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/25s] 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 ... [158s/124s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
readMzTabData    26.491  0.068  26.991
quantify-methods 13.224  7.862   7.520
MzTab-class      16.201  0.040  19.740
averageMSnSet     8.304  0.180  10.012
MSnSet-class      7.437  0.079   7.605
MSnSetList-class  5.102  0.021   5.123
writeMzTabData    3.600  0.064  10.032
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [107s/68s]
 [108s/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	0.492	0.014	0.691
FeaturesOfInterest-class	0.090	0.004	0.093
MSmap-class	0.002	0.001	0.002
MSnExp-class	0.396	0.007	0.476
MSnProcess-class	0.003	0.000	0.003
MSnSet-class	7.437	0.079	7.605
MSnSetList-class	5.102	0.021	5.123
MzTab-class	16.201	0.040	19.740
NAnnotatedDataFrame-class	0.021	0.001	0.021
ReporterIons-class	0.019	0.001	0.019
TMT6	0.014	0.001	0.015
addIdentificationData-methods	0.695	0.004	0.698
averageMSnSet	8.304	0.180	10.012
bin-methods	0.760	0.016	0.776
calculateFragments-methods	0.711	0.015	0.725
chromatogram-methods	0.062	0.021	0.247
clean-methods	1.162	0.036	1.199
combineFeatures	0.968	0.012	0.979
commonFeatureNames	0.749	0.013	0.762
compareSpectra-methods	0.186	0.007	0.194
exprsToRatios-methods	0.097	0.002	0.098
extractPrecSpectra-methods	0.632	0.003	0.635
featureCV	0.058	0.001	0.058
fillUp	0.009	0.001	0.009
formatRt	0.002	0.000	0.001
get.amino.acids	0.007	0.001	0.008
get.atomic.mass	0	0	0
getVariableName	0.002	0.000	0.003
iPQF	0.392	0.002	0.393
iTRAQ4	0.023	0.001	0.023
imageNA2	2.836	0.032	2.874
impute-methods	1.035	0.018	1.281
itraqdata	0.048	0.002	0.050
listOf	0.004	0.000	0.004
missing-data	2.618	0.020	2.645
nQuants	0.256	0.001	0.257
normalise-methods	0.024	0.001	0.025
npcv	0.003	0.001	0.003
pSet-class	0.002	0.000	0.003
pickPeaks-method	0.230	0.012	0.242
plot-methods	1.213	0.029	1.489
plot2d-methods	1.168	0.005	1.173
plotDensity-methods	0.749	0.005	0.754
plotMzDelta-methods	1.885	0.050	1.935
plotNA-methods	0.657	0.051	0.709
plotSpectrumSpectrum-methods	0.863	0.025	0.890
precSelection	0.018	0.000	0.019
purityCorrect-methods	0.032	0.002	0.033
quantify-methods	13.224	7.862	7.520
readIspyData	0.000	0.000	0.001
readMSData	0.588	0.006	0.594
readMSnSet	0.000	0.000	0.001
readMgfData	3.061	0.080	3.149
readMzTabData	26.491	0.068	26.991
readMzTabData_v0.9	0.227	0.002	0.368
removeNoId-methods	1.290	0.013	1.303
removePeaks-methods	1.332	0.038	1.369
removeReporters-methods	0.665	0.009	0.673
smooth-methods	0.205	0.009	0.214
trimMz-methods	0.120	0.008	0.128
writeMgfData-methods	0.002	0.000	0.001
writeMzTabData	3.600	0.064	10.032
xic-methods	0.001	0.000	0.001

BioC 3.2: CHECK report for MSnbase on perceval

Summary

Command output