Lorenz Gerber
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/tofsims |
| Branch: RELEASE_3_6 |
| Last Commit: 8dc3f02 |
| Last Changed Date: 2017-10-30 12:41:11 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:42:07 -0400 (Thu, 12 Apr 2018).
| Package 1406/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tofsims 1.6.0 Lorenz Gerber
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: tofsims |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tofsims_1.6.0.tar.gz |
| StartedAt: 2018-04-12 10:21:40 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 10:26:37 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 296.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tofsims.Rcheck |
| Warnings: 0 |
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tofsims_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/tofsims.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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
findPeakWidth 6.872 1.187 8.202
peakWidths 6.135 1.082 7.318
bwApply 5.270 0.255 5.584
image 4.984 0.122 5.179
* 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 clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c LapackEigen.cpp -o LapackEigen.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c c_importer.cpp -o c_importer.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c nn.cpp -o nn.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c tofsims_init.c -o tofsims_init.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utilities.cpp -o utilities.o clang++ -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 /Users/biocbuild/bbs-3.6-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/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 119 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
74.281 8.603 84.156
tofsims.Rcheck/tofsims-Ex.timings
| name | user | system | elapsed | |
| MAF | 1.382 | 0.064 | 1.469 | |
| MCR | 0.130 | 0.014 | 0.147 | |
| MNF | 0.124 | 0.016 | 0.145 | |
| MassImage | 0.007 | 0.001 | 0.007 | |
| MassSpectra | 0.022 | 0.001 | 0.024 | |
| PCAnalysis | 0.021 | 0.001 | 0.024 | |
| PeakList | 3.041 | 0.758 | 3.860 | |
| PrComp | 0.025 | 0.002 | 0.027 | |
| PrinComp | 0.019 | 0.002 | 0.021 | |
| addFixedWidth | 3.353 | 0.607 | 4.008 | |
| addPeaks | 1.259 | 0.081 | 1.353 | |
| analysis | 3.673 | 0.097 | 3.790 | |
| analysisName | 1.018 | 0.056 | 1.076 | |
| binning | 0.145 | 0.017 | 0.164 | |
| bwApply | 5.270 | 0.255 | 5.584 | |
| calibPointNew | 1.445 | 0.079 | 1.548 | |
| calibPoints | 1.195 | 0.019 | 1.221 | |
| calibration | 1.271 | 0.042 | 1.329 | |
| changePeakWidth | 1.501 | 0.096 | 1.623 | |
| findPeakWidth | 6.872 | 1.187 | 8.202 | |
| getTOFs | 1.348 | 0.021 | 1.380 | |
| image | 4.984 | 0.122 | 5.179 | |
| imageMatrix | 2.231 | 0.299 | 2.575 | |
| instrument | 1.318 | 0.013 | 1.348 | |
| mz | 1.342 | 0.058 | 1.429 | |
| nComp | 4.681 | 0.120 | 4.868 | |
| nPeaks | 3.013 | 1.168 | 4.253 | |
| nnMNF | 0.216 | 0.103 | 0.321 | |
| nz | 1.341 | 0.062 | 1.416 | |
| overlayPlot | 1.662 | 0.186 | 1.876 | |
| pcaLoadings | 4.488 | 0.197 | 4.741 | |
| pcaScores | 4.454 | 0.122 | 4.657 | |
| peakIDs | 2.729 | 1.088 | 3.860 | |
| peakMzs | 2.749 | 1.044 | 3.849 | |
| peakPick | 2.340 | 0.404 | 2.796 | |
| peakWidths | 6.135 | 1.082 | 7.318 | |
| peaks2Spectra | 2.043 | 0.658 | 2.727 | |
| plot | 1.289 | 0.064 | 1.372 | |
| points | 1.581 | 0.241 | 1.852 | |
| poissonScaling | 0.010 | 0.000 | 0.011 | |
| recalibrate | 1.361 | 0.069 | 1.447 | |
| reduceSpectrumResolution | 1.259 | 0.060 | 1.338 | |
| removePeaks | 1.25 | 0.08 | 1.35 | |
| scale | 0.021 | 0.003 | 0.023 | |
| smoothScatter | 4.322 | 0.198 | 4.585 | |
| smootherGolay | 1.412 | 0.083 | 1.516 | |
| smootherSpline | 3.315 | 1.104 | 4.503 | |
| subset | 1.399 | 0.062 | 1.472 | |
| unitMassPeaks | 3.331 | 1.238 | 4.634 | |
| xy | 1.374 | 0.064 | 1.450 | |
| xySpec | 1.447 | 0.061 | 1.537 | |