Lorenz Gerber
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/tofsims |
| Branch: RELEASE_3_8 |
| Last Commit: 59e42aa |
| Last Changed Date: 2019-01-04 13:52:26 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:51:47 -0400 (Tue, 16 Apr 2019).
| Package 1570/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tofsims 1.10.1 Lorenz Gerber
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: tofsims |
| Version: 1.10.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:tofsims.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings tofsims_1.10.1.tar.gz |
| StartedAt: 2019-04-16 03:26:57 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:31:05 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 248.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tofsims.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:tofsims.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings tofsims_1.10.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/tofsims.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.1’
* 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 6.996 0.268 7.306
findPeakWidth 5.432 0.544 5.995
image 5.520 0.092 5.625
analysis 5.448 0.072 5.530
peakWidths 4.896 0.468 5.384
* 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-3.8-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-3.8-bioc/R/bin/R CMD INSTALL tofsims
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘tofsims’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from LapackEigen.cpp:1:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:514:108: 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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/RcppArmadillo/include/armadillo:54:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadilloForward.h:46,
from /home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:31,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:514:108: 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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c nn.cpp -o nn.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I/usr/local/include -fpic -g -O2 -Wall -c readRawPhi.cpp -o readRawPhi.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
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: 119 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
86.460 5.972 93.148
tofsims.Rcheck/tofsims-Ex.timings
| name | user | system | elapsed | |
| MAF | 1.484 | 0.048 | 1.615 | |
| MCR | 0.104 | 0.016 | 0.120 | |
| MNF | 0.072 | 0.000 | 0.114 | |
| MassImage | 0.008 | 0.000 | 0.006 | |
| MassSpectra | 0.020 | 0.000 | 0.023 | |
| PCAnalysis | 0.020 | 0.000 | 0.024 | |
| PeakList | 2.668 | 0.108 | 2.783 | |
| PrComp | 0.060 | 0.004 | 0.061 | |
| PrinComp | 0.032 | 0.000 | 0.031 | |
| addFixedWidth | 2.944 | 0.144 | 3.093 | |
| addPeaks | 1.548 | 0.000 | 1.548 | |
| analysis | 5.448 | 0.072 | 5.530 | |
| analysisName | 1.252 | 0.052 | 1.308 | |
| binning | 0.236 | 0.104 | 0.381 | |
| bwApply | 6.996 | 0.268 | 7.306 | |
| calibPointNew | 1.788 | 0.032 | 1.826 | |
| calibPoints | 1.312 | 0.044 | 1.357 | |
| calibration | 1.352 | 0.020 | 1.374 | |
| changePeakWidth | 1.528 | 0.028 | 1.557 | |
| findPeakWidth | 5.432 | 0.544 | 5.995 | |
| getTOFs | 1.296 | 0.024 | 1.321 | |
| image | 5.520 | 0.092 | 5.625 | |
| imageMatrix | 1.736 | 0.104 | 1.845 | |
| instrument | 1.144 | 0.036 | 1.186 | |
| mz | 1.268 | 0.048 | 1.322 | |
| nComp | 4.504 | 0.040 | 4.548 | |
| nPeaks | 2.000 | 0.176 | 2.176 | |
| nnMNF | 0.156 | 0.000 | 0.154 | |
| nz | 1.152 | 0.000 | 1.155 | |
| overlayPlot | 1.428 | 0.000 | 1.429 | |
| pcaLoadings | 4.356 | 0.012 | 4.367 | |
| pcaScores | 4.424 | 0.060 | 4.490 | |
| peakIDs | 1.964 | 0.060 | 2.029 | |
| peakMzs | 2.028 | 0.028 | 2.062 | |
| peakPick | 2.404 | 0.032 | 2.445 | |
| peakWidths | 4.896 | 0.468 | 5.384 | |
| peaks2Spectra | 1.652 | 0.076 | 1.729 | |
| plot | 1.380 | 0.016 | 1.396 | |
| points | 1.584 | 0.048 | 1.631 | |
| poissonScaling | 0.008 | 0.000 | 0.007 | |
| recalibrate | 1.556 | 0.004 | 1.565 | |
| reduceSpectrumResolution | 1.268 | 0.032 | 1.306 | |
| removePeaks | 1.276 | 0.072 | 1.347 | |
| scale | 0.02 | 0.00 | 0.02 | |
| smoothScatter | 4.568 | 0.008 | 4.577 | |
| smootherGolay | 1.108 | 0.000 | 1.111 | |
| smootherSpline | 2.232 | 0.000 | 2.237 | |
| subset | 1.220 | 0.000 | 1.223 | |
| unitMassPeaks | 2.096 | 0.000 | 2.098 | |
| xy | 1.268 | 0.036 | 1.307 | |
| xySpec | 1.460 | 0.028 | 1.492 | |