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BioC 3.4: CHECK report for tofsims on zin1

This page was generated on 2016-09-21 03:40:29 -0700 (Wed, 21 Sep 2016).

Package 1205/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tofsims 1.1.2
Lorenz Gerber
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/tofsims
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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

tofsims.Rcheck/00install.out:

* 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)

tofsims.Rcheck/tofsims-Ex.timings:

nameusersystemelapsed
MAF0.9040.0200.944
MCR0.0840.0040.088
MNF0.0480.0040.117
MassImage0.0080.0000.007
MassSpectra0.0240.0000.023
PCAnalysis0.0160.0000.019
PeakList2.1800.0882.269
PrComp0.0280.0000.029
PrinComp0.0240.0000.020
addFixedWidth2.0600.2922.357
addPeaks1.0120.1561.168
analysis3.9800.1844.165
analysisName0.9200.0320.951
binning0.1040.0320.143
bwApply5.7360.4486.204
calibPointNew1.1360.1601.297
calibPoints0.9520.1241.076
calibration1.0720.0441.115
changePeakWidth1.0000.1561.155
findPeakWidth4.3361.7726.107
getTOFs0.9120.1401.053
image4.2640.2604.526
imageMatrix1.7200.3002.021
instrument0.9360.0440.979
mz0.9320.1641.097
nComp4.0960.2684.362
nPeaks2.0600.2482.314
nnMNF0.1000.0000.102
nz0.860.000.86
overlayPlot1.240.001.24
pcaLoadings4.2600.2644.526
pcaScores4.2280.1564.385
peakIDs1.8600.1442.003
peakMzs1.8080.0401.849
peakPick1.7800.3162.097
peakWidths4.0162.0166.031
peaks2Spectra1.4440.2401.684
plot1.0880.0041.094
points1.3720.0241.396
poissonScaling0.0120.0000.012
recalibrate1.0280.0041.030
reduceSpectrumResolution0.8320.0000.829
removePeaks0.8640.1561.021
scale0.0200.0000.023
smoothScatter4.0960.0084.104
smootherGolay1.0280.1321.159
smootherSpline2.6280.0122.640
subset1.0080.0921.101
unitMassPeaks2.1040.1562.263
xy0.8640.0000.866
xySpec1.0120.0001.011