BioC 3.4: CHECK report for tofsims on malbec1

Package: tofsims

Version: 1.2.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.2.0.tar.gz

StartedAt: 2017-04-15 01:39:36 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:43:12 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 215.9 seconds

RetCode: 0

Status:  OK

CheckDir: tofsims.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/tofsims.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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 6.464  0.092   6.584
* 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c LapackEigen.cpp -o LapackEigen.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c c_importer.cpp -o c_importer.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c nn.cpp -o nn.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c readRawPhi.cpp -o readRawPhi.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c tofsims_init.c -o tofsims_init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c utilities.cpp -o utilities.o
g++ -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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	1.192	0.004	1.224
MCR	0.124	0.000	0.124
MNF	0.076	0.000	0.113
MassImage	0.008	0.000	0.010
MassSpectra	0.028	0.004	0.034
PCAnalysis	0.020	0.004	0.026
PeakList	2.276	0.080	2.355
PrComp	0.024	0.000	0.025
PrinComp	0.02	0.00	0.02
addFixedWidth	2.168	0.064	2.233
addPeaks	1.196	0.016	1.214
analysis	4.304	0.028	4.339
analysisName	1.048	0.012	1.060
binning	0.092	0.020	0.127
bwApply	6.464	0.092	6.584
calibPointNew	1.396	0.020	1.417
calibPoints	1.084	0.004	1.086
calibration	1.104	0.004	1.107
changePeakWidth	1.400	0.008	1.408
findPeakWidth	3.984	0.116	4.101
getTOFs	1.028	0.012	1.040
image	4.284	0.016	4.302
imageMatrix	1.812	0.028	1.843
instrument	1.060	0.004	1.062
mz	1.076	0.000	1.078
nComp	4.460	0.024	4.488
nPeaks	1.876	0.176	2.055
nnMNF	0.096	0.000	0.098
nz	1.000	0.004	1.005
overlayPlot	1.324	0.004	1.331
pcaLoadings	4.548	0.004	4.555
pcaScores	4.812	0.004	4.818
peakIDs	2.028	0.136	2.169
peakMzs	1.960	0.004	1.965
peakPick	1.924	0.008	1.933
peakWidths	4.488	0.100	4.594
peaks2Spectra	1.596	0.052	1.650
plot	1.196	0.004	1.201
points	1.356	0.008	1.367
poissonScaling	0.008	0.000	0.009
recalibrate	1.192	0.000	1.193
reduceSpectrumResolution	1.036	0.012	1.050
removePeaks	1.028	0.000	1.031
scale	0.02	0.00	0.02
smoothScatter	4.392	0.012	4.409
smootherGolay	1.120	0.008	1.127
smootherSpline	2.592	0.116	2.709
subset	1.116	0.020	1.135
unitMassPeaks	2.180	0.016	2.197
xy	1.104	0.028	1.131
xySpec	1.196	0.008	1.203