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Package 520/609HostnameOS / ArchBUILDCHECKBUILD BIN
rSFFreader 0.6.0
Matt Settles
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/rSFFreader
Last Changed Rev: 70144 / Revision: 74773
Last Changed Date: 2012-10-03 08:43:48 -0700 (Wed, 03 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: rSFFreader
Version: 0.6.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rSFFreader_0.6.0.tar.gz
StartedAt: 2013-03-25 01:12:09 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:15:16 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 187.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rSFFreader.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/rSFFreader.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '0.6.0'
* 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 whether package 'rSFFreader' can be installed ... 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-2.11-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 for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/rSFFreader.Rcheck/00check.log'
for details.

rSFFreader.Rcheck/00install.out:

* 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/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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-2.11-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)

rSFFreader.Rcheck/rSFFreader-Ex.timings:

nameusersystemelapsed
SffHeader-class0.2510.0380.295
SffReads-class0.3270.0290.360
SffReadsQ-class0.5290.0270.560
availableClipModes0.1600.0260.191
load454SampleData0.4670.0280.498
loadIonSampleData0.1470.0180.167
readsff0.1570.0240.186
readsffgeometry0.0060.0110.018
readsffheader0.0030.0020.005