BioC 3.3: CHECK report for MSnbase on morelia

Package: MSnbase

Version: 1.19.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.19.1.tar.gz

StartedAt: 2015-10-22 08:49:07 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 08:53:00 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 232.6 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_1.19.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MSnbase.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.19.1’
* 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 ... [17s/17s] 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 ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
quantify-methods 9.774  3.331   4.145
averageMSnSet    6.272  0.123   7.037
MSnSet-class     4.740  0.087   5.253
writeMzTabData   2.922  0.053   8.987
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [58s/42s]
 [59s/43s] 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-3.3-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/3.3/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/3.3/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-3.3-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	0.204	0.020	0.357
FeaturesOfInterest-class	0.060	0.007	0.067
MSmap-class	0.000	0.001	0.002
MSnExp-class	0.298	0.005	0.379
MSnProcess-class	0.002	0.000	0.002
MSnSet-class	4.740	0.087	5.253
MSnSetList-class	3.502	0.015	3.518
MzTab-class	1.201	0.039	4.591
NAnnotatedDataFrame-class	0.016	0.001	0.016
ReporterIons-class	0.012	0.000	0.013
TMT6	0.009	0.001	0.010
addIdentificationData-methods	0.597	0.004	0.601
averageMSnSet	6.272	0.123	7.037
bin-methods	0.652	0.012	0.666
calculateFragments-methods	0.551	0.011	0.562
chromatogram-methods	0.065	0.013	0.175
clean-methods	0.590	0.021	0.610
combineFeatures	0.639	0.010	0.654
commonFeatureNames	0.419	0.010	0.429
compareSpectra-methods	0.177	0.001	0.179
exprsToRatios-methods	0.093	0.001	0.094
extractPrecSpectra-methods	0.482	0.002	0.485
featureCV	0.054	0.000	0.055
fillUp	0.008	0.000	0.008
formatRt	0.001	0.000	0.001
get.amino.acids	0.004	0.000	0.004
get.atomic.mass	0.001	0.000	0.000
getVariableName	0.001	0.000	0.002
iPQF	0.322	0.001	0.323
iTRAQ4	0.012	0.000	0.012
imageNA2	1.593	0.053	1.653
impute-methods	0.612	0.014	0.844
itraqdata	0.043	0.002	0.045
listOf	0.004	0.000	0.004
missing-data	1.949	0.052	2.008
nQuants	0.227	0.002	0.229
normalise-methods	0.022	0.001	0.023
npcv	0.003	0.000	0.003
pSet-class	0.003	0.001	0.003
pickPeaks-method	0.150	0.002	0.152
plot-methods	0.908	0.009	0.920
plot2d-methods	0.486	0.003	1.126
plotDensity-methods	0.564	0.002	0.567
plotMzDelta-methods	1.198	0.024	1.224
plotNA-methods	0.389	0.002	0.391
plotSpectrumSpectrum-methods	0.485	0.006	0.492
precSelection	0.009	0.001	0.009
purityCorrect-methods	0.017	0.001	0.018
quantify-methods	9.774	3.331	4.145
readIspyData	0.000	0.000	0.001
readMSData	0.398	0.004	0.403
readMSnSet	0.001	0.000	0.001
readMgfData	2.601	0.056	2.661
readMzTabData	2.703	0.032	3.149
readMzTabData_v0.9	0.171	0.002	0.261
removeNoId-methods	0.806	0.014	0.821
removePeaks-methods	1.033	0.012	1.046
removeReporters-methods	0.549	0.007	0.556
smooth-methods	0.153	0.007	0.159
trimMz-methods	0.058	0.001	0.059
writeMgfData-methods	0.000	0.000	0.001
writeMzTabData	2.922	0.053	8.987
xic-methods	0.000	0.000	0.001