BioC 3.5: CHECK report for tofsims on malbec2

Package: tofsims

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.4.0.tar.gz

StartedAt: 2017-08-16 02:41:21 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:44:53 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 211.7 seconds

RetCode: 0

Status:  OK

CheckDir: tofsims.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/tofsims.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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
bwApply 5.628  0.044   5.674
* 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
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c LapackEigen.cpp -o LapackEigen.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c c_importer.cpp -o c_importer.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c nn.cpp -o nn.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c readRawPhi.cpp -o readRawPhi.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c tofsims_init.c -o tofsims_init.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utilities.cpp -o utilities.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/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 -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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	1.132	0.016	1.183
MCR	0.132	0.008	0.140
MNF	0.076	0.004	0.110
MassImage	0.004	0.004	0.007
MassSpectra	0.012	0.008	0.021
PCAnalysis	0.016	0.000	0.018
PeakList	2.408	0.076	2.484
PrComp	0.024	0.000	0.025
PrinComp	0.016	0.000	0.019
addFixedWidth	2.584	0.088	2.670
addPeaks	1.104	0.012	1.119
analysis	4.256	0.012	4.274
analysisName	1.060	0.012	1.072
binning	0.072	0.000	0.074
bwApply	5.628	0.044	5.674
calibPointNew	1.344	0.024	1.368
calibPoints	0.992	0.016	1.008
calibration	1.064	0.012	1.074
changePeakWidth	1.068	0.008	1.074
findPeakWidth	4.300	0.160	4.464
getTOFs	1.016	0.012	1.029
image	4.308	0.024	4.336
imageMatrix	1.700	0.020	1.723
instrument	1.036	0.020	1.059
mz	1.028	0.016	1.045
nComp	4.192	0.012	4.207
nPeaks	2.044	0.072	2.114
nnMNF	0.168	0.000	0.167
nz	1.064	0.000	1.064
overlayPlot	1.332	0.008	1.343
pcaLoadings	4.152	0.008	4.163
pcaScores	4.296	0.020	4.316
peakIDs	2.012	0.060	2.074
peakMzs	1.9	0.0	1.9
peakPick	1.864	0.084	1.948
peakWidths	3.928	0.156	4.089
peaks2Spectra	1.572	0.120	1.691
plot	1.164	0.004	1.170
points	1.304	0.024	1.328
poissonScaling	0.008	0.000	0.009
recalibrate	1.168	0.004	1.171
reduceSpectrumResolution	1.068	0.000	1.066
removePeaks	1.036	0.000	1.034
scale	0.020	0.000	0.019
smoothScatter	4.216	0.004	4.222
smootherGolay	1.196	0.008	1.203
smootherSpline	2.632	0.116	2.749
subset	1.208	0.000	1.209
unitMassPeaks	2.252	0.004	2.257
xy	1.012	0.020	1.034
xySpec	1.204	0.008	1.210