BioC 3.3: CHECK report for tofsims on zin2

Package: tofsims

Version: 1.0.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.0.2.tar.gz

StartedAt: 2016-10-13 07:27:58 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:32:06 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 248.0 seconds

RetCode: 0

Status:  OK

CheckDir: tofsims.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings tofsims_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.0.2’
* 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
bwApply       6.588  0.123   6.785
peakWidths    5.564  0.459   6.038
findPeakWidth 5.233  0.642   5.895
smoothScatter 5.070  0.012   5.110
image         4.880  0.111   5.025
* 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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c LapackEigen.cpp -o LapackEigen.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c c_importer.cpp -o c_importer.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c nn.cpp -o nn.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c readRawPhi.cpp -o readRawPhi.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c tofsims_init.c -o tofsims_init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c utilities.cpp -o utilities.o
g++ -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lR
installing to /home/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	1.155	0.007	1.205
MCR	0.094	0.012	0.106
MNF	0.058	0.000	0.079
MassImage	0.010	0.000	0.018
MassSpectra	0.035	0.000	0.038
PCAnalysis	0.023	0.000	0.023
PeakList	3.500	0.115	3.649
PrComp	0.036	0.000	0.037
PrinComp	0.026	0.000	0.026
addFixedWidth	2.717	0.215	2.976
addPeaks	1.273	0.275	1.574
analysis	4.472	0.029	4.504
analysisName	1.024	0.004	1.027
binning	0.113	0.027	0.143
bwApply	6.588	0.123	6.785
calibPointNew	1.332	0.032	1.364
calibPoints	1.062	0.017	1.086
calibration	1.240	0.008	1.252
changePeakWidth	1.185	0.032	1.224
findPeakWidth	5.233	0.642	5.895
getTOFs	1.053	0.119	1.173
image	4.880	0.111	5.025
imageMatrix	1.876	0.123	2.012
instrument	0.982	0.008	0.994
mz	1.135	0.012	1.148
nComp	4.830	0.040	4.879
nPeaks	3.335	0.323	3.692
nnMNF	0.116	0.000	0.115
nz	1.071	0.000	1.072
overlayPlot	1.507	0.000	1.509
pcaLoadings	4.712	0.025	4.742
pcaScores	4.869	0.032	4.911
peakIDs	3.179	0.016	3.197
peakMzs	3.175	0.032	3.212
peakPick	2.109	0.044	2.221
peakWidths	5.564	0.459	6.038
peaks2Spectra	2.229	0.183	2.440
plot	1.260	0.004	1.282
points	1.610	0.027	1.645
poissonScaling	0.013	0.000	0.013
recalibrate	1.366	0.000	1.384
reduceSpectrumResolution	1.263	0.004	1.279
removePeaks	1.218	0.000	1.220
scale	0.027	0.000	0.028
smoothScatter	5.070	0.012	5.110
smootherGolay	1.281	0.016	1.303
smootherSpline	3.619	0.008	3.635
subset	1.246	0.008	1.257
unitMassPeaks	3.581	0.003	3.665
xy	1.164	0.020	1.183
xySpec	1.238	0.008	1.258