BioC 3.2: CHECK report for MSnbase on perceval

Package: MSnbase

Version: 1.17.14

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.17.14.tar.gz

StartedAt: 2015-08-18 05:31:19 -0700 (Tue, 18 Aug 2015)

EndedAt: 2015-08-18 05:37:46 -0700 (Tue, 18 Aug 2015)

EllapsedTime: 386.2 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_1.17.14.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MSnbase.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.17.14’
* 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 ... [25s/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 ... [130s/126s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
quantify-methods 17.547  9.933   9.410
readMzTabData    23.803  0.108  25.367
MzTab-class      11.388  0.045  15.527
MSnSet-class      9.026  0.130   9.209
averageMSnSet     8.304  0.230   9.433
MSnSetList-class  5.205  0.046   5.252
writeMzTabData    5.073  0.099  11.950
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [105s/74s]
 [105s/75s] 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 ‘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	0.271	0.025	0.392
FeaturesOfInterest-class	0.087	0.007	0.094
MSmap-class	0.001	0.000	0.002
MSnExp-class	0.520	0.008	0.528
MSnProcess-class	0.002	0.000	0.003
MSnSet-class	9.026	0.130	9.209
MSnSetList-class	5.205	0.046	5.252
MzTab-class	11.388	0.045	15.527
NAnnotatedDataFrame-class	0.022	0.000	0.023
ReporterIons-class	0.02	0.00	0.02
TMT6	0.013	0.001	0.015
addIdentificationData-methods	0.933	0.008	0.942
averageMSnSet	8.304	0.230	9.433
bin-methods	1.156	0.033	1.190
calculateFragments-methods	0.916	0.021	0.937
chromatogram-methods	0.065	0.033	0.189
clean-methods	1.078	0.054	1.132
combineFeatures	0.911	0.017	0.927
commonFeatureNames	0.618	0.017	0.634
compareSpectra-methods	0.150	0.008	0.159
exprsToRatios-methods	0.076	0.001	0.078
extractPrecSpectra-methods	0.771	0.004	0.776
featureCV	0.045	0.000	0.046
fillUp	0.006	0.000	0.007
formatRt	0.001	0.000	0.001
get.amino.acids	0.006	0.001	0.007
get.atomic.mass	0	0	0
getVariableName	0.002	0.000	0.002
iPQF	0.071	0.001	0.073
iTRAQ4	0.018	0.000	0.019
imageNA2	2.642	0.038	2.754
impute-methods	1.127	0.033	1.301
itraqdata	0.059	0.003	0.063
listOf	0.005	0.000	0.005
missing-data	3.540	0.034	3.581
nQuants	0.270	0.002	0.272
normalise-methods	0.022	0.002	0.023
npcv	0.003	0.000	0.003
pSet-class	0.002	0.001	0.003
pickPeaks-method	0.214	0.015	0.229
plot-methods	1.248	0.042	1.293
plot2d-methods	0.718	0.007	0.724
plotDensity-methods	0.702	0.006	0.709
plotMzDelta-methods	1.770	0.081	1.851
plotNA-methods	0.681	0.010	0.690
plotSpectrumSpectrum-methods	1.175	0.017	1.193
precSelection	0.022	0.001	0.023
purityCorrect-methods	0.032	0.002	0.034
quantify-methods	17.547	9.933	9.410
readIspyData	0.001	0.000	0.001
readMSData	0.786	0.020	0.805
readMSnSet	0.001	0.000	0.001
readMgfData	3.193	0.080	3.276
readMzTabData	23.803	0.108	25.367
readMzTabData_v0.9	0.251	0.017	0.398
removeNoId-methods	1.892	0.036	1.931
removePeaks-methods	1.209	0.034	1.337
removeReporters-methods	0.657	0.012	0.668
smooth-methods	0.187	0.006	0.192
trimMz-methods	0.123	0.005	0.127
writeMgfData-methods	0.001	0.001	0.001
writeMzTabData	5.073	0.099	11.950
xic-methods	0.001	0.000	0.001