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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:08:04 -0400 (Wed, 16 Oct 2019).
| Package 1656/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tofsims 1.12.0 Lorenz Gerber
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
##############################################################################
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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
###
##############################################################################
##############################################################################
* 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.
tofsims.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
tofsims.Rcheck/tofsims-Ex.timings
| name | user | system | elapsed | |
| MAF | 1.301 | 0.040 | 1.386 | |
| MCR | 0.067 | 0.008 | 0.074 | |
| MNF | 0.059 | 0.004 | 0.087 | |
| MassImage | 0.008 | 0.000 | 0.007 | |
| MassSpectra | 0.022 | 0.001 | 0.022 | |
| PCAnalysis | 0.019 | 0.003 | 0.022 | |
| PeakList | 2.942 | 0.104 | 3.047 | |
| PrComp | 0.038 | 0.000 | 0.038 | |
| PrinComp | 0.029 | 0.000 | 0.030 | |
| addFixedWidth | 3.014 | 0.156 | 3.170 | |
| addPeaks | 1.639 | 0.100 | 1.738 | |
| analysis | 6.039 | 0.100 | 6.140 | |
| analysisName | 1.278 | 0.032 | 1.310 | |
| binning | 0.440 | 0.163 | 0.598 | |
| bwApply | 7.051 | 0.284 | 7.537 | |
| calibPointNew | 1.708 | 0.068 | 1.777 | |
| calibPoints | 1.233 | 0.032 | 1.265 | |
| calibration | 1.191 | 0.036 | 1.227 | |
| changePeakWidth | 1.504 | 0.048 | 1.552 | |
| findPeakWidth | 5.265 | 0.552 | 5.819 | |
| getTOFs | 1.055 | 0.036 | 1.091 | |
| image | 4.768 | 0.060 | 4.828 | |
| imageMatrix | 2.069 | 0.120 | 2.188 | |
| instrument | 1.245 | 0.056 | 1.301 | |
| mz | 1.381 | 0.020 | 1.401 | |
| nComp | 5.921 | 0.155 | 6.080 | |
| nPeaks | 2.27 | 0.22 | 2.49 | |
| nnMNF | 0.099 | 0.004 | 0.102 | |
| nz | 1.203 | 0.004 | 1.206 | |
| overlayPlot | 1.337 | 0.028 | 1.364 | |
| pcaLoadings | 4.774 | 0.077 | 4.850 | |
| pcaScores | 5.619 | 0.103 | 5.723 | |
| peakIDs | 2.152 | 0.124 | 2.277 | |
| peakMzs | 2.255 | 0.004 | 2.258 | |
| peakPick | 2.090 | 0.084 | 2.173 | |
| peakWidths | 5.230 | 0.396 | 5.633 | |
| peaks2Spectra | 2.211 | 0.243 | 2.455 | |
| plot | 1.686 | 0.009 | 1.693 | |
| points | 1.561 | 0.000 | 1.560 | |
| poissonScaling | 0.008 | 0.000 | 0.008 | |
| recalibrate | 1.353 | 0.040 | 1.392 | |
| reduceSpectrumResolution | 1.274 | 0.000 | 1.273 | |
| removePeaks | 1.247 | 0.000 | 1.247 | |
| scale | 0.034 | 0.000 | 0.034 | |
| smoothScatter | 4.794 | 0.000 | 4.794 | |
| smootherGolay | 1.274 | 0.024 | 1.298 | |
| smootherSpline | 2.839 | 0.008 | 2.847 | |
| subset | 1.302 | 0.044 | 1.346 | |
| unitMassPeaks | 2.191 | 0.176 | 2.367 | |
| xy | 1.177 | 0.000 | 1.177 | |
| xySpec | 1.293 | 0.000 | 1.293 | |