rSFFreader 0.7.0
Matt Settles
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rSFFreader | | Last Changed Rev: 71491 / Revision: 74774 | | Last Changed Date: 2012-11-27 11:14:04 -0800 (Tue, 27 Nov 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rSFFreader.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rSFFreader/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rSFFreader' version '0.7.0'
* 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 ... [24s/24s] WARNING
Found the following significant warnings:
R_init_rSFFreader.c:21: warning: ISO C does not allow extra ';' outside of a function
See '/Users/biocbuild/bbs-2.12-bioc/meat/rSFFreader.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 8.8Mb
sub-directories of 1Mb or more:
extdata 8.2Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [15s/15s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/rSFFreader.Rcheck/00check.log'
for details.
* installing *source* package 'rSFFreader' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -g -O2 -Wall -pedantic -c R_init_rSFFreader.c -o R_init_rSFFreader.o
R_init_rSFFreader.c:21: warning: ISO C does not allow extra ';' outside of a function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -g -O2 -Wall -pedantic -c SFF-io.c -o SFF-io.o
SFF-io.c: In function 'readCommonHeader':
SFF-io.c:280: warning: value computed is not used
SFF-io.c:258: warning: unused variable 'size'
SFF-io.c:250: warning: unused variable 'uint8'
SFF-io.c:249: warning: unused variable 'uint16'
SFF-io.c:247: warning: unused variable 'padding_size'
SFF-io.c: In function 'read_sff':
SFF-io.c:542: warning: 'loader_ext.lkup_length_seq' may be used uninitialized in this function
SFF-io.c:542: note: 'loader_ext.lkup_length_seq' was declared here
SFF-io.c:542: warning: 'loader_ext.lkup_length_qual' may be used uninitialized in this function
SFF-io.c:542: note: 'loader_ext.lkup_length_qual' was declared here
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rSFFreader.so Biostrings_stubs.o IRanges_stubs.o R_init_rSFFreader.o SFF-io.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rSFFreader.Rcheck/rSFFreader/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'rSFFreader.Rnw'
** testing if installed package can be loaded
* DONE (rSFFreader)