BioC 3.4: CHECK report for tofsims on zin1

Package: tofsims

Version: 1.1.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.1.2.tar.gz

StartedAt: 2016-09-20 13:23:01 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:26:52 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 231.5 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_1.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/tofsims.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.2’
* 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
bwApply       5.736  0.448   6.204
findPeakWidth 4.336  1.772   6.107
peakWidths    4.016  2.016   6.031
* 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	0.904	0.020	0.944
MCR	0.084	0.004	0.088
MNF	0.048	0.004	0.117
MassImage	0.008	0.000	0.007
MassSpectra	0.024	0.000	0.023
PCAnalysis	0.016	0.000	0.019
PeakList	2.180	0.088	2.269
PrComp	0.028	0.000	0.029
PrinComp	0.024	0.000	0.020
addFixedWidth	2.060	0.292	2.357
addPeaks	1.012	0.156	1.168
analysis	3.980	0.184	4.165
analysisName	0.920	0.032	0.951
binning	0.104	0.032	0.143
bwApply	5.736	0.448	6.204
calibPointNew	1.136	0.160	1.297
calibPoints	0.952	0.124	1.076
calibration	1.072	0.044	1.115
changePeakWidth	1.000	0.156	1.155
findPeakWidth	4.336	1.772	6.107
getTOFs	0.912	0.140	1.053
image	4.264	0.260	4.526
imageMatrix	1.720	0.300	2.021
instrument	0.936	0.044	0.979
mz	0.932	0.164	1.097
nComp	4.096	0.268	4.362
nPeaks	2.060	0.248	2.314
nnMNF	0.100	0.000	0.102
nz	0.86	0.00	0.86
overlayPlot	1.24	0.00	1.24
pcaLoadings	4.260	0.264	4.526
pcaScores	4.228	0.156	4.385
peakIDs	1.860	0.144	2.003
peakMzs	1.808	0.040	1.849
peakPick	1.780	0.316	2.097
peakWidths	4.016	2.016	6.031
peaks2Spectra	1.444	0.240	1.684
plot	1.088	0.004	1.094
points	1.372	0.024	1.396
poissonScaling	0.012	0.000	0.012
recalibrate	1.028	0.004	1.030
reduceSpectrumResolution	0.832	0.000	0.829
removePeaks	0.864	0.156	1.021
scale	0.020	0.000	0.023
smoothScatter	4.096	0.008	4.104
smootherGolay	1.028	0.132	1.159
smootherSpline	2.628	0.012	2.640
subset	1.008	0.092	1.101
unitMassPeaks	2.104	0.156	2.263
xy	0.864	0.000	0.866
xySpec	1.012	0.000	1.011