Lorenz Gerber
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/tofsims |
| Branch: RELEASE_3_7 |
| Last Commit: dfdd7e4 |
| Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:28:23 -0400 (Wed, 17 Oct 2018).
| Package 1490/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tofsims 1.8.0 Lorenz Gerber
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: tofsims |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:tofsims.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings tofsims_1.8.0.tar.gz |
| StartedAt: 2018-10-16 04:13:45 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 04:17:01 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 195.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tofsims.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:tofsims.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings tofsims_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/tofsims.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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 5.768 0.228 6.107
* 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-3.7-bioc/meat/tofsims.Rcheck/00check.log’
for details.
tofsims.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL tofsims
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘tofsims’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c LapackEigen.cpp -o LapackEigen.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from LapackEigen.cpp:1:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
#pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
^
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:509:108: note: #pragma message: NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags
#pragma message ("NOTE: suggest to enable C++14 mode for faster code; add -std=c++14 to compiler flags")
^
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c c_importer.cpp -o c_importer.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c nn.cpp -o nn.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c readRawPhi.cpp -o readRawPhi.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c tofsims_init.c -o tofsims_init.o
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c utilities.cpp -o utilities.o
g++ -shared -L/home/biocbuild/bbs-3.7-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-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (tofsims)
tofsims.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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: 119 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
68.020 5.800 73.996
tofsims.Rcheck/tofsims-Ex.timings
| name | user | system | elapsed | |
| MAF | 1.200 | 0.040 | 1.272 | |
| MCR | 0.060 | 0.012 | 0.074 | |
| MNF | 0.068 | 0.000 | 0.095 | |
| MassImage | 0.008 | 0.000 | 0.007 | |
| MassSpectra | 0.008 | 0.016 | 0.022 | |
| PCAnalysis | 0.020 | 0.000 | 0.022 | |
| PeakList | 2.112 | 0.064 | 2.180 | |
| PrComp | 0.028 | 0.000 | 0.027 | |
| PrinComp | 0.02 | 0.00 | 0.02 | |
| addFixedWidth | 2.020 | 0.132 | 2.158 | |
| addPeaks | 1.192 | 0.060 | 1.256 | |
| analysis | 4.204 | 0.068 | 4.276 | |
| analysisName | 1.120 | 0.032 | 1.153 | |
| binning | 0.148 | 0.088 | 0.254 | |
| bwApply | 5.768 | 0.228 | 6.107 | |
| calibPointNew | 1.324 | 0.032 | 1.357 | |
| calibPoints | 1.052 | 0.020 | 1.076 | |
| calibration | 1.152 | 0.044 | 1.197 | |
| changePeakWidth | 1.244 | 0.052 | 1.296 | |
| findPeakWidth | 4.264 | 0.524 | 4.790 | |
| getTOFs | 1.012 | 0.056 | 1.070 | |
| image | 4.516 | 0.080 | 4.602 | |
| imageMatrix | 1.672 | 0.116 | 1.795 | |
| instrument | 1.064 | 0.048 | 1.115 | |
| mz | 1.024 | 0.016 | 1.040 | |
| nComp | 4.048 | 0.080 | 4.129 | |
| nPeaks | 1.896 | 0.144 | 2.041 | |
| nnMNF | 0.096 | 0.000 | 0.098 | |
| nz | 0.996 | 0.000 | 0.999 | |
| overlayPlot | 1.156 | 0.004 | 1.160 | |
| pcaLoadings | 4.220 | 0.004 | 4.228 | |
| pcaScores | 4.312 | 0.032 | 4.346 | |
| peakIDs | 2.012 | 0.112 | 2.129 | |
| peakMzs | 1.996 | 0.000 | 1.997 | |
| peakPick | 1.792 | 0.004 | 1.797 | |
| peakWidths | 4.196 | 0.384 | 4.586 | |
| peaks2Spectra | 1.500 | 0.044 | 1.547 | |
| plot | 1.208 | 0.004 | 1.215 | |
| points | 1.276 | 0.032 | 1.306 | |
| poissonScaling | 0.008 | 0.000 | 0.008 | |
| recalibrate | 1.188 | 0.000 | 1.191 | |
| reduceSpectrumResolution | 1.072 | 0.000 | 1.074 | |
| removePeaks | 1.196 | 0.008 | 1.204 | |
| scale | 0.020 | 0.000 | 0.021 | |
| smoothScatter | 4.36 | 0.04 | 4.41 | |
| smootherGolay | 1.200 | 0.040 | 1.239 | |
| smootherSpline | 2.276 | 0.172 | 2.450 | |
| subset | 1.084 | 0.004 | 1.090 | |
| unitMassPeaks | 2.156 | 0.020 | 2.179 | |
| xy | 1.128 | 0.024 | 1.153 | |
| xySpec | 1.308 | 0.028 | 1.337 | |