BioC 3.2: CHECK report for MSnbase on oaxaca

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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_1.17.14.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 ‘1.17.14’
* 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 ... [83s/85s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
quantify-methods 7.289  2.178   5.873
averageMSnSet    8.124  0.146   9.086
MSnSet-class     7.450  0.112   7.705
MSnSetList-class 5.647  0.052   5.748
writeMzTabData   3.190  0.041   9.831
MzTab-class      1.608  0.041   5.797
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [80s/66s]
 [80s/66s] 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 ‘lengths’ from package ‘base’ 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	0.472	0.015	0.776
FeaturesOfInterest-class	0.079	0.004	0.085
MSmap-class	0.002	0.000	0.002
MSnExp-class	0.355	0.005	0.444
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	7.450	0.112	7.705
MSnSetList-class	5.647	0.052	5.748
MzTab-class	1.608	0.041	5.797
NAnnotatedDataFrame-class	0.024	0.000	0.024
ReporterIons-class	0.021	0.001	0.022
TMT6	0.014	0.001	0.016
addIdentificationData-methods	0.610	0.010	0.634
averageMSnSet	8.124	0.146	9.086
bin-methods	0.724	0.013	0.738
calculateFragments-methods	0.653	0.018	0.677
chromatogram-methods	0.082	0.018	0.213
clean-methods	1.084	0.033	1.118
combineFeatures	1.038	0.006	1.057
commonFeatureNames	0.736	0.017	0.774
compareSpectra-methods	0.172	0.005	0.177
exprsToRatios-methods	0.097	0.001	0.098
extractPrecSpectra-methods	0.473	0.002	0.483
featureCV	0.059	0.001	0.060
fillUp	0.010	0.000	0.011
formatRt	0.001	0.000	0.002
get.amino.acids	0.007	0.001	0.007
get.atomic.mass	0.001	0.000	0.001
getVariableName	0.002	0.000	0.003
iPQF	0.087	0.000	0.088
iTRAQ4	0.022	0.000	0.023
imageNA2	2.604	0.071	2.724
impute-methods	0.978	0.017	1.126
itraqdata	0.054	0.002	0.056
listOf	0.006	0.000	0.006
missing-data	2.630	0.039	2.723
nQuants	0.311	0.002	0.314
normalise-methods	0.027	0.000	0.027
npcv	0.004	0.000	0.004
pSet-class	0.002	0.000	0.002
pickPeaks-method	0.247	0.002	0.249
plot-methods	1.696	0.006	1.815
plot2d-methods	0.784	0.003	0.790
plotDensity-methods	0.914	0.003	0.946
plotMzDelta-methods	1.780	0.046	1.841
plotNA-methods	0.762	0.002	0.766
plotSpectrumSpectrum-methods	0.849	0.008	0.870
precSelection	0.018	0.001	0.019
purityCorrect-methods	0.038	0.001	0.040
quantify-methods	7.289	2.178	5.873
readIspyData	0.000	0.000	0.001
readMSData	0.547	0.006	0.555
readMSnSet	0.000	0.000	0.001
readMgfData	3.623	0.050	3.767
readMzTabData	3.567	0.041	3.935
readMzTabData_v0.9	0.267	0.002	0.429
removeNoId-methods	1.219	0.021	1.240
removePeaks-methods	1.372	0.023	1.399
removeReporters-methods	0.820	0.005	0.828
smooth-methods	0.265	0.006	0.277
trimMz-methods	0.122	0.005	0.128
writeMgfData-methods	0.001	0.001	0.001
writeMzTabData	3.190	0.041	9.831
xic-methods	0.001	0.000	0.001

BioC 3.2: CHECK report for MSnbase on oaxaca

Summary

Command output