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 12:56:59 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tofsims.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tofsims_1.12.0.tar.gz |
| StartedAt: 2019-10-16 07:25:29 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:32:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 405.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tofsims.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tofsims.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tofsims_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/tofsims.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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
findPeakWidth 10.051 2.857 12.907
peakWidths 9.886 2.951 12.838
bwApply 11.055 0.778 11.846
image 7.131 0.313 7.446
smoothScatter 6.943 0.417 7.361
analysis 6.906 0.220 7.125
pcaLoadings 6.822 0.291 7.116
pcaScores 6.726 0.306 7.032
unitMassPeaks 4.227 2.677 6.905
smootherSpline 4.296 2.601 6.898
peakIDs 4.011 2.696 6.708
peakMzs 4.106 2.512 6.619
nComp 6.241 0.262 6.503
nPeaks 3.715 2.376 6.090
PeakList 3.987 2.066 6.053
addFixedWidth 3.920 1.480 5.398
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/tofsims.Rcheck/00check.log’
for details.
tofsims.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tofsims ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘tofsims’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c LapackEigen.cpp -o LapackEigen.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c c_importer.cpp -o c_importer.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nn.cpp -o nn.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c readRawPhi.cpp -o readRawPhi.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c tofsims_init.c -o tofsims_init.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utilities.cpp -o utilities.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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-apple-darwin15.6.0 (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
118.040 19.783 138.030
tofsims.Rcheck/tofsims-Ex.timings
| name | user | system | elapsed | |
| MAF | 1.974 | 0.148 | 2.125 | |
| MCR | 0.218 | 0.056 | 0.274 | |
| MNF | 0.111 | 0.031 | 0.141 | |
| MassImage | 0.010 | 0.004 | 0.014 | |
| MassSpectra | 0.026 | 0.006 | 0.032 | |
| PCAnalysis | 0.041 | 0.008 | 0.050 | |
| PeakList | 3.987 | 2.066 | 6.053 | |
| PrComp | 0.032 | 0.006 | 0.039 | |
| PrinComp | 0.031 | 0.004 | 0.035 | |
| addFixedWidth | 3.920 | 1.480 | 5.398 | |
| addPeaks | 2.106 | 0.201 | 2.307 | |
| analysis | 6.906 | 0.220 | 7.125 | |
| analysisName | 1.856 | 0.143 | 1.999 | |
| binning | 0.541 | 0.181 | 0.725 | |
| bwApply | 11.055 | 0.778 | 11.846 | |
| calibPointNew | 2.357 | 0.215 | 2.574 | |
| calibPoints | 1.751 | 0.045 | 1.796 | |
| calibration | 1.756 | 0.030 | 1.784 | |
| changePeakWidth | 1.845 | 0.157 | 2.001 | |
| findPeakWidth | 10.051 | 2.857 | 12.907 | |
| getTOFs | 1.469 | 0.034 | 1.503 | |
| image | 7.131 | 0.313 | 7.446 | |
| imageMatrix | 3.252 | 0.509 | 3.763 | |
| instrument | 1.639 | 0.033 | 1.672 | |
| mz | 1.777 | 0.136 | 1.914 | |
| nComp | 6.241 | 0.262 | 6.503 | |
| nPeaks | 3.715 | 2.376 | 6.090 | |
| nnMNF | 0.137 | 0.016 | 0.152 | |
| nz | 1.619 | 0.140 | 1.758 | |
| overlayPlot | 2.261 | 0.587 | 2.849 | |
| pcaLoadings | 6.822 | 0.291 | 7.116 | |
| pcaScores | 6.726 | 0.306 | 7.032 | |
| peakIDs | 4.011 | 2.696 | 6.708 | |
| peakMzs | 4.106 | 2.512 | 6.619 | |
| peakPick | 3.189 | 0.742 | 3.931 | |
| peakWidths | 9.886 | 2.951 | 12.838 | |
| peaks2Spectra | 3.119 | 1.814 | 4.934 | |
| plot | 2.056 | 0.334 | 2.391 | |
| points | 2.534 | 0.496 | 3.032 | |
| poissonScaling | 0.015 | 0.003 | 0.018 | |
| recalibrate | 2.030 | 0.336 | 2.367 | |
| reduceSpectrumResolution | 1.787 | 0.155 | 1.943 | |
| removePeaks | 1.882 | 0.206 | 2.088 | |
| scale | 0.031 | 0.005 | 0.036 | |
| smoothScatter | 6.943 | 0.417 | 7.361 | |
| smootherGolay | 2.082 | 0.199 | 2.283 | |
| smootherSpline | 4.296 | 2.601 | 6.898 | |
| subset | 1.790 | 0.477 | 2.268 | |
| unitMassPeaks | 4.227 | 2.677 | 6.905 | |
| xy | 1.782 | 0.140 | 1.921 | |
| xySpec | 1.815 | 0.122 | 1.948 | |