| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-03 02:36:16 -0000 (Fri, 03 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4039 |
| 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 ptairMS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ptairMS.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 1537/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ptairMS 1.7.0 (landing page) camille Roquencourt
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ptairMS |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ptairMS_1.7.0.tar.gz |
| StartedAt: 2023-02-02 16:43:16 -0000 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 17:00:01 -0000 (Thu, 02 Feb 2023) |
| EllapsedTime: 1005.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ptairMS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ptairMS_1.7.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ptairMS.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.7.0’
* 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 ‘ptairMS’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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
detectPeak 125.758 0.196 126.358
alignSamples 27.380 0.175 29.815
imputeMat 24.468 0.212 24.991
annotation 24.455 0.151 27.447
impute 24.084 0.080 24.172
writeEset 24.072 0.084 24.363
getPeakList 23.484 0.104 23.602
plot 18.551 0.100 18.725
plotRaw 17.850 0.060 17.924
plotTIC 17.728 0.076 17.812
plotFeatures 17.176 0.044 17.223
plotCalib 16.682 0.108 16.825
defineKnots 16.516 0.064 16.586
getDirectory 16.317 0.048 16.371
setSampleMetadata 16.284 0.056 16.508
updatePtrSet 15.907 0.072 16.278
exportSampleMetada 15.848 0.064 15.918
getFileNames 15.773 0.040 15.819
getSampleMetadata 15.744 0.032 15.786
importSampleMetadata 15.688 0.028 15.720
changeTimeLimits 15.651 0.054 15.874
rmPeakList 15.435 0.040 15.881
resetSampleMetadata 15.432 0.028 15.466
createPtrSet 12.108 0.073 12.228
convert_to_mzML 7.711 0.106 7.846
* 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 ...
‘ptairMS.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/ptairMS.Rcheck/00check.log’
for details.
ptairMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ptairMS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘ptairMS’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c align.cpp -o align.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c findEqualGreaterM.cpp -o findEqualGreaterM.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-ptairMS/00new/ptairMS/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘annotateVOC’ with signature ‘"ExpressionSet"’: no definition for class “ExpressionSet” in method for ‘writeEset’ with signature ‘"ExpressionSet"’: no definition for class “ExpressionSet” ** 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 (ptairMS)
ptairMS.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(ptairMS)
>
> test_check("ptairMS")
Control1.h5 : 3 peaks detected
Control2.h5 : 4 peaks detected
Specie-a1.h5 : 2 peaks detected
Specie-a2.h5 : 3 peaks detected
specie-b1.h5 : 4 peaks detected
specie-b2.h5 : 3 peaks detected
Control1.h5 : 2 peaks detected
Control2.h5 : 2 peaks detected
Specie-a1.h5 : 3 peaks detected
Specie-a2.h5 : 3 peaks detected
specie-b1.h5 : 2 peaks detected
specie-b2.h5 : 3 peaks detected
Control1.h5 : 4 peaks detected
Control2.h5 : 6 peaks detected
Specie-a1.h5 : 3 peaks detected
Specie-a2.h5 : 4 peaks detected
specie-b1.h5 : 5 peaks detected
specie-b2.h5 : 4 peaks detected
Control1.h5 : 3 peaks detected
Control2.h5 : 2 peaks detected
Specie-a1.h5 : 3 peaks detected
Specie-a2.h5 : 3 peaks detected
specie-b1.h5 : 4 peaks detected
specie-b2.h5 : 4 peaks detected
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ]
>
> proc.time()
user system elapsed
115.664 0.556 116.509
ptairMS.Rcheck/ptairMS-Ex.timings
| name | user | system | elapsed | |
| LocalMaximaSG | 0.033 | 0.000 | 0.033 | |
| PeakList | 1.202 | 0.064 | 1.594 | |
| alignSamples | 27.380 | 0.175 | 29.815 | |
| annotation | 24.455 | 0.151 | 27.447 | |
| calibration | 1.155 | 0.004 | 1.181 | |
| changeTimeLimits | 15.651 | 0.054 | 15.874 | |
| convert_to_mzML | 7.711 | 0.106 | 7.846 | |
| createPtrSet | 12.108 | 0.073 | 12.228 | |
| defineKnots | 16.516 | 0.064 | 16.586 | |
| detectPeak | 125.758 | 0.196 | 126.358 | |
| exportSampleMetada | 15.848 | 0.064 | 15.918 | |
| formula2mass | 0.004 | 0.000 | 0.004 | |
| getDirectory | 16.317 | 0.048 | 16.371 | |
| getFileNames | 15.773 | 0.040 | 15.819 | |
| getPeakList | 23.484 | 0.104 | 23.602 | |
| getSampleMetadata | 15.744 | 0.032 | 15.786 | |
| importSampleMetadata | 15.688 | 0.028 | 15.720 | |
| impute | 24.084 | 0.080 | 24.172 | |
| imputeMat | 24.468 | 0.212 | 24.991 | |
| plot | 18.551 | 0.100 | 18.725 | |
| plotCalib | 16.682 | 0.108 | 16.825 | |
| plotFeatures | 17.176 | 0.044 | 17.223 | |
| plotRaw | 17.850 | 0.060 | 17.924 | |
| plotTIC | 17.728 | 0.076 | 17.812 | |
| readRaw | 0.161 | 0.004 | 0.166 | |
| resetSampleMetadata | 15.432 | 0.028 | 15.466 | |
| rmPeakList | 15.435 | 0.040 | 15.881 | |
| setSampleMetadata | 16.284 | 0.056 | 16.508 | |
| timeLimits | 1.764 | 0.012 | 1.777 | |
| updatePtrSet | 15.907 | 0.072 | 16.278 | |
| writeEset | 24.072 | 0.084 | 24.363 | |