BioC 3.6: CHECK report for tofsims on malbec1

Package: tofsims

Version: 1.5.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.5.0.tar.gz

StartedAt: 2017-08-16 02:48:48 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:52:24 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 216.1 seconds

RetCode: 0

Status:  OK

CheckDir: tofsims.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.5.0’
* 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 5.98  0.056   6.041
* 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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c LapackEigen.cpp -o LapackEigen.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c nn.cpp -o nn.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RcppArmadillo/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c readRawPhi.cpp -o readRawPhi.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	1.124	0.016	1.186
MCR	0.136	0.000	0.139
MNF	0.080	0.004	0.109
MassImage	0.008	0.000	0.006
MassSpectra	0.020	0.000	0.021
PCAnalysis	0.020	0.000	0.019
PeakList	2.368	0.132	2.499
PrComp	0.028	0.000	0.025
PrinComp	0.02	0.00	0.02
addFixedWidth	3.244	0.104	3.356
addPeaks	1.224	0.040	1.267
analysis	4.288	0.028	4.317
analysisName	1.068	0.016	1.085
binning	0.068	0.008	0.079
bwApply	5.980	0.056	6.041
calibPointNew	1.356	0.012	1.369
calibPoints	0.996	0.000	0.995
calibration	1.088	0.008	1.095
changePeakWidth	1.136	0.020	1.156
findPeakWidth	4.164	0.208	4.374
getTOFs	1.048	0.004	1.051
image	4.292	0.032	4.322
imageMatrix	1.760	0.020	1.779
instrument	1.068	0.012	1.083
mz	1.056	0.004	1.062
nComp	4.236	0.012	4.251
nPeaks	1.908	0.108	2.018
nnMNF	0.164	0.004	0.169
nz	1.028	0.004	1.032
overlayPlot	1.324	0.012	1.336
pcaLoadings	4.648	0.028	4.683
pcaScores	4.364	0.020	4.387
peakIDs	2.176	0.096	2.275
peakMzs	2.400	0.000	2.403
peakPick	1.844	0.012	1.858
peakWidths	4.164	0.124	4.290
peaks2Spectra	1.556	0.088	1.647
plot	1.340	0.012	1.354
points	1.808	0.020	1.831
poissonScaling	0.016	0.000	0.015
recalibrate	1.264	0.012	1.278
reduceSpectrumResolution	1.152	0.012	1.168
removePeaks	1.096	0.000	1.096
scale	0.02	0.00	0.02
smoothScatter	4.328	0.008	4.339
smootherGolay	1.236	0.016	1.257
smootherSpline	2.648	0.076	2.723
subset	1.132	0.000	1.134
unitMassPeaks	2.172	0.000	2.172
xy	0.992	0.024	1.015
xySpec	1.152	0.020	1.171