytes (2.0 Mb) > opened URL > ================================================== > downloaded 2.0 Mb > > * installing *source* package ?Rsamtools? ... > checking for gcc... gcc > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking for gzeof in -lz... yes > checking for bzero... yes > checking for memset... yes > checking for pow... no > checking for sqrt... no > checking for strcasecmp... yes > checking for strdup... yes > checking for strstr... yes > checking for strtol... yes > checking how to run the C preprocessor... gcc -E > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking zlib.h usability... yes > checking zlib.h presence... yes > checking for zlib.h... yes > checking fcntl.h usability... yes > checking fcntl.h presence... yes > checking for fcntl.h... yes > checking malloc.h usability... yes > checking malloc.h presence... yes > checking for malloc.h... yes > checking stddef.h usability... yes > checking stddef.h presence... yes > checking for stddef.h... yes > checking for ptrdiff_t... yes > checking for an ANSI C-conforming const... yes > checking for inline... inline > checking for _LARGEFILE_SOURCE value needed for large files... no > checking for stdlib.h... (cached) yes > checking for GNU libc compatible malloc... yes > checking for working memcmp... yes > checking for stdlib.h... (cached) yes > checking for GNU libc compatible realloc... yes > checking for stdbool.h that conforms to C99... yes > checking for _Bool... yes > checking for off_t... yes > checking for size_t... yes > configure: creating ./config.status > config.status: creating src/Makevars > config.status: creating src/Rsamtools.mk > ** libs > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c Biostrings_stubs.c -o Biostrings_stubs.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c IRanges_stubs.c -o IRanges_stubs.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c R_init_Rsamtools.c -o R_init_Rsamtools.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c as_bam.c -o as_bam.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c bamfile.c -o bamfile.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c bcffile.c -o bcffile.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c encode.c -o encode.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c fafile.c -o fafile.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c io_sam.c -o io_sam.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools_patch.c -o samtools_patch.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c utilities.c -o utilities.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bgzf.c -o samtools/bgzf.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/kstring.c -o samtools/kstring.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam_aux.c -o samtools/bam_aux.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam.c -o samtools/bam.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam_import.c -o samtools/bam_import.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/sam.c -o samtools/sam.o > samtools/sam.c: In function ?samopen?: > samtools/sam.c:96: warning: ignoring return value of ?fwrite?, declared with > attribute warn_unused_result > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam_index.c -o samtools/bam_index.o > samtools/bam_index.c: In function ?bam_index_save?: > samtools/bam_index.c:258: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:261: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:262: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:270: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:271: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:277: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:278: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:283: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:289: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:290: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:291: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:298: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:299: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:304: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:307: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c:312: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bam_index.c: In function ?bam_index_load_core?: > samtools/bam_index.c:326: warning: ignoring return value of ?fread?, > declared with attribute warn_unused_result > samtools/bam_index.c:333: warning: ignoring return value of ?fread?, > declared with attribute warn_unused_result > samtools/bam_index.c:346: warning: ignoring return value of ?fread?, > declared with attribute warn_unused_result > samtools/bam_index.c:349: warning: ignoring return value of ?fread?, > declared with attribute warn_unused_result > samtools/bam_index.c:353: warning: ignoring return value of ?fread?, > declared with attribute warn_unused_result > samtools/bam_index.c:357: warning: ignoring return value of ?fread?, > declared with attribute warn_unused_result > samtools/bam_index.c:367: warning: ignoring return value of ?fread?, > declared with attribute warn_unused_result > samtools/bam_index.c:371: warning: ignoring return value of ?fread?, > declared with attribute warn_unused_result > samtools/bam_index.c: In function ?download_from_remote?: > samtools/bam_index.c:437: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam_pileup.c -o samtools/bam_pileup.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam_md.c -o samtools/bam_md.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/glf.c -o samtools/glf.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/razf.c -o samtools/razf.o > samtools/razf.c: In function ?save_zindex?: > samtools/razf.c:96: warning: ignoring return value of ?write?, declared with > attribute warn_unused_result > samtools/razf.c:99: warning: ignoring return value of ?write?, declared with > attribute warn_unused_result > samtools/razf.c:106: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c:107: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c: In function ?_razf_write?: > samtools/razf.c:201: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c: In function ?razf_flush?: > samtools/razf.c:221: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c:234: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c: In function ?razf_end_flush?: > samtools/razf.c:258: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c: In function ?razf_close?: > samtools/razf.c:807: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c:808: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c:811: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/razf.c:813: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/faidx.c -o samtools/faidx.o > samtools/faidx.c: In function ?download_and_open?: > samtools/faidx.c:252: warning: ignoring return value of ?fwrite?, declared > with attribute warn_unused_result > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/knetfile.c -o samtools/knetfile.o > samtools/knetfile.c: In function ?kftp_send_cmd?: > samtools/knetfile.c:236: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > samtools/knetfile.c: In function ?khttp_connect_file?: > samtools/knetfile.c:415: warning: ignoring return value of ?write?, declared > with attribute warn_unused_result > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam_sort.c -o samtools/bam_sort.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/sam_header.c -o samtools/sam_header.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bam_reheader.c -o samtools/bam_reheader.o > samtools/bam_reheader.c: In function ?bam_reheader?: > samtools/bam_reheader.c:25: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/kprobaln.c -o samtools/kprobaln.o > ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o > samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o > samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o > samtools/glf.o samtools/razf.o samtools/faidx.o samtools/knetfile.o > samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o > samtools/kprobaln.o samtools_patch.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o > samtools/bcftools/vcf.c: In function ?vcf_hdr_write?: > samtools/bcftools/vcf.c:128: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > samtools/bcftools/vcf.c: In function ?vcf_write?: > samtools/bcftools/vcf.c:144: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/ld.c -o samtools/bcftools/ld.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/index.c -o samtools/bcftools/index.o > samtools/bcftools/index.c: In function ?download_from_remote?: > samtools/bcftools/index.c:195: warning: ignoring return value of ?fwrite?, > declared with attribute warn_unused_result > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Biostrings/include" > -I"/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/IRanges/include" > -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o > ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o > samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o > samtools/bcftools/ld.o samtools/bcftools/kfunc.o samtools/bcftools/index.o > samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o > mkdir -p > /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/usretc > cp Rsamtools.mk > /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/usretc > mkdir -p > /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/include/samtoo > ls/bcftools > cp samtools/*.h > /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/include/samtoo > ls/ > cp samtools/bcftools/*h > /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/include/samtoo > ls/bcftools/ > mkdir -p > /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/usrlib > cp libbam.a libbcf.a > /home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools/usrlib > gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so > Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o > bcffile.o encode.o fafile.o io_sam.o samtools_patch.o utilities.o -L. -lbam > -lbcf -lz -L/usr/lib64/R/lib -lR > /usr/bin/ld: /usr/local/lib64/libbam.a(bgzf.o): relocation R_X86_64_32 > against `a local symbol' can not be used when making a shared object; > recompile with -fPIC > /usr/local/lib64/libbam.a: could not read symbols: Bad value > collect2: ld returned 1 exit status > make: *** [Rsamtools.so] Error 1 > ERROR: compilation failed for package ?Rsamtools? > * removing ?/home/kiverson/R/x86_64-redhat-linux-gnu- library/2.13/Rsamtools? > > The downloaded packages are in > ?/tmp/Rtmpc9YtaR/downloaded_packages? > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'Rsamtools' had non-zero exit status > > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.13.1 > > > > Thank you very much for your help, > Kathryn > > -- > Kathryn Iverson, MS Bioinformatics > kiverson at umich.edu > www.kathryniverson.com > University of Michigan | Department of Microbiology and Immunology > University of Michigan | Center for Computational Medicine and Biology > > [[alternative HTML version deleted]] > NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:16}}