BioC 3.5: CHECK report for tofsims on veracruz2

Package: tofsims

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tofsims_1.4.0.tar.gz

StartedAt: 2017-10-18 09:46:09 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:51:15 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 306.3 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/tofsims.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.4.0’
* 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
peakWidths    6.150  1.037   7.422
bwApply       6.184  0.301   6.647
findPeakWidth 5.156  0.934   6.224
nComp         4.831  0.128   5.115
image         4.808  0.142   5.253
pcaScores     4.782  0.136   5.064
pcaLoadings   4.761  0.125   5.016
* 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-3.5-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	1.411	0.064	1.520
MCR	0.131	0.012	0.145
MNF	0.136	0.018	0.158
MassImage	0.007	0.001	0.014
MassSpectra	0.024	0.002	0.027
PCAnalysis	0.020	0.003	0.022
PeakList	3.127	0.765	4.015
PrComp	0.031	0.002	0.034
PrinComp	0.020	0.002	0.022
addFixedWidth	3.654	0.617	4.382
addPeaks	1.391	0.086	1.516
analysis	4.618	0.119	4.882
analysisName	1.390	0.069	1.492
binning	0.094	0.003	0.101
bwApply	6.184	0.301	6.647
calibPointNew	1.631	0.087	1.774
calibPoints	1.213	0.023	1.293
calibration	1.200	0.045	1.283
changePeakWidth	1.129	0.089	1.238
findPeakWidth	5.156	0.934	6.224
getTOFs	1.290	0.024	1.346
image	4.808	0.142	5.253
imageMatrix	2.288	0.285	2.639
instrument	1.324	0.019	1.400
mz	1.397	0.060	1.492
nComp	4.831	0.128	5.115
nPeaks	2.952	1.051	4.120
nnMNF	0.187	0.025	0.219
nz	1.286	0.062	1.378
overlayPlot	1.578	0.236	1.853
pcaLoadings	4.761	0.125	5.016
pcaScores	4.782	0.136	5.064
peakIDs	2.928	1.064	4.075
peakMzs	2.917	1.191	4.210
peakPick	2.431	0.357	2.880
peakWidths	6.150	1.037	7.422
peaks2Spectra	2.053	0.641	2.778
plot	1.506	0.077	1.632
points	1.822	0.235	2.123
poissonScaling	0.012	0.001	0.014
recalibrate	1.481	0.072	1.601
reduceSpectrumResolution	1.295	0.065	1.399
removePeaks	1.342	0.131	1.518
scale	0.026	0.002	0.032
smoothScatter	4.668	0.158	4.986
smootherGolay	1.543	0.167	1.786
smootherSpline	3.315	0.986	4.450
subset	1.410	0.067	1.537
unitMassPeaks	3.021	1.030	4.167
xy	1.366	0.060	1.458
xySpec	1.490	0.061	1.593