Rsamtools 1.8.0
Bioconductor Package Maintainer
| Snapshot Date: 2012-03-31 17:01:49 -0700 (Sat, 31 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/Rsamtools | | Last Changed Rev: 64678 / Revision: 64719 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| puck5 | Linux (Ubuntu 12.04) / x86_64 | OK | [ ERROR ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rsamtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsamtools' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'Rsamtools' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
extdata 1.7Mb
libs 1.3Mb
usrlib 1.8Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/libs/Rsamtools.so':
Found 'stderr', possibly from 'stderr' (C)
Object: 'samtools_patch.o'
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'Rsamtools_unit_tests.R'
ERROR
Running the tests in 'tests/Rsamtools_unit_tests.R' failed.
Last 13 lines of output:
1 Test Suite :
Rsamtools RUnit Tests - 62 test functions, 0 errors, 1 failure
FAILURE in test_catch_samtools: Error in checkTrue(warn) : Test not TRUE
Test files with failing tests
test_utilities.R
test_catch_samtools
Error in Rsamtools:::.test() : unit tests failed for package Rsamtools
Execution halted
* installing *source* package 'Rsamtools' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c as_bam.c -o as_bam.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c bamfile.c -o bamfile.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c bcffile.c -o bcffile.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c encode.c -o encode.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c fafile.c -o fafile.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c io_sam.c -o io_sam.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c pileupbam.c -o pileupbam.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c tabixfile.c -o tabixfile.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c zip_compression.c -o zip_compression.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bgzf.c -o samtools/bgzf.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/kstring.c -o samtools/kstring.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam.c -o samtools/bam.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_import.c -o samtools/bam_import.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/sam.c -o samtools/sam.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_index_load_core':
samtools/bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
samtools/bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
samtools/bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
samtools/bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
samtools/bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
samtools/bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
samtools/bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
samtools/bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_md.c -o samtools/bam_md.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_close':
samtools/razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c:809:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c:812:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c:814:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c: In function 'razf_end_flush':
samtools/razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c: In function '_razf_write':
samtools/razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c: In function 'save_zindex':
samtools/razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c: In function 'razf_flush':
samtools/razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
samtools/razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/faidx.c -o samtools/faidx.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/knetfile.c -o samtools/knetfile.o
In file included from /usr/include/fcntl.h:252:0,
from samtools/knetfile.h:5,
from samtools/knetfile.c:46:
/usr/include/x86_64-linux-gnu/bits/fcntl2.h: In function 'khttp_connect_file':
samtools/knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
In file included from /usr/include/string.h:642:0,
from samtools/knetfile.c:35:
/usr/include/x86_64-linux-gnu/bits/string3.h: In function 'kftp_send_cmd':
samtools/knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_reheader.c -o samtools/bam_reheader.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -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/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 -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -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/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c tabix/index.c -o tabix/index.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/hpages/test-puck5/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usretc"
cp ../Rsamtools.mk "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usretc"
mkdir -p "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools"
mkdir -p "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix"
cp samtools/*.h "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/"
mkdir -p "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib"
gcc -std=gnu99 -shared -L/usr/local/lib -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 pileupbam.o samtools_patch.o tabixfile.o utilities.o zip_compression.o -fopenmp /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libbam.a /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libbcf.a /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libtabix.a -lz -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'Rsamtools-Overview.Rnw'
'Rsamtools-UsingCLibraries.Rnw'
** testing if installed package can be loaded
* DONE (Rsamtools)