BioC 3.2: CHECK report for MSnbase on oaxaca

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.18.1’
* 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 ... [23s/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 ... [81s/115s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
quantify-methods 8.809  2.925   5.712
averageMSnSet    8.168  0.169  10.354
MSnSet-class     6.555  0.070   6.651
MSnSetList-class 5.122  0.026   5.151
writeMzTabData   4.655  0.049  39.455
MzTab-class      1.639  0.046   7.062
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [76s/62s]
 [77s/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	0.236	0.018	0.385
FeaturesOfInterest-class	0.238	0.006	0.245
MSmap-class	0.002	0.000	0.002
MSnExp-class	0.366	0.006	0.431
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	6.555	0.070	6.651
MSnSetList-class	5.122	0.026	5.151
MzTab-class	1.639	0.046	7.062
NAnnotatedDataFrame-class	0.021	0.000	0.021
ReporterIons-class	0.019	0.001	0.019
TMT6	0.015	0.001	0.015
addIdentificationData-methods	0.612	0.008	0.620
averageMSnSet	8.168	0.169	10.354
bin-methods	0.431	0.011	0.442
calculateFragments-methods	0.682	0.015	0.698
chromatogram-methods	0.077	0.016	0.232
clean-methods	1.074	0.036	1.112
combineFeatures	0.979	0.010	0.989
commonFeatureNames	0.719	0.014	0.734
compareSpectra-methods	0.184	0.006	0.189
exprsToRatios-methods	0.103	0.002	0.105
extractPrecSpectra-methods	0.535	0.003	0.539
featureCV	0.059	0.002	0.061
fillUp	0.009	0.000	0.009
formatRt	0.001	0.001	0.001
get.amino.acids	0.006	0.001	0.007
get.atomic.mass	0	0	0
getVariableName	0.002	0.000	0.003
iPQF	0.448	0.005	0.454
iTRAQ4	0.022	0.000	0.023
imageNA2	2.911	0.058	2.990
impute-methods	0.886	0.018	1.169
itraqdata	0.049	0.004	0.053
listOf	0.005	0.000	0.005
missing-data	2.453	0.045	2.506
nQuants	0.255	0.002	0.257
normalise-methods	0.026	0.002	0.027
npcv	0.003	0.000	0.004
pSet-class	0.003	0.001	0.004
pickPeaks-method	0.241	0.003	0.244
plot-methods	1.366	0.007	1.381
plot2d-methods	0.807	0.004	0.812
plotDensity-methods	0.940	0.008	0.950
plotMzDelta-methods	2.013	0.040	2.054
plotNA-methods	0.628	0.010	0.638
plotSpectrumSpectrum-methods	0.819	0.010	0.829
precSelection	0.016	0.001	0.017
purityCorrect-methods	0.036	0.003	0.039
quantify-methods	8.809	2.925	5.712
readIspyData	0.001	0.000	0.001
readMSData	0.504	0.004	0.509
readMSnSet	0.000	0.000	0.001
readMgfData	3.301	0.050	3.357
readMzTabData	3.315	0.038	3.776
readMzTabData_v0.9	0.257	0.002	0.897
removeNoId-methods	1.200	0.016	1.217
removePeaks-methods	1.250	0.018	1.269
removeReporters-methods	0.879	0.006	0.885
smooth-methods	0.255	0.006	0.261
trimMz-methods	0.123	0.007	0.130
writeMgfData-methods	0.001	0.000	0.002
writeMzTabData	4.655	0.049	39.455
xic-methods	0.000	0.000	0.001

BioC 3.2: CHECK report for MSnbase on oaxaca

Summary

Command output