BioC 3.0: CHECK report for MSnbase on moscato1

Package: MSnbase

Version: 1.14.2

Command: rm -rf MSnbase.buildbin-libdir MSnbase.Rcheck && mkdir MSnbase.buildbin-libdir MSnbase.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_1.14.2.tar.gz >MSnbase.Rcheck\00install.out 2>&1 && cp MSnbase.Rcheck\00install.out MSnbase-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_1.14.2.tar.gz

StartedAt: 2015-04-10 03:28:10 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:37:39 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 568.9 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 MSnbase.Rcheck && mkdir MSnbase.buildbin-libdir MSnbase.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_1.14.2.tar.gz >MSnbase.Rcheck\00install.out 2>&1 && cp MSnbase.Rcheck\00install.out MSnbase-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_1.14.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/MSnbase.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.14.2'
* 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 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
'library' or 'require' call to 'rols' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'Biobase:::.showAnnotatedDataFrame' 'MALDIquant:::.estimateNoise'
  'MALDIquant:::.localMaxima' 'MALDIquant:::.movingAverage'
  'MALDIquant:::.savitzkyGolay' 'MALDIquant:::.which.closest'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeMTD: no visible global function definition for 'olsQuery'
makeMTD: no visible global function definition for 'term'
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [97s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareSpectra-methods 9.47   0.03    9.50
averageMSnSet          8.58   0.28   10.61
readMgfData            6.82   0.06    6.99
writeMzTabData         6.54   0.06   16.58
quantify-methods       5.76   0.00    5.75
** running examples for arch 'x64' ... [113s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
averageMSnSet          13.28   0.32   14.72
compareSpectra-methods 13.02   0.02   13.04
writeMzTabData          9.37   0.09   16.10
quantify-methods        6.17   0.01    6.19
readMgfData             5.84   0.00    5.85
plotNA-methods          4.14   0.00    5.60
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [37s]
 [38s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [47s]
 [47s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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 new generic function for 'smooth' in package 'MSnbase'
Creating a generic function for 't' from package 'base' in package 'MSnbase'
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_1.14.2.zip
* DONE (MSnbase)

name	user	system	elapsed
FeatComp-class	0.30	0.01	0.54
FeaturesOfInterest-class	0.06	0.00	0.06
MSmap-class	0	0	0
MSnExp-class	0.44	0.00	0.44
MSnProcess-class	0	0	0
MSnSet-class	0.72	0.00	0.72
NAnnotatedDataFrame-class	0.01	0.00	0.02
ReporterIons-class	0.02	0.00	0.01
TMT6	0.02	0.00	0.02
addIdentificationData-methods	0.48	0.02	0.50
averageMSnSet	8.58	0.28	10.61
bin-methods	0.56	0.00	0.56
calculateFragments-methods	0.41	0.00	0.41
chromatogram-methods	0.11	0.01	0.97
clean-methods	1.07	0.00	1.07
combineFeatures	0.94	0.02	0.95
compareSpectra-methods	9.47	0.03	9.50
exprsToRatios-methods	3.87	0.00	3.87
extractPrecSpectra-methods	0.35	0.01	0.38
featureCV	0.39	0.00	0.39
fillUp	0	0	0
formatRt	0.02	0.00	0.01
get.amino.acids	0	0	0
get.atomic.mass	0	0	0
getVariableName	0	0	0
iTRAQ4	0.02	0.00	0.02
impute-methods	3.08	0.00	3.09
itraqdata	0.04	0.00	0.03
listOf	0.01	0.00	0.01
nQuants	3.23	0.00	3.23
normalise-methods	2.90	0.02	2.92
npcv	0	0	0
pSet-class	0	0	0
pickPeaks-method	0.44	0.01	0.45
plot-methods	1.03	0.00	1.03
plot2d-methods	1.06	0.00	2.30
plotDensity-methods	0.75	0.00	0.74
plotMzDelta-methods	2.45	0.04	2.48
plotNA-methods	3.51	0.00	3.51
plotSpectrumSpectrum-methods	0.43	0.00	0.44
precSelection	0.02	0.00	0.02
purityCorrect-methods	3.12	0.00	3.12
quantify-methods	5.76	0.00	5.75
readIspyData	0	0	0
readMSData	0.5	0.0	0.5
readMSnSet	0	0	0
readMgfData	6.82	0.06	6.99
readMzTabData	0.25	0.01	0.47
removeNoId-methods	1.04	0.02	1.06
removePeaks-methods	1.36	0.00	1.35
removeReporters-methods	0.69	0.00	0.69
smooth-methods	0.2	0.0	0.2
trimMz-methods	0.12	0.00	0.13
writeMgfData-methods	0	0	0
writeMzTabData	6.54	0.06	16.58
xic-methods	0	0	0

name	user	system	elapsed
FeatComp-class	0.42	0.03	1.42
FeaturesOfInterest-class	0.08	0.00	0.08
MSmap-class	0	0	0
MSnExp-class	0.56	0.00	2.11
MSnProcess-class	0	0	0
MSnSet-class	0.94	0.00	0.94
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	0.70	0.01	0.72
averageMSnSet	13.28	0.32	14.72
bin-methods	1.00	0.00	0.99
calculateFragments-methods	0.65	0.00	0.65
chromatogram-methods	0.08	0.11	0.21
clean-methods	1.62	0.01	1.63
combineFeatures	1.61	0.00	1.61
compareSpectra-methods	13.02	0.02	13.04
exprsToRatios-methods	3.56	0.00	3.56
extractPrecSpectra-methods	0.5	0.0	0.5
featureCV	0.44	0.00	0.43
fillUp	0	0	0
formatRt	0	0	0
get.amino.acids	0	0	0
get.atomic.mass	0	0	0
getVariableName	0	0	0
iTRAQ4	0.02	0.00	0.02
impute-methods	3.94	0.03	3.97
itraqdata	0.02	0.00	0.02
listOf	0.01	0.00	0.01
nQuants	4.15	0.00	4.15
normalise-methods	3.93	0.00	3.93
npcv	0	0	0
pSet-class	0	0	0
pickPeaks-method	0.24	0.01	0.25
plot-methods	1.23	0.00	1.23
plot2d-methods	0.83	0.00	0.83
plotDensity-methods	0.85	0.00	0.86
plotMzDelta-methods	2.34	0.07	2.40
plotNA-methods	4.14	0.00	5.60
plotSpectrumSpectrum-methods	0.56	0.00	0.56
precSelection	0.02	0.00	0.02
purityCorrect-methods	3.29	0.00	3.29
quantify-methods	6.17	0.01	6.19
readIspyData	0	0	0
readMSData	0.58	0.00	0.58
readMSnSet	0	0	0
readMgfData	5.84	0.00	5.85
readMzTabData	0.42	0.02	0.47
removeNoId-methods	1.62	0.00	1.62
removePeaks-methods	1.42	0.00	1.42
removeReporters-methods	0.86	0.00	0.86
smooth-methods	0.22	0.00	0.22
trimMz-methods	0.14	0.00	0.14
writeMgfData-methods	0	0	0
writeMzTabData	9.37	0.09	16.10
xic-methods	0	0	0