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BUILD report for rSFFreader on malbec2

This page was generated on 2019-10-16 12:01:54 -0400 (Wed, 16 Oct 2019).

Package 1424/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rSFFreader 0.32.0
Matt Settles
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/rSFFreader
Branch: RELEASE_3_9
Last Commit: f200828
Last Changed Date: 2019-05-02 11:53:39 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  ERROR [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
celaya2 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 

Summary

Package: rSFFreader
Version: 0.32.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rSFFreader
StartedAt: 2019-10-15 20:32:47 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:32:50 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 3.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rSFFreader
###
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* checking for file ‘rSFFreader/DESCRIPTION’ ... OK
* preparing ‘rSFFreader’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘rSFFreader’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_init_rSFFreader.c -o R_init_rSFFreader.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c SFF-io.c -o SFF-io.o
SFF-io.c: In function ‘readCommonHeader’:
SFF-io.c:262:5: 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:265:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread( commonHeader.version, sizeof(char), 4, file);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SFF-io.c:267:5: 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:270:5: 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:273:5: 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:276:5: 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:279:5: 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:282:5: 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:285:5: 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:297:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
         fread(&ch, sizeof(char), 1, file);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SFF-io.c:309:9: 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:778:13: 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:780:13: 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:782:13: 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:784:13: 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:786:13: 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:788:13: 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:790:13: 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:628:9: 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:630:9: 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:632:9: 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:634:9: 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:636:9: 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:638:9: 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:640:9: 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:656:9: 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:674:13: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
             fread( &uint16, sizeof(uint16_t), 1, file);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SFF-io.c:682:13: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
             fread( &uint8, sizeof(uint8_t), 1, file);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SFF-io.c:691:13: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
             fread( &ch, sizeof(char), 1, file);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SFF-io.c:708:13: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
             fread( &uint8, sizeof(uint8_t), 1, file);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /tmp/Rtmp6g5XQ1/Rinstfdf445db309/00LOCK-rSFFreader/00new/rSFFreader/libs
** R
Error in .install_package_code_files(".", instdir) : 
files in '/tmp/Rtmp6g5XQ1/Rbuildfdf4c2c9c93/rSFFreader/R' missing from 'Collate' field:
  zzz.R
ERROR: unable to collate and parse R files for package ‘rSFFreader’
* removing ‘/tmp/Rtmp6g5XQ1/Rinstfdf445db309/rSFFreader’
      -----------------------------------
ERROR: package installation failed