BioC 3.1: CHECK report for MSnbase on petty

Package: MSnbase

Version: 1.16.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.16.2.tar.gz

StartedAt: 2015-10-09 00:40:28 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:50:45 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 617.6 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_1.16.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.16.2’
* 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 ... [33s/55s] 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 ... NOTE
curveStats,Spectrum : .local: no visible global function definition for
  ‘curveStats_Spectrum’
exprsToRatios,matrix : .local: no visible global function definition
  for ‘conames<-’
impute,MSnSet : .local: no visible global function definition for
  ‘prelim.norm’
impute,MSnSet : .local: no visible global function definition for
  ‘em.norm’
impute,MSnSet : .local: no visible global function definition for
  ‘rngseed’
impute,MSnSet : .local: no visible global function definition for
  ‘imp.norm’
plot3D,MSmap : .local: no visible global function definition for
  ‘plot3d’
plot3D,MSmap : .local: no visible binding for global variable ‘ms’
plotMzDelta,mzRramp : .local: no visible binding for global variable
  ‘ms’
* 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 ... [115s/199s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
quantify-methods 11.404  7.728  30.177
averageMSnSet    11.572  0.313  18.744
imageNA2          4.784  0.061   8.350
missing-data      4.536  0.038   5.740
readMgfData       4.231  0.075  10.806
writeMzTabData    3.898  0.100  76.021
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [109s/81s]
 [110s/82s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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-3.1-bioc/meat/MSnbase.Rcheck/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (MSnbase)

name	user	system	elapsed
FeatComp-class	0.400	0.023	0.516
FeaturesOfInterest-class	0.142	0.008	0.150
MSmap-class	0.002	0.000	0.003
MSnExp-class	0.605	0.010	0.768
MSnProcess-class	0.003	0.000	0.004
MSnSet-class	0.554	0.026	0.582
NAnnotatedDataFrame-class	0.037	0.001	0.039
ReporterIons-class	0.033	0.001	0.034
TMT6	0.027	0.001	0.027
addIdentificationData-methods	0.766	0.004	0.771
averageMSnSet	11.572	0.313	18.744
bin-methods	0.609	0.014	1.056
calculateFragments-methods	1.591	0.025	2.695
chromatogram-methods	0.093	0.030	0.251
clean-methods	1.933	0.065	3.476
combineFeatures	0.874	0.008	1.494
compareSpectra-methods	0.286	0.014	0.508
exprsToRatios-methods	0.150	0.002	0.256
extractPrecSpectra-methods	0.788	0.005	1.346
featureCV	0.088	0.001	0.158
fillUp	0.013	0.000	0.024
formatRt	0.002	0.000	0.002
get.amino.acids	0.011	0.002	0.022
get.atomic.mass	0.001	0.000	0.001
getVariableName	0.003	0.000	0.003
iTRAQ4	0.034	0.001	0.053
imageNA2	4.784	0.061	8.350
impute-methods	1.698	0.030	3.263
itraqdata	0.087	0.003	0.160
listOf	0.008	0.001	0.015
missing-data	4.536	0.038	5.740
nQuants	0.413	0.002	0.417
normalise-methods	0.034	0.002	0.037
npcv	0.004	0.000	0.004
pSet-class	0.003	0.000	0.004
pickPeaks-method	0.316	0.022	0.339
plot-methods	1.886	0.036	1.974
plot2d-methods	1.021	0.007	1.050
plotDensity-methods	1.195	0.007	1.204
plotMzDelta-methods	2.595	0.073	2.673
plotNA-methods	0.656	0.026	0.683
plotSpectrumSpectrum-methods	1.141	0.017	1.161
precSelection	0.030	0.002	0.032
purityCorrect-methods	0.032	0.002	0.034
quantify-methods	11.404	7.728	30.177
readIspyData	0.000	0.001	0.001
readMSData	0.551	0.009	0.560
readMSnSet	0.001	0.000	0.088
readMgfData	4.231	0.075	10.806
readMzTabData	0.292	0.004	0.783
removeNoId-methods	1.313	0.016	1.331
removePeaks-methods	1.415	0.025	1.440
removeReporters-methods	0.814	0.008	0.822
smooth-methods	0.285	0.014	0.298
trimMz-methods	0.139	0.010	0.167
writeMgfData-methods	0.001	0.000	0.001
writeMzTabData	3.898	0.100	76.021
xic-methods	0.001	0.000	0.002