BioC 3.2: CHECK report for MSnbase on oaxaca

Package: MSnbase

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.18.0.tar.gz

StartedAt: 2015-10-27 05:58:34 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:03:47 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 312.6 seconds

RetCode: 0

Status:  OK

CheckDir: MSnbase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnbase/DESCRIPTION’ ... OK
* this is package ‘MSnbase’ version ‘1.18.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSnbase’ can be installed ... [22s/22s] 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
* 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 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [78s/81s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
quantify-methods 10.247  3.360   5.559
averageMSnSet     7.705  0.132   9.121
MSnSet-class      6.734  0.093   7.191
MSnSetList-class  5.117  0.027   5.152
writeMzTabData    3.660  0.040   9.762
MzTab-class       1.650  0.041   5.544
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [76s/61s]
 [76s/62s] 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck/00check.log’
for details.

* installing *source* package ‘MSnbase’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MSnbase.so RcppExports.o imp_neighbour_avg.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck/MSnbase/libs
** 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’
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
Creating a generic function for ‘split’ from package ‘base’ in package ‘MSnbase’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnbase)

name	user	system	elapsed
FeatComp-class	0.436	0.024	0.532
FeaturesOfInterest-class	0.077	0.007	0.084
MSmap-class	0.001	0.001	0.002
MSnExp-class	0.318	0.005	0.405
MSnProcess-class	0.002	0.001	0.001
MSnSet-class	6.734	0.093	7.191
MSnSetList-class	5.117	0.027	5.152
MzTab-class	1.650	0.041	5.544
NAnnotatedDataFrame-class	0.032	0.000	0.033
ReporterIons-class	0.024	0.000	0.025
TMT6	0.017	0.001	0.017
addIdentificationData-methods	0.598	0.004	0.602
averageMSnSet	7.705	0.132	9.121
bin-methods	0.616	0.010	0.625
calculateFragments-methods	0.617	0.016	0.634
chromatogram-methods	0.067	0.014	0.177
clean-methods	0.961	0.032	0.993
combineFeatures	0.921	0.005	0.925
commonFeatureNames	0.711	0.013	0.725
compareSpectra-methods	0.150	0.005	0.156
exprsToRatios-methods	0.072	0.001	0.073
extractPrecSpectra-methods	0.419	0.001	0.421
featureCV	0.035	0.001	0.035
fillUp	0.006	0.000	0.007
formatRt	0.001	0.000	0.001
get.amino.acids	0.004	0.000	0.004
get.atomic.mass	0.001	0.000	0.001
getVariableName	0.002	0.001	0.001
iPQF	0.392	0.002	0.394
iTRAQ4	0.020	0.000	0.021
imageNA2	2.446	0.065	2.582
impute-methods	0.947	0.018	1.132
itraqdata	0.038	0.003	0.040
listOf	0.005	0.000	0.005
missing-data	2.912	0.042	2.987
nQuants	0.275	0.002	0.277
normalise-methods	0.026	0.001	0.027
npcv	0.004	0.000	0.004
pSet-class	0.003	0.000	0.003
pickPeaks-method	0.263	0.003	0.267
plot-methods	1.254	0.007	1.274
plot2d-methods	0.711	0.003	0.716
plotDensity-methods	0.771	0.004	0.775
plotMzDelta-methods	1.659	0.044	1.704
plotNA-methods	0.637	0.026	0.663
plotSpectrumSpectrum-methods	0.815	0.023	0.838
precSelection	0.019	0.001	0.020
purityCorrect-methods	0.032	0.002	0.033
quantify-methods	10.247	3.360	5.559
readIspyData	0.000	0.000	0.001
readMSData	0.480	0.005	0.485
readMSnSet	0.000	0.000	0.001
readMgfData	3.345	0.047	3.398
readMzTabData	3.353	0.043	3.816
readMzTabData_v0.9	0.264	0.002	0.458
removeNoId-methods	1.108	0.011	1.120
removePeaks-methods	1.272	0.022	1.554
removeReporters-methods	0.922	0.005	1.344
smooth-methods	0.234	0.004	0.238
trimMz-methods	0.099	0.005	0.104
writeMgfData-methods	0.001	0.001	0.002
writeMzTabData	3.660	0.040	9.762
xic-methods	0.001	0.000	0.001