BioC 3.6: CHECK report for tofsims on veracruz1

Package: tofsims

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tofsims_1.5.0.tar.gz

StartedAt: 2017-08-16 09:11:04 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:15:53 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 288.5 seconds

RetCode: 0

Status:  OK

CheckDir: tofsims.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 tofsims_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/tofsims.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tofsims/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tofsims’ version ‘1.5.0’
* 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 ‘tofsims’ can be installed ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
findPeakWidth 5.940  0.969   7.111
peakWidths    5.891  0.993   7.132
bwApply       6.353  0.290   6.837
pcaLoadings   4.792  0.203   5.137
smoothScatter 4.835  0.126   5.104
pcaScores     4.796  0.109   5.063
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: OK

* installing *source* package ‘tofsims’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c LapackEigen.cpp -o LapackEigen.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c c_importer.cpp -o c_importer.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c nn.cpp -o nn.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c readRawPhi.cpp -o readRawPhi.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c tofsims_init.c -o tofsims_init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c utilities.cpp -o utilities.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 tofsims.so LapackEigen.o RcppExports.o c_importer.o nn.o readRawPhi.o tofsims_init.o utilities.o -llapack -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/tofsims.Rcheck/tofsims/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tofsims)

name	user	system	elapsed
MAF	1.383	0.056	1.480
MCR	0.111	0.011	0.122
MNF	0.140	0.017	0.164
MassImage	0.007	0.001	0.008
MassSpectra	0.026	0.002	0.033
PCAnalysis	0.018	0.001	0.019
PeakList	3.078	0.831	4.003
PrComp	0.027	0.001	0.029
PrinComp	0.020	0.001	0.022
addFixedWidth	3.296	0.568	3.980
addPeaks	1.412	0.105	1.588
analysis	4.530	0.090	4.766
analysisName	1.293	0.046	1.383
binning	0.094	0.007	0.106
bwApply	6.353	0.290	6.837
calibPointNew	1.608	0.072	1.748
calibPoints	1.216	0.018	1.258
calibration	1.308	0.044	1.370
changePeakWidth	1.405	0.081	1.514
findPeakWidth	5.940	0.969	7.111
getTOFs	1.290	0.095	1.425
image	4.742	0.093	4.985
imageMatrix	2.187	0.261	2.507
instrument	1.312	0.012	1.372
mz	1.283	0.019	1.344
nComp	4.722	0.108	4.919
nPeaks	2.737	1.034	3.880
nnMNF	0.237	0.105	0.357
nz	1.321	0.056	1.420
overlayPlot	1.635	0.173	1.858
pcaLoadings	4.792	0.203	5.137
pcaScores	4.796	0.109	5.063
peakIDs	2.647	1.013	3.773
peakMzs	2.749	1.041	3.901
peakPick	2.555	0.423	3.054
peakWidths	5.891	0.993	7.132
peaks2Spectra	1.757	0.466	2.283
plot	1.157	0.052	1.221
points	1.503	0.203	1.754
poissonScaling	0.010	0.001	0.011
recalibrate	1.435	0.200	1.677
reduceSpectrumResolution	1.304	0.063	1.385
removePeaks	1.355	0.086	1.452
scale	0.027	0.002	0.029
smoothScatter	4.835	0.126	5.104
smootherGolay	1.428	0.191	1.687
smootherSpline	3.088	0.910	4.117
subset	1.430	0.096	1.581
unitMassPeaks	2.873	1.127	4.128
xy	1.372	0.057	1.452
xySpec	1.548	0.059	1.655