Lorenz Gerber
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/tofsims |
| git_branch: RELEASE_3_14 |
| git_last_commit: 6cfbd33 |
| git_last_commit_date: 2021-10-26 12:24:38 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:03 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the tofsims package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tofsims.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1970/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| tofsims 1.22.0 (landing page) Lorenz Gerber
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: tofsims |
| Version: 1.22.0 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:tofsims.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings tofsims_1.22.0.tar.gz |
| StartedAt: 2022-04-12 09:41:19 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 09:44:51 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 211.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tofsims.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:tofsims.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings tofsims_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/tofsims.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.22.0’
* 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 ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
libs 4.6Mb
* 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 7.014 0.332 7.346
pcaScores 5.305 0.096 5.401
findPeakWidth 4.506 0.756 5.262
analysis 4.982 0.136 5.117
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.14-bioc/meat/tofsims.Rcheck/00check.log’
for details.
tofsims.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL tofsims ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘tofsims’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c LapackEigen.cpp -o LapackEigen.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c c_importer.cpp -o c_importer.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c nn.cpp -o nn.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c readRawPhi.cpp -o readRawPhi.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -Wall -c utilities.cpp -o utilities.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o tofsims.so LapackEigen.o RcppExports.o c_importer.o nn.o readRawPhi.o utilities.o -llapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
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 ]
[ FAIL 0 | WARN 53 | SKIP 0 | PASS 73 ]
>
> proc.time()
user system elapsed
82.690 7.343 90.031
tofsims.Rcheck/tofsims-Ex.timings
| name | user | system | elapsed | |
| MAF | 0.964 | 0.044 | 1.009 | |
| MCR | 0.045 | 0.024 | 0.070 | |
| MNF | 0.060 | 0.001 | 0.067 | |
| MassImage | 0.004 | 0.004 | 0.007 | |
| MassSpectra | 0.016 | 0.004 | 0.020 | |
| PCAnalysis | 0.024 | 0.000 | 0.024 | |
| PeakList | 2.254 | 0.068 | 2.321 | |
| PrComp | 0.026 | 0.000 | 0.027 | |
| PrinComp | 0.034 | 0.000 | 0.034 | |
| addFixedWidth | 2.369 | 0.212 | 2.581 | |
| addPeaks | 1.130 | 0.048 | 1.179 | |
| analysis | 4.982 | 0.136 | 5.117 | |
| analysisName | 1.030 | 0.048 | 1.078 | |
| binning | 0.400 | 0.024 | 0.440 | |
| bwApply | 7.014 | 0.332 | 7.346 | |
| calibPointNew | 1.230 | 0.044 | 1.274 | |
| calibPoints | 0.934 | 0.052 | 0.986 | |
| calibration | 1.056 | 0.076 | 1.131 | |
| changePeakWidth | 0.978 | 0.076 | 1.053 | |
| findPeakWidth | 4.506 | 0.756 | 5.262 | |
| getTOFs | 0.937 | 0.048 | 0.985 | |
| image | 4.774 | 0.092 | 4.866 | |
| imageMatrix | 1.696 | 0.172 | 1.869 | |
| instrument | 0.932 | 0.040 | 0.972 | |
| mz | 0.938 | 0.060 | 0.998 | |
| nComp | 4.375 | 0.192 | 4.567 | |
| nPeaks | 1.962 | 0.348 | 2.310 | |
| nnMNF | 0.091 | 0.004 | 0.095 | |
| nz | 0.953 | 0.004 | 0.957 | |
| overlayPlot | 1.212 | 0.000 | 1.212 | |
| pcaLoadings | 4.837 | 0.132 | 4.969 | |
| pcaScores | 5.305 | 0.096 | 5.401 | |
| peakIDs | 1.943 | 0.320 | 2.263 | |
| peakMzs | 2.116 | 0.016 | 2.132 | |
| peakPick | 2.856 | 0.028 | 2.884 | |
| peakWidths | 4.378 | 0.376 | 4.754 | |
| peaks2Spectra | 1.445 | 0.048 | 1.493 | |
| plot | 1.083 | 0.003 | 1.087 | |
| points | 1.303 | 0.000 | 1.302 | |
| poissonScaling | 0.007 | 0.000 | 0.008 | |
| recalibrate | 1.050 | 0.052 | 1.102 | |
| reduceSpectrumResolution | 1.003 | 0.004 | 1.007 | |
| removePeaks | 1.042 | 0.028 | 1.069 | |
| scale | 0.021 | 0.000 | 0.022 | |
| smoothScatter | 4.542 | 0.032 | 4.574 | |
| smootherGolay | 1.072 | 0.028 | 1.100 | |
| smootherSpline | 2.033 | 0.052 | 2.085 | |
| subset | 0.973 | 0.048 | 1.021 | |
| unitMassPeaks | 2.241 | 0.060 | 2.301 | |
| xy | 0.957 | 0.004 | 0.961 | |
| xySpec | 1.036 | 0.020 | 1.056 | |