Package: R453Plus1Toolbox

Version: 1.6.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.6.0.tar.gz

StartedAt: 2012-04-01 02:55:18 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:58:49 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 211.0 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.6.0'
* 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 '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
.getEnsemblInfo: no visible binding for global variable 'cds_length'
.getEnsemblInfo: no visible binding for global variable
  'ensembl_transcript_id'
.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'
.plotVariants: no visible binding for global variable 'mutation'
* 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 ... 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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.

* installing *source* package 'R453Plus1Toolbox' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c readSFF.c -o readSFF.o
readSFF.c: In function 'readSFF':
readSFF.c:46:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -shared -L/usr/local/lib -o R453Plus1Toolbox.so readSFF.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'boxplot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
   'vignette.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'boxplot' when loading 'graphics'

* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.088	0.008	0.106
AVASet	0.020	0.004	0.034
AnnotatedVariants-class	0.004	0.000	0.002
MapperSet-class	0.040	0.000	0.049
MapperSet	0.012	0.000	0.023
SFFContainer-class	0.000	0.000	0.001
SFFRead-class	0.000	0.004	0.000
alignShortReads	0.876	0.004	0.886
annotateVariants	0.000	0.000	0.001
assayDataAmp	0.004	0.000	0.017
avaSetExample	0.020	0.000	0.025
avaSetFiltered	0.032	0.008	0.049
avaSetFiltered_annot	0.000	0.004	0.019
breakpoints	0.004	0.000	0.017
calculateTiTv	0.012	0.004	0.026
captureArray	0.000	0.000	0.014
coverageOnTarget	0.340	0.020	0.382
demultiplexReads	0.356	0.000	0.365
detectBreakpoints	0.460	0.000	0.466
fDataAmp	0.024	0.000	0.030
featureDataAmp	0.028	0.000	0.035
filterChimericReads	1.692	0.004	1.731
genomeSequencerMIDs	0.044	0.000	0.042
getAlignedReads	0.140	0.000	0.158
getVariantPercentages	0.048	0.004	0.063
htmlReport	3.820	0.060	4.195
mapperSetExample	0.004	0.004	0.016
mergeBreakpoints	6.273	0.040	6.350
mutationInfo	0.000	0.004	0.015
plotAmpliconCoverage	0	0	0
plotChimericReads	3.960	0.000	3.969
plotVariants	0.004	0.000	0.004
plotVariationFrequency	0	0	0
readSFF	0	0	0
readsOnTarget	0.452	0.008	0.477
referenceSequences	0.012	0.000	0.022
regions	0.004	0.000	0.013
removeLinker	0.024	0.000	0.026
sequenceCaptureLinkers	0.004	0.000	0.006
setVariantFilter	0.080	0.004	0.094
variants	0.004	0.000	0.013