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: 2017-10-18 02:54:53 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:58:38 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 225.1 seconds

RetCode: 0

Status:  OK

CheckDir: tofsims.Rcheck

Warnings: 0

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###
### Running command:
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###   /home/biocbuild/bbs-3.5-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 3.4.2 (2017-09-28)
* 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 5.72  0.024   5.993
* 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
In file included from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo:53:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from LapackEigen.cpp:1:
/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: note: #pragma message: WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+
   #pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+")
                                                                                                ^
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
In file included from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo:53:0,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
                 from /home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: note: #pragma message: WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+
   #pragma message ("WARNING: use of OpenMP disabled; this compiler doesn't support OpenMP 3.0+")
                                                                                                ^
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	1.212	0.012	1.252
MCR	0.104	0.000	0.101
MNF	0.088	0.000	0.118
MassImage	0.008	0.000	0.007
MassSpectra	0.020	0.000	0.021
PCAnalysis	0.020	0.000	0.019
PeakList	2.260	0.100	2.359
PrComp	0.024	0.000	0.025
PrinComp	0.020	0.000	0.019
addFixedWidth	2.624	0.092	2.717
addPeaks	1.184	0.016	1.199
analysis	4.180	0.032	4.214
analysisName	1.052	0.004	1.056
binning	0.072	0.000	0.072
bwApply	5.720	0.024	5.993
calibPointNew	1.372	0.016	1.385
calibPoints	1.100	0.008	1.109
calibration	1.048	0.008	1.057
changePeakWidth	1.104	0.020	1.127
findPeakWidth	4.232	0.500	4.735
getTOFs	0.988	0.024	1.012
image	4.356	0.112	4.470
imageMatrix	1.668	0.120	1.786
instrument	1.092	0.004	1.096
mz	1.036	0.008	1.041
nComp	4.268	0.008	4.278
nPeaks	1.924	0.136	2.061
nnMNF	0.156	0.000	0.159
nz	1.068	0.012	1.081
overlayPlot	1.388	0.004	1.390
pcaLoadings	4.404	0.004	4.410
pcaScores	4.320	0.024	4.346
peakIDs	2.396	0.028	2.423
peakMzs	2.208	0.020	2.229
peakPick	1.936	0.008	1.946
peakWidths	4.300	0.412	4.715
peaks2Spectra	1.644	0.152	1.796
plot	1.172	0.008	1.182
points	1.400	0.032	1.429
poissonScaling	0.008	0.000	0.008
recalibrate	1.172	0.004	1.176
reduceSpectrumResolution	1.120	0.012	1.130
removePeaks	1.244	0.052	1.299
scale	0.032	0.000	0.032
smoothScatter	4.320	0.032	4.356
smootherGolay	1.124	0.008	1.134
smootherSpline	2.796	0.052	2.851
subset	1.112	0.012	1.125
unitMassPeaks	2.092	0.204	2.299
xy	1.004	0.000	1.005
xySpec	1.12	0.00	1.12