BioC 2.14: CHECK report for MSnbase on moscato2

Package: MSnbase

Version: 1.12.1

Command: rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_1.12.1.tar.gz >MSnbase-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_1.12.1.tar.gz

StartedAt: 2014-10-08 03:15:26 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:22:49 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 443.3 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_1.12.1.tar.gz >MSnbase-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_1.12.1.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/MSnbase.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSnbase/DESCRIPTION' ... OK
* this is package 'MSnbase' version '1.12.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MSnbase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'Biobase:::.showAnnotatedDataFrame'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [88s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
readMgfData    7.31   0.06    7.70
writeMzTabData 6.54   0.13   35.27
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
writeMzTabData 6.52   0.11   32.35
readMgfData    5.26   0.02    5.33
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [34s]
 [34s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [38s]
 [38s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'multicore'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/MSnbase.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MSnbase' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'scale' from package 'base' in package 'MSnbase'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MSnbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSnbase' as MSnbase_1.12.1.zip
* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	0.44	0.00	0.64
MSnProcess-class	0	0	0
MSnSet-class	0.94	0.00	0.94
NAnnotatedDataFrame-class	0.03	0.00	0.03
ReporterIons-class	0	0	0
TMT6	0	0	0
addIdentificationData-methods	0.44	0.01	0.49
chromatogram-methods	0.06	0.06	0.64
clean-methods	1.53	0.02	1.54
combineFeatures	1.01	0.00	1.01
exprsToRatios-methods	3.51	0.02	3.53
extractPrecSpectra-methods	0.25	0.01	0.26
featureCV	0.39	0.02	0.41
fillUp	0	0	0
formatRt	0	0	0
getVariableName	0	0	0
iTRAQ4	0	0	0
impute-methods	3.12	0.00	3.12
itraqdata	0.03	0.00	0.04
nQuants	3.56	0.00	3.57
normalise-methods	3.29	0.00	3.30
pSet-class	0.01	0.00	0.02
plot-methods	1.22	0.00	1.22
plot2d-methods	0.7	0.0	0.7
plotDensity-methods	0.75	0.00	0.75
plotMzDelta-methods	1.78	0.04	1.82
plotNA-methods	3.34	0.00	3.34
precSelection	0.03	0.00	0.03
purityCorrect-methods	3.34	0.02	3.36
quantify-methods	4.18	0.00	4.18
readIspyData	0	0	0
readMSData	0.32	0.00	0.32
readMSnSet	0	0	0
readMgfData	7.31	0.06	7.70
readMzTabData	0.24	0.00	0.36
removeNoId-methods	0.55	0.00	0.55
removePeaks-methods	1.79	0.00	1.79
removeReporters-methods	1.16	0.00	1.16
trimMz-methods	0.25	0.00	0.25
writeMgfData-methods	0	0	0
writeMzTabData	6.54	0.13	35.27
xic-methods	0.01	0.00	0.02

name	user	system	elapsed
MSnExp-class	0.53	0.00	1.09
MSnProcess-class	0	0	0
MSnSet-class	1.02	0.00	1.02
NAnnotatedDataFrame-class	0.03	0.00	0.03
ReporterIons-class	0.01	0.00	0.01
TMT6	0.02	0.00	0.02
addIdentificationData-methods	0.59	0.01	0.61
chromatogram-methods	0.11	0.06	0.17
clean-methods	1.56	0.02	1.58
combineFeatures	1.09	0.00	1.09
exprsToRatios-methods	4.07	0.01	4.09
extractPrecSpectra-methods	0.36	0.02	0.37
featureCV	0.42	0.00	0.45
fillUp	0	0	0
formatRt	0	0	0
getVariableName	0	0	0
iTRAQ4	0.02	0.00	0.01
impute-methods	3.52	0.00	3.53
itraqdata	0.05	0.00	0.05
nQuants	3.94	0.00	3.94
normalise-methods	3.76	0.02	3.78
pSet-class	0	0	0
plot-methods	1.52	0.01	1.53
plot2d-methods	0.79	0.00	0.79
plotDensity-methods	0.85	0.00	0.84
plotMzDelta-methods	2.04	0.00	2.05
plotNA-methods	4.12	0.00	4.12
precSelection	0.03	0.00	0.03
purityCorrect-methods	3.6	0.0	3.6
quantify-methods	4.88	0.00	4.88
readIspyData	0	0	0
readMSData	0.27	0.00	0.27
readMSnSet	0	0	0
readMgfData	5.26	0.02	5.33
readMzTabData	0.23	0.00	0.30
removeNoId-methods	0.66	0.00	0.66
removePeaks-methods	1.7	0.0	1.7
removeReporters-methods	0.75	0.00	0.75
trimMz-methods	0.14	0.00	0.14
writeMgfData-methods	0	0	0
writeMzTabData	6.52	0.11	32.35
xic-methods	0	0	0