BioC 3.2: CHECK report for MSnbase on perceval

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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 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [24s/24s] 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 ... [161s/130s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
readMzTabData    31.501  0.060  31.985
quantify-methods 17.623 10.731   7.505
MzTab-class      13.566  0.046  16.812
averageMSnSet     8.547  0.186  10.036
MSnSet-class      7.573  0.081   7.833
MSnSetList-class  5.080  0.016   5.096
writeMzTabData    3.534  0.105  13.268
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [107s/68s]
 [107s/68s] 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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
llvm-g++-4.2 -arch x86_64 -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 -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	0.483	0.014	0.616
FeaturesOfInterest-class	0.088	0.005	0.093
MSmap-class	0.001	0.000	0.002
MSnExp-class	0.400	0.007	0.448
MSnProcess-class	0.002	0.001	0.003
MSnSet-class	7.573	0.081	7.833
MSnSetList-class	5.080	0.016	5.096
MzTab-class	13.566	0.046	16.812
NAnnotatedDataFrame-class	0.023	0.000	0.023
ReporterIons-class	0.019	0.001	0.019
TMT6	0.014	0.001	0.014
addIdentificationData-methods	0.691	0.003	0.694
averageMSnSet	8.547	0.186	10.036
bin-methods	0.835	0.020	0.856
calculateFragments-methods	0.728	0.015	0.744
chromatogram-methods	0.060	0.019	0.167
clean-methods	1.135	0.034	1.170
combineFeatures	0.903	0.011	0.915
commonFeatureNames	0.686	0.015	0.702
compareSpectra-methods	0.161	0.007	0.168
exprsToRatios-methods	0.093	0.001	0.093
extractPrecSpectra-methods	0.645	0.003	0.648
featureCV	0.053	0.000	0.053
fillUp	0.008	0.001	0.009
formatRt	0.001	0.000	0.001
get.amino.acids	0.007	0.001	0.007
get.atomic.mass	0.000	0.000	0.001
getVariableName	0.002	0.000	0.002
iPQF	0.380	0.002	0.380
iTRAQ4	0.022	0.000	0.022
imageNA2	2.764	0.032	2.825
impute-methods	1.010	0.016	1.247
itraqdata	0.049	0.002	0.051
listOf	0.004	0.001	0.004
missing-data	3.592	0.023	3.624
nQuants	0.252	0.002	0.253
normalise-methods	0.022	0.001	0.023
npcv	0.003	0.001	0.003
pSet-class	0.002	0.000	0.003
pickPeaks-method	0.212	0.002	0.215
plot-methods	1.213	0.035	1.250
plot2d-methods	0.679	0.007	0.687
plotDensity-methods	0.776	0.005	0.810
plotMzDelta-methods	2.368	0.053	2.422
plotNA-methods	0.604	0.032	0.636
plotSpectrumSpectrum-methods	0.875	0.032	0.907
precSelection	0.024	0.002	0.024
purityCorrect-methods	0.033	0.002	0.035
quantify-methods	17.623	10.731	7.505
readIspyData	0.001	0.000	0.000
readMSData	0.604	0.010	0.613
readMSnSet	0	0	0
readMgfData	3.095	0.075	3.178
readMzTabData	31.501	0.060	31.985
readMzTabData_v0.9	0.250	0.004	0.418
removeNoId-methods	1.301	0.036	1.337
removePeaks-methods	1.335	0.021	1.356
removeReporters-methods	0.698	0.004	0.702
smooth-methods	0.208	0.005	0.212
trimMz-methods	0.116	0.005	0.121
writeMgfData-methods	0.002	0.000	0.001
writeMzTabData	3.534	0.105	13.268
xic-methods	0.001	0.000	0.001

BioC 3.2: CHECK report for MSnbase on perceval

Summary

Command output