rSFFreader 0.19.0
Matt Settles
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rSFFreader | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL rSFFreader
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* installing to library ‘/home/biocbuild/bbs-3.3-bioc/R/library’
* installing *source* package ‘rSFFreader’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c R_init_rSFFreader.c -o R_init_rSFFreader.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c SFF-io.c -o SFF-io.o
SFF-io.c: In function ‘readCommonHeader’:
SFF-io.c:262:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &commonHeader.magic_number, sizeof(uint32_t), 1, file);
^
SFF-io.c:265:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( commonHeader.version, sizeof(char), 4, file);
^
SFF-io.c:267:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &commonHeader.index_offset, sizeof(uint64_t), 1, file);
^
SFF-io.c:270:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &commonHeader.index_length, sizeof(uint32_t), 1, file);
^
SFF-io.c:273:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &commonHeader.number_of_reads, sizeof(uint32_t), 1, file);
^
SFF-io.c:276:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &commonHeader.commonHeader_length, sizeof(uint16_t), 1, file);
^
SFF-io.c:279:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &commonHeader.key_length, sizeof(uint16_t), 1, file);
^
SFF-io.c:282:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &commonHeader.number_of_flows_per_read, sizeof(uint16_t), 1, file);
^
SFF-io.c:285:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &commonHeader.flowgram_format_code, sizeof(uint8_t),1, file);
^
SFF-io.c:297:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&ch, sizeof(char), 1, file);
^
SFF-io.c:309:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&ch, sizeof(char), 1, file);
^
SFF-io.c: In function ‘sff_geometry’:
SFF-io.c:778:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.read_header_length, sizeof(uint16_t), 1, file);
^
SFF-io.c:780:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.name_length, sizeof(uint16_t), 1, file);
^
SFF-io.c:782:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.number_of_bases, sizeof(uint32_t), 1, file);
^
SFF-io.c:784:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.clip_qual_left, sizeof(uint16_t), 1, file);
^
SFF-io.c:786:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.clip_qual_right, sizeof(uint16_t), 1, file);
^
SFF-io.c:788:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.clip_adapter_left, sizeof(uint16_t), 1, file);
^
SFF-io.c:790:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.clip_adapter_right, sizeof(uint16_t), 1, file);
^
SFF-io.c: In function ‘readSFF’:
SFF-io.c:628:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.read_header_length, sizeof(uint16_t), 1, file);
^
SFF-io.c:630:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.name_length, sizeof(uint16_t), 1, file);
^
SFF-io.c:632:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.number_of_bases, sizeof(uint32_t), 1, file);
^
SFF-io.c:634:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.clip_qual_left, sizeof(uint16_t), 1, file);
^
SFF-io.c:636:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.clip_qual_right, sizeof(uint16_t), 1, file);
^
SFF-io.c:638:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.clip_adapter_left, sizeof(uint16_t), 1, file);
^
SFF-io.c:640:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &header.clip_adapter_right, sizeof(uint16_t), 1, file);
^
SFF-io.c:656:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( data.name, sizeof(char),header.name_length, file);
^
SFF-io.c:674:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &uint16, sizeof(uint16_t), 1, file);
^
SFF-io.c:682:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &uint8, sizeof(uint8_t), 1, file);
^
SFF-io.c:691:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &ch, sizeof(char), 1, file);
^
SFF-io.c:708:18: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( &uint8, sizeof(uint8_t), 1, file);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o rSFFreader.so Biostrings_stubs.o IRanges_stubs.o R_init_rSFFreader.o S4Vectors_stubs.o SFF-io.o XVector_stubs.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/R/library/rSFFreader/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rSFFreader)