| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:40 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 1562/2195 | 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/site-library --timings ptairMS_1.7.0.tar.gz |
| StartedAt: 2023-03-25 09:39:29 -0000 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 09:54:52 -0000 (Sat, 25 Mar 2023) |
| EllapsedTime: 923.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ptairMS.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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/site-library --timings ptairMS_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ptairMS.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 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 117.613 0.632 118.248
alignSamples 24.288 0.360 24.709
imputeMat 23.072 0.220 23.293
annotation 22.445 0.212 22.660
writeEset 21.788 0.156 21.946
getPeakList 21.287 0.148 21.436
impute 21.125 0.180 21.306
plot 17.894 0.084 17.978
plotTIC 17.214 0.116 17.331
plotRaw 17.109 0.112 17.222
plotFeatures 17.103 0.104 17.207
defineKnots 16.037 0.320 16.357
plotCalib 15.901 0.100 16.002
rmPeakList 15.214 0.088 15.303
resetSampleMetadata 15.174 0.124 15.299
updatePtrSet 15.152 0.072 15.225
setSampleMetadata 14.580 0.068 14.648
changeTimeLimits 14.554 0.072 14.626
importSampleMetadata 14.536 0.040 14.577
getSampleMetadata 14.489 0.044 14.533
getFileNames 14.390 0.120 14.511
exportSampleMetada 14.293 0.052 14.345
getDirectory 14.295 0.036 14.330
createPtrSet 12.130 0.049 12.228
convert_to_mzML 7.443 0.190 7.642
* 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-devel_2023-03-12_r83975-bin/site-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++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c align.cpp -o align.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c findEqualGreaterM.cpp -o findEqualGreaterM.o g++ -std=gnu++17 -shared -L/usr/local/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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) (2023-03-12 r83975) -- "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
108.167 0.963 109.119
ptairMS.Rcheck/ptairMS-Ex.timings
| name | user | system | elapsed | |
| LocalMaximaSG | 0.024 | 0.008 | 0.032 | |
| PeakList | 1.176 | 0.180 | 1.373 | |
| alignSamples | 24.288 | 0.360 | 24.709 | |
| annotation | 22.445 | 0.212 | 22.660 | |
| calibration | 1.147 | 0.016 | 1.163 | |
| changeTimeLimits | 14.554 | 0.072 | 14.626 | |
| convert_to_mzML | 7.443 | 0.190 | 7.642 | |
| createPtrSet | 12.130 | 0.049 | 12.228 | |
| defineKnots | 16.037 | 0.320 | 16.357 | |
| detectPeak | 117.613 | 0.632 | 118.248 | |
| exportSampleMetada | 14.293 | 0.052 | 14.345 | |
| formula2mass | 0.004 | 0.000 | 0.004 | |
| getDirectory | 14.295 | 0.036 | 14.330 | |
| getFileNames | 14.390 | 0.120 | 14.511 | |
| getPeakList | 21.287 | 0.148 | 21.436 | |
| getSampleMetadata | 14.489 | 0.044 | 14.533 | |
| importSampleMetadata | 14.536 | 0.040 | 14.577 | |
| impute | 21.125 | 0.180 | 21.306 | |
| imputeMat | 23.072 | 0.220 | 23.293 | |
| plot | 17.894 | 0.084 | 17.978 | |
| plotCalib | 15.901 | 0.100 | 16.002 | |
| plotFeatures | 17.103 | 0.104 | 17.207 | |
| plotRaw | 17.109 | 0.112 | 17.222 | |
| plotTIC | 17.214 | 0.116 | 17.331 | |
| readRaw | 0.155 | 0.000 | 0.155 | |
| resetSampleMetadata | 15.174 | 0.124 | 15.299 | |
| rmPeakList | 15.214 | 0.088 | 15.303 | |
| setSampleMetadata | 14.580 | 0.068 | 14.648 | |
| timeLimits | 1.677 | 0.000 | 1.678 | |
| updatePtrSet | 15.152 | 0.072 | 15.225 | |
| writeEset | 21.788 | 0.156 | 21.946 | |