BioC 2.11: CHECK report for R453Plus1Toolbox on pitt

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.7.1'
* 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 ... NOTE
  No methods found in "IRanges" for requests: matchMatrix
* 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 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log'
for details.

* installing *source* package 'R453Plus1Toolbox' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -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-2.11-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'boxplot' when loading 'graphics'
No methods found in "IRanges" for requests: matchMatrix
** 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'
No methods found in "IRanges" for requests: matchMatrix

* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.141	0.017	0.158
AVASet	0.026	0.002	0.028
AnnotatedVariants-class	0.003	0.000	0.004
MapperSet-class	0.045	0.013	0.060
MapperSet	0.012	0.001	0.013
SFFContainer-class	0.001	0.000	0.003
SFFRead-class	0.000	0.000	0.001
alignShortReads	1.243	0.006	1.315
annotateVariants	0.002	0.000	0.002
assayDataAmp	0.008	0.002	0.009
avaSetExample	0.028	0.002	0.030
avaSetFiltered	0.065	0.009	0.073
avaSetFiltered_annot	0.003	0.001	0.004
breakpoints	0.006	0.001	0.006
calculateTiTv	0.024	0.005	0.029
captureArray	0.002	0.001	0.004
coverageOnTarget	0.571	0.029	0.710
demultiplexReads	0.397	0.005	0.510
detectBreakpoints	0.777	0.022	0.864
fDataAmp	0.030	0.002	0.033
featureDataAmp	0.029	0.002	0.032
filterChimericReads	2.709	0.025	2.941
genomeSequencerMIDs	0.064	0.001	0.069
getAlignedReads	0.247	0.006	0.269
getVariantPercentages	0.078	0.003	0.093
htmlReport	7.454	0.424	8.797
mapperSetExample	0.012	0.001	0.013
mergeBreakpoints	12.298	1.507	14.490
mutationInfo	0.003	0.001	0.005
plotAmpliconCoverage	0.000	0.000	0.001
plotChimericReads	7.032	0.028	7.308
plotVariants	0.005	0.001	0.006
plotVariationFrequency	0	0	0
readSFF	0.000	0.001	0.000
readsOnTarget	0.903	0.012	0.984
referenceSequences	0.014	0.001	0.017
regions	0.004	0.000	0.006
removeLinker	0.044	0.001	0.049
sequenceCaptureLinkers	0.011	0.001	0.013
setVariantFilter	0.140	0.004	0.159
variants	0.004	0.001	0.005

Summary

Command output