Package: R453Plus1Toolbox

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.4.0.tar.gz

StartedAt: 2012-03-24 03:30:21 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:36:00 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 338.3 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.4.0'
* 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 'R453Plus1Toolbox' can be installed ... OK
* checking installed package size ... OK
* 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 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 ... NOTE
.getMutations: no visible binding for global variable 'PatternStart'
.getMutations: no visible binding for global variable 'PatternEnd'
.htmlReport: no visible binding for global variable 'VarFreqForward'
.htmlReport: no visible binding for global variable 'VarFreqReverse'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... NOTE
File '/Users/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386/R453Plus1Toolbox.so':
  Found '___stderrp', possibly from 'stderr' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under '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

* installing *source* package 'R453Plus1Toolbox' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c readSFF.c -o readSFF.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignette.Rnw' 
** testing if installed package can be loaded

* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.111	0.008	0.193
AVASet	0.031	0.002	0.039
AnnotatedVariants-class	0.004	0.000	0.004
MapperSet-class	0.044	0.014	0.185
MapperSet	0.013	0.002	0.016
SFFContainer-class	0.001	0.000	0.001
SFFRead-class	0.001	0.000	0.002
alignShortReads	1.305	0.018	1.439
annotateVariants	0.002	0.000	0.002
assayDataAmp	0.009	0.001	0.011
avaSetExample	0.029	0.003	0.033
avaSetFiltered	0.060	0.009	0.071
avaSetFiltered_annot	0.004	0.002	0.005
breakpoints	0.005	0.001	0.007
calculateTiTv	0.025	0.004	0.030
captureArray	0.004	0.001	0.005
coverageOnTarget	0.545	0.032	0.579
demultiplexReads	0.124	0.002	0.125
detectBreakpoints	0.959	0.020	0.998
fDataAmp	0.031	0.002	0.033
featureDataAmp	0.030	0.001	0.032
filterChimericReads	2.482	0.020	2.516
genomeSequencerMIDs	0.068	0.002	0.070
getAlignedReads	0.232	0.006	0.239
getVariantPercentages	0.071	0.002	0.074
htmlReport	7.430	0.428	10.153
mapperSetExample	0.012	0.001	0.015
mergeBreakpoints	11.604	1.548	15.083
plotAmpliconCoverage	0.001	0.000	0.000
plotChimericReads	6.487	0.016	6.602
plotVariants	0.002	0.001	0.002
plotVariationFrequency	0.000	0.000	0.001
readSFF	0	0	0
readsOnTarget	0.796	0.010	0.808
referenceSequences	0.014	0.001	0.016
removeLinker	0.043	0.001	0.043
sequenceCaptureLinkers	0.01	0.00	0.01
setVariantFilter	0.120	0.003	0.124
transcriptdf	0.002	0.001	0.003