Lorenz Gerber
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/tofsims |
| Branch: RELEASE_3_12 |
| Last Commit: aa3c69c |
| Last Changed Date: 2020-10-27 11:10:23 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:37:13 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the tofsims package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1874/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| tofsims 1.18.0 (landing page) Lorenz Gerber
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: tofsims |
| Version: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2021-05-06 06:56:41 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:01:21 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 279.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tofsims.Rcheck |
| Warnings: 0 |
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### 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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/tofsims.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.18.0’
* package encoding: UTF-8
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bwApply 8.116 0.183 8.314
findPeakWidth 7.290 0.663 7.962
peakWidths 7.087 0.371 7.478
pcaScores 5.532 0.126 5.668
image 5.568 0.067 5.646
nComp 5.456 0.112 5.574
smoothScatter 5.332 0.021 5.359
analysis 5.226 0.042 5.273
pcaLoadings 4.934 0.104 5.045
* 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-3.12-bioc/meat/tofsims.Rcheck/00check.log’
for details.
tofsims.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tofsims
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘tofsims’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c LapackEigen.cpp -o LapackEigen.o
In file included from LapackEigen.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c c_importer.cpp -o c_importer.o
In file included from c_importer.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nn.cpp -o nn.o
In file included from nn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c readRawPhi.cpp -o readRawPhi.o
In file included from readRawPhi.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utilities.cpp -o utilities.o
In file included from utilities.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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 utilities.o -llapack -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
> 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
[ FAIL 0 | WARN 53 | SKIP 0 | PASS 73 ]
>
> proc.time()
user system elapsed
95.092 5.246 100.511
tofsims.Rcheck/tofsims-Ex.timings
| name | user | system | elapsed | |
| MAF | 1.798 | 0.069 | 1.871 | |
| MCR | 0.133 | 0.018 | 0.152 | |
| MNF | 0.080 | 0.009 | 0.090 | |
| MassImage | 0.012 | 0.003 | 0.015 | |
| MassSpectra | 0.024 | 0.004 | 0.028 | |
| PCAnalysis | 0.035 | 0.005 | 0.039 | |
| PeakList | 2.932 | 0.620 | 3.579 | |
| PrComp | 0.032 | 0.002 | 0.034 | |
| PrinComp | 0.023 | 0.001 | 0.024 | |
| addFixedWidth | 3.130 | 0.427 | 3.568 | |
| addPeaks | 1.720 | 0.108 | 1.831 | |
| analysis | 5.226 | 0.042 | 5.273 | |
| analysisName | 1.522 | 0.050 | 1.573 | |
| binning | 0.709 | 0.044 | 0.757 | |
| bwApply | 8.116 | 0.183 | 8.314 | |
| calibPointNew | 2.095 | 0.060 | 2.161 | |
| calibPoints | 1.617 | 0.008 | 1.626 | |
| calibration | 1.588 | 0.009 | 1.598 | |
| changePeakWidth | 1.692 | 0.033 | 1.728 | |
| findPeakWidth | 7.290 | 0.663 | 7.962 | |
| getTOFs | 1.668 | 0.009 | 1.679 | |
| image | 5.568 | 0.067 | 5.646 | |
| imageMatrix | 2.668 | 0.139 | 2.811 | |
| instrument | 1.573 | 0.012 | 1.586 | |
| mz | 1.618 | 0.012 | 1.633 | |
| nComp | 5.456 | 0.112 | 5.574 | |
| nPeaks | 3.141 | 1.277 | 4.422 | |
| nnMNF | 0.119 | 0.008 | 0.126 | |
| nz | 1.572 | 0.020 | 1.592 | |
| overlayPlot | 1.960 | 0.103 | 2.066 | |
| pcaLoadings | 4.934 | 0.104 | 5.045 | |
| pcaScores | 5.532 | 0.126 | 5.668 | |
| peakIDs | 2.845 | 1.133 | 3.986 | |
| peakMzs | 2.696 | 0.693 | 3.391 | |
| peakPick | 3.874 | 0.164 | 4.047 | |
| peakWidths | 7.087 | 0.371 | 7.478 | |
| peaks2Spectra | 2.320 | 0.430 | 2.753 | |
| plot | 1.712 | 0.018 | 1.734 | |
| points | 1.935 | 0.138 | 2.076 | |
| poissonScaling | 0.01 | 0.00 | 0.01 | |
| recalibrate | 1.806 | 0.018 | 1.827 | |
| reduceSpectrumResolution | 1.549 | 0.010 | 1.560 | |
| removePeaks | 1.715 | 0.078 | 1.797 | |
| scale | 0.027 | 0.002 | 0.029 | |
| smoothScatter | 5.332 | 0.021 | 5.359 | |
| smootherGolay | 1.770 | 0.048 | 1.820 | |
| smootherSpline | 3.065 | 0.621 | 3.690 | |
| subset | 1.712 | 0.253 | 1.975 | |
| unitMassPeaks | 3.042 | 0.604 | 3.650 | |
| xy | 1.546 | 0.116 | 1.663 | |
| xySpec | 1.620 | 0.011 | 1.635 | |