BioC 3.3: CHECK report for MSnbase on morelia

Package: MSnbase

Version: 1.19.19

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MSnbase_1.19.19.tar.gz

StartedAt: 2016-04-21 05:23:11 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:27:35 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 263.9 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_1.19.19.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MSnbase.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.19.19’
* 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 ... [20s/21s] 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
naplot: no visible global function definition for ‘par’
naplot: no visible global function definition for ‘layout’
naplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  barplot layout par
Consider adding
  importFrom("graphics", "barplot", "layout", "par")
to your NAMESPACE file.
* 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 ... [75s/66s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
averageMSnSet    7.133  0.136   7.972
MSnSet-class     5.602  0.104   5.745
quantify-methods 1.850  0.237   6.802
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [81s/59s]
 [81s/59s] 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-3.3-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
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ 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’
** inst
** preparing package for lazy loading
Creating a new generic function for ‘smooth’ in package ‘MSnbase’
Creating a new generic function for ‘trimws’ 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	0.230	0.017	0.355
FeaturesOfInterest-class	0.068	0.005	0.074
MSmap-class	0.002	0.000	0.002
MSnExp-class	0.376	0.006	0.641
MSnProcess-class	0.002	0.000	0.001
MSnSet-class	5.602	0.104	5.745
MSnSetList-class	4.375	0.015	4.395
MzTab-class	1.355	0.045	4.896
NAnnotatedDataFrame-class	0.026	0.000	0.026
ReporterIons-class	0.024	0.000	0.024
TMT6	0.016	0.001	0.016
addIdentificationData-methods	0.624	0.006	0.632
averageMSnSet	7.133	0.136	7.972
bin-methods	0.754	0.015	0.770
calculateFragments-methods	0.601	0.013	0.614
chromatogram-methods	0.075	0.016	0.274
clean-methods	1.434	0.031	1.466
combineFeatures	0.742	0.009	0.752
commonFeatureNames	0.598	0.022	0.623
compareSpectra-methods	0.165	0.005	0.170
estimateNoise-method	0.014	0.000	0.015
exprsToRatios-methods	0.067	0.001	0.068
extractPrecSpectra-methods	0.454	0.002	0.456
featureCV	0.036	0.001	0.037
fillUp	0.008	0.000	0.008
formatRt	0.001	0.000	0.001
get.amino.acids	0.006	0.000	0.006
get.atomic.mass	0.001	0.000	0.001
getVariableName	0.002	0.000	0.002
iPQF	0.330	0.007	0.337
iTRAQ4	0.018	0.000	0.018
imageNA2	1.941	0.076	2.026
impute-methods	0.666	0.020	0.891
itraqdata	0.048	0.004	0.053
listOf	0.004	0.000	0.005
missing-data	2.071	0.050	2.132
nQuants	0.228	0.002	0.229
naplot	0.093	0.003	0.099
normalise-methods	0.025	0.002	0.027
npcv	0.003	0.000	0.003
pSet-class	0.002	0.000	0.003
pickPeaks-method	0.344	0.005	0.350
plot-methods	1.448	0.010	1.463
plot2d-methods	0.850	0.005	0.857
plotDensity-methods	0.845	0.004	0.850
plotMzDelta-methods	1.614	0.038	1.652
plotNA-methods	0.509	0.022	0.532
plotSpectrumSpectrum-methods	0.905	0.018	0.950
precSelection	0.018	0.001	0.019
purityCorrect-methods	0.032	0.002	0.035
quantify-methods	1.850	0.237	6.802
readIspyData	0.001	0.000	0.000
readMSData	0.518	0.003	0.521
readMSnSet	0.001	0.000	0.001
readMgfData	3.412	0.050	3.480
readMzTabData	3.004	0.046	3.512
readMzTabData_v0.9	0.234	0.002	0.798
removeNoId-methods	1.078	0.017	1.095
removePeaks-methods	1.090	0.019	1.110
removeReporters-methods	0.690	0.005	0.694
selectFeatureData	0.141	0.013	0.171
smooth-methods	0.329	0.008	0.337
trimMz-methods	0.195	0.001	0.196
writeMgfData-methods	0.002	0.000	0.001
xic-methods	0.001	0.000	0.001