BioC 2.13: CHECK report for MSnbase on moscato1

Package: MSnbase

Version: 1.10.4

Command: rm -rf MSnbase.buildbin-libdir && mkdir MSnbase.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSnbase.buildbin-libdir MSnbase_1.10.4.tar.gz >MSnbase-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=MSnbase.buildbin-libdir --install="check:MSnbase-install.out" --force-multiarch --no-vignettes --timings MSnbase_1.10.4.tar.gz && mv MSnbase.buildbin-libdir/* MSnbase.Rcheck/ && rmdir MSnbase.buildbin-libdir

StartedAt: 2014-04-05 05:23:20 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:31:13 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 472.5 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/MSnbase.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.10.4'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'MSnbase-demo.Rnw', 'MSnbase-development.Rnw', 'MSnbase-io.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [119s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
writeMzTabData        7.72   0.04   14.75
readMgfData           6.40   0.02    7.88
purityCorrect-methods 5.22   0.00    5.23
chromatogram-methods  0.11   0.04   43.48
** running examples for arch 'x64' ... [81s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
writeMzTabData 8.77   0.11   15.69
readMgfData    6.88   0.00    6.91
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'test-all.R' [33s]
 [34s] OK
** running tests for arch 'x64'
  Running 'test-all.R' [37s]
 [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 4 notes.
See
  'D:/biocbld/bbs-2.13-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_1.10.4.zip
* DONE (MSnbase)

name	user	system	elapsed
MSnExp-class	0.47	0.00	0.72
MSnProcess-class	0.00	0.01	0.01
MSnSet-class	1.29	0.04	1.38
NAnnotatedDataFrame-class	0.03	0.00	0.03
ReporterIons-class	0.04	0.00	0.03
TMT6	0.01	0.00	0.01
chromatogram-methods	0.11	0.04	43.48
clean-methods	1.62	0.02	1.64
combineFeatures	0.58	0.00	0.62
exprsToRatios-methods	3.53	0.00	3.55
extractPrecSpectra-methods	0.21	0.01	0.22
featureCV	0.43	0.00	0.95
fillUp	0.00	0.02	0.02
formatRt	0.02	0.00	0.01
getVariableName	0	0	0
iTRAQ4	0.02	0.00	0.01
impute-methods	3.58	0.00	3.57
itraqdata	0.14	0.00	0.14
nQuants	3.59	0.00	3.59
normalise-methods	3.37	0.00	3.40
pSet-class	0	0	0
plot-methods	1.35	0.00	1.36
plot2d-methods	0.89	0.00	0.89
plotDensity-methods	1.03	0.00	1.03
plotMzDelta-methods	2.93	0.06	3.71
plotNA-methods	4.12	0.00	4.12
precSelection	0.07	0.00	0.06
purityCorrect-methods	5.22	0.00	5.23
quantify-methods	4.26	0.00	4.26
readIspyData	0	0	0
readMSData	0.2	0.0	0.2
readMSnSet	0	0	0
readMgfData	6.40	0.02	7.88
readMzTabData	0.37	0.00	0.50
removePeaks-methods	2.45	0.01	2.49
removeReporters-methods	0.86	0.00	0.85
trimMz-methods	0.17	0.02	0.19
writeMgfData-methods	0.00	0.01	0.02
writeMzTabData	7.72	0.04	14.75
xic-methods	0	0	0

name	user	system	elapsed
MSnExp-class	0.72	0.00	1.19
MSnProcess-class	0	0	0
MSnSet-class	1.81	0.00	1.81
NAnnotatedDataFrame-class	0.06	0.00	0.06
ReporterIons-class	0.03	0.00	0.03
TMT6	0.2	0.0	0.2
chromatogram-methods	0.14	0.00	0.14
clean-methods	2.22	0.00	2.21
combineFeatures	1.19	0.03	1.22
exprsToRatios-methods	4.76	0.00	4.77
extractPrecSpectra-methods	0.36	0.00	0.36
featureCV	0.73	0.00	0.73
fillUp	0.01	0.00	0.01
formatRt	0	0	0
getVariableName	0.01	0.00	0.01
iTRAQ4	0.04	0.00	0.05
impute-methods	4.9	0.0	4.9
itraqdata	0.05	0.00	0.04
nQuants	4.36	0.01	4.38
normalise-methods	3.7	0.0	3.7
pSet-class	0	0	0
plot-methods	1.70	0.02	1.72
plot2d-methods	1.18	0.00	1.19
plotDensity-methods	1.39	0.00	1.38
plotMzDelta-methods	3.82	0.05	3.87
plotNA-methods	4.72	0.00	4.72
precSelection	0.07	0.00	0.09
purityCorrect-methods	3.95	0.00	3.95
quantify-methods	3.96	0.00	3.96
readIspyData	0	0	0
readMSData	0.28	0.00	0.29
readMSnSet	0	0	0
readMgfData	6.88	0.00	6.91
readMzTabData	0.28	0.00	0.32
removePeaks-methods	2.34	0.01	2.36
removeReporters-methods	1.22	0.00	1.21
trimMz-methods	0.21	0.00	0.20
writeMgfData-methods	0.03	0.00	0.03
writeMzTabData	8.77	0.11	15.69
xic-methods	0.02	0.00	0.02