BioC 3.5: CHECK report for tofsims on toluca2

Package: tofsims

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tofsims_1.3.2.tar.gz

StartedAt: 2017-04-23 10:48:43 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:53:40 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 297.0 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_1.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/tofsims.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.2’
* 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    6.737  1.210   7.998
findPeakWidth 6.803  1.108   8.951
bwApply       7.186  0.251   8.148
image         4.698  0.123   5.448
nComp         4.661  0.113   5.455
* 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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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	1.156	0.059	1.392
MCR	0.152	0.014	0.191
MNF	0.150	0.019	0.191
MassImage	0.008	0.001	0.010
MassSpectra	0.026	0.002	0.034
PCAnalysis	0.022	0.002	0.023
PeakList	2.912	0.972	4.084
PrComp	0.035	0.001	0.042
PrinComp	0.025	0.002	0.028
addFixedWidth	3.531	0.677	4.721
addPeaks	1.259	0.128	1.441
analysis	4.687	0.099	4.925
analysisName	1.018	0.055	1.082
binning	0.252	0.015	0.274
bwApply	7.186	0.251	8.148
calibPointNew	1.476	0.094	1.784
calibPoints	1.079	0.015	1.242
calibration	1.102	0.041	1.301
changePeakWidth	1.239	0.097	1.542
findPeakWidth	6.803	1.108	8.951
getTOFs	1.050	0.016	1.226
image	4.698	0.123	5.448
imageMatrix	2.016	0.288	2.626
instrument	1.051	0.007	1.197
mz	1.079	0.060	1.295
nComp	4.661	0.113	5.455
nPeaks	2.698	1.118	4.039
nnMNF	0.217	0.013	0.232
nz	1.057	0.109	1.173
overlayPlot	1.454	0.197	1.663
pcaLoadings	4.696	0.195	4.922
pcaScores	4.772	0.096	4.891
peakIDs	2.681	1.363	4.065
peakMzs	2.640	1.112	3.789
peakPick	2.375	0.464	2.864
peakWidths	6.737	1.210	7.998
peaks2Spectra	1.940	0.828	2.783
plot	1.138	0.068	1.220
points	1.610	0.260	1.915
poissonScaling	0.014	0.001	0.016
recalibrate	1.297	0.078	1.480
reduceSpectrumResolution	1.106	0.066	1.199
removePeaks	1.122	0.150	1.278
scale	0.028	0.002	0.030
smoothScatter	4.810	0.155	4.979
smootherGolay	1.246	0.040	1.291
smootherSpline	2.984	1.113	4.101
subset	1.177	0.101	1.351
unitMassPeaks	2.719	1.157	4.154
xy	0.907	0.050	0.956
xySpec	0.939	0.048	0.987