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: 2017-08-16 08:54:45 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:59:38 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 292.2 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 3.4.1 (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 ‘1.4.0’
* 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
findPeakWidth 6.105  1.064   7.327
peakWidths    5.859  1.037   7.038
bwApply       6.275  0.256   6.764
pcaScores     4.854  0.232   5.201
smoothScatter 4.752  0.141   5.031
image         4.742  0.114   5.009
* 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	1.322	0.056	1.435
MCR	0.126	0.013	0.142
MNF	0.126	0.018	0.147
MassImage	0.006	0.001	0.008
MassSpectra	0.022	0.002	0.022
PCAnalysis	0.018	0.001	0.019
PeakList	2.960	0.874	3.939
PrComp	0.027	0.001	0.028
PrinComp	0.024	0.002	0.026
addFixedWidth	3.173	0.544	3.834
addPeaks	1.498	0.118	1.649
analysis	4.596	0.085	4.827
analysisName	1.285	0.045	1.385
binning	0.096	0.001	0.100
bwApply	6.275	0.256	6.764
calibPointNew	1.738	0.086	1.864
calibPoints	1.317	0.018	1.358
calibration	1.316	0.043	1.389
changePeakWidth	1.398	0.081	1.503
findPeakWidth	6.105	1.064	7.327
getTOFs	1.241	0.016	1.283
image	4.742	0.114	5.009
imageMatrix	2.099	0.252	2.438
instrument	1.248	0.013	1.293
mz	1.343	0.056	1.444
nComp	4.483	0.105	4.733
nPeaks	2.658	0.942	3.724
nnMNF	0.166	0.008	0.174
nz	1.192	0.051	1.272
overlayPlot	1.617	0.209	1.864
pcaLoadings	4.657	0.121	4.882
pcaScores	4.854	0.232	5.201
peakIDs	2.807	1.009	3.937
peakMzs	2.560	0.899	3.551
peakPick	2.106	0.328	2.495
peakWidths	5.859	1.037	7.038
peaks2Spectra	2.189	0.658	2.935
plot	1.455	0.069	1.566
points	1.752	0.222	2.028
poissonScaling	0.008	0.001	0.009
recalibrate	1.477	0.067	1.589
reduceSpectrumResolution	1.332	0.060	1.420
removePeaks	1.450	0.142	1.633
scale	0.027	0.002	0.030
smoothScatter	4.752	0.141	5.031
smootherGolay	1.519	0.045	1.597
smootherSpline	3.096	1.014	4.197
subset	1.416	0.094	1.572
unitMassPeaks	2.778	0.892	3.737
xy	1.340	0.068	1.445
xySpec	1.442	0.055	1.534