rSFFreader 0.24.0
Matt Settles
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/rSFFreader | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rSFFreader_0.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/rSFFreader.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rSFFreader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rSFFreader’ version ‘0.24.0’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rSFFreader’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.1Mb
sub-directories of 1Mb or more:
extdata 8.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘S4Vectors’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over 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 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 ... NOTE
readSff: no visible global function definition for ‘isTRUEorFALSE’
readSffHeader: no visible global function definition for
‘isTRUEorFALSE’
Undefined global functions or variables:
isTRUEorFALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'SffReads,ANY,ANY,ANY'
generic '[' and siglist 'SffReads,ANY,missing,ANY'
generic '[' and siglist 'SffReads,missing,ANY,ANY'
generic '[' and siglist 'SffReads,missing,missing,ANY'
generic '[' and siglist 'SffReadsQ,ANY,ANY,ANY'
generic '[' and siglist 'SffReadsQ,ANY,missing,ANY'
generic '[' and siglist 'SffReadsQ,missing,ANY,ANY'
generic '[' and siglist 'SffReadsQ,missing,missing,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/rSFFreader.Rcheck/00check.log’
for details.
* installing *source* package ‘rSFFreader’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/rSFFreader.Rcheck/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)