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BioC 3.2: INSTALL report for rSFFreader on zin1

This page was generated on 2015-08-24 10:48:58 -0700 (Mon, 24 Aug 2015).

Package 891/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rSFFreader 0.17.1
Matt Settles
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rSFFreader
Last Changed Rev: 104492 / Revision: 107696
Last Changed Date: 2015-06-02 18:27:24 -0700 (Tue, 02 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rSFFreader
Version: 0.17.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL rSFFreader
StartedAt: 2015-08-23 17:05:33 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 17:05:49 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 15.7 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL rSFFreader
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.2-bioc/R/library’
* installing *source* package ‘rSFFreader’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c R_init_rSFFreader.c -o R_init_rSFFreader.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-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-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)