BioC 3.3: CHECK report for tofsims on oaxaca

Package: tofsims

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tofsims_1.0.2.tar.gz

StartedAt: 2016-10-13 06:54:11 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:58:55 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 284.2 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_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/tofsims.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.0.2’
* 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    6.833  1.260   8.105
findPeakWidth 6.636  1.180   7.822
bwApply       7.226  0.324   7.638
analysis      5.169  0.113   5.291
pcaScores     5.098  0.095   5.198
image         4.878  0.130   5.014
* 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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c LapackEigen.cpp -o LapackEigen.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" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/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" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c nn.cpp -o nn.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" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c readRawPhi.cpp -o readRawPhi.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" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/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-3.3-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	1.263	0.063	1.395
MCR	0.123	0.014	0.145
MNF	0.057	0.005	0.063
MassImage	0.010	0.001	0.011
MassSpectra	0.028	0.003	0.030
PCAnalysis	0.024	0.002	0.026
PeakList	2.994	0.889	3.885
PrComp	0.030	0.002	0.033
PrinComp	0.027	0.003	0.030
addFixedWidth	2.846	0.681	3.535
addPeaks	1.290	0.146	1.439
analysis	5.169	0.113	5.291
analysisName	1.217	0.056	1.276
binning	0.144	0.019	0.163
bwApply	7.226	0.324	7.638
calibPointNew	1.459	0.082	1.562
calibPoints	1.191	0.041	1.233
calibration	1.207	0.099	1.306
changePeakWidth	1.216	0.082	1.299
findPeakWidth	6.636	1.180	7.822
getTOFs	1.190	0.016	1.206
image	4.878	0.130	5.014
imageMatrix	2.41	0.34	2.77
instrument	1.151	0.006	1.158
mz	1.231	0.068	1.302
nComp	4.800	0.121	4.925
nPeaks	2.787	1.339	4.129
nnMNF	0.117	0.013	0.137
nz	1.142	0.058	1.201
overlayPlot	1.542	0.203	1.749
pcaLoadings	4.782	0.141	4.931
pcaScores	5.098	0.095	5.198
peakIDs	2.657	1.128	3.785
peakMzs	2.814	1.171	3.991
peakPick	2.419	0.408	2.828
peakWidths	6.833	1.260	8.105
peaks2Spectra	1.896	0.715	2.612
plot	1.259	0.069	1.329
points	1.654	0.303	1.965
poissonScaling	0.015	0.001	0.016
recalibrate	1.409	0.080	1.499
reduceSpectrumResolution	1.322	0.071	1.403
removePeaks	1.297	0.090	1.390
scale	0.028	0.003	0.032
smoothScatter	4.476	0.231	4.713
smootherGolay	1.248	0.081	1.334
smootherSpline	3.362	1.213	4.578
subset	1.413	0.087	1.504
unitMassPeaks	3.089	1.350	4.442
xy	1.190	0.062	1.264
xySpec	1.244	0.061	1.316