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CHECK report for tofsims on malbec2

This page was generated on 2019-10-16 12:08:04 -0400 (Wed, 16 Oct 2019).

Package 1656/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tofsims 1.12.0
Lorenz Gerber
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/tofsims
Branch: RELEASE_3_9
Last Commit: 53cc0c3
Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tofsims
Version: 1.12.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:tofsims.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings tofsims_1.12.0.tar.gz
StartedAt: 2019-10-16 05:28:32 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:32:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 251.8 seconds
RetCode: 0
Status:  OK 
CheckDir: tofsims.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:tofsims.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings tofsims_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/tofsims.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
bwApply       7.051  0.284   7.537
analysis      6.039  0.100   6.140
nComp         5.921  0.155   6.080
findPeakWidth 5.265  0.552   5.819
pcaScores     5.619  0.103   5.723
peakWidths    5.230  0.396   5.633
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/tofsims.Rcheck/00check.log’
for details.



Installation output

tofsims.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL tofsims
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘tofsims’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c LapackEigen.cpp -o LapackEigen.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c c_importer.cpp -o c_importer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c nn.cpp -o nn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c readRawPhi.cpp -o readRawPhi.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c tofsims_init.c -o tofsims_init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c utilities.cpp -o utilities.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-tofsims/00new/tofsims/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tofsims)

Tests output

tofsims.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(tofsims)
Loading required package: ProtGenerics
> library(tofsimsData)
> 
> test_check("tofsims")
                                             analysisName instrument no.spectra
1 /Users/loge/Data/ULVACPHI/RAW/080414/trift_test_001.RAW   ulvacphi     65'536
  spectra.points total.ion.count x.image.dimension y.image.dimention analysis
1            200       1'859'292               256               256     none
                                             analysisName instrument no.spectra
1 /Users/loge/Data/ULVACPHI/RAW/080414/trift_test_001.RAW   ulvacphi          1
  spectra.points total.ion.count analysis
1        162'255       2'033'289     none
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 73 | SKIPPED: 0 | WARNINGS: 53 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 83.837   5.775  89.738 

Example timings

tofsims.Rcheck/tofsims-Ex.timings

nameusersystemelapsed
MAF1.3010.0401.386
MCR0.0670.0080.074
MNF0.0590.0040.087
MassImage0.0080.0000.007
MassSpectra0.0220.0010.022
PCAnalysis0.0190.0030.022
PeakList2.9420.1043.047
PrComp0.0380.0000.038
PrinComp0.0290.0000.030
addFixedWidth3.0140.1563.170
addPeaks1.6390.1001.738
analysis6.0390.1006.140
analysisName1.2780.0321.310
binning0.4400.1630.598
bwApply7.0510.2847.537
calibPointNew1.7080.0681.777
calibPoints1.2330.0321.265
calibration1.1910.0361.227
changePeakWidth1.5040.0481.552
findPeakWidth5.2650.5525.819
getTOFs1.0550.0361.091
image4.7680.0604.828
imageMatrix2.0690.1202.188
instrument1.2450.0561.301
mz1.3810.0201.401
nComp5.9210.1556.080
nPeaks2.270.222.49
nnMNF0.0990.0040.102
nz1.2030.0041.206
overlayPlot1.3370.0281.364
pcaLoadings4.7740.0774.850
pcaScores5.6190.1035.723
peakIDs2.1520.1242.277
peakMzs2.2550.0042.258
peakPick2.0900.0842.173
peakWidths5.2300.3965.633
peaks2Spectra2.2110.2432.455
plot1.6860.0091.693
points1.5610.0001.560
poissonScaling0.0080.0000.008
recalibrate1.3530.0401.392
reduceSpectrumResolution1.2740.0001.273
removePeaks1.2470.0001.247
scale0.0340.0000.034
smoothScatter4.7940.0004.794
smootherGolay1.2740.0241.298
smootherSpline2.8390.0082.847
subset1.3020.0441.346
unitMassPeaks2.1910.1762.367
xy1.1770.0001.177
xySpec1.2930.0001.293