| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:38 -0000 (Wed, 10 May 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" | 6211 |
| 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: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1553/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ptairMS 1.9.0 (landing page) camille Roquencourt
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ptairMS |
| Version: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2023-05-10 01:07:50 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 01:23:17 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 927.2 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_1.9.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ptairMS.Rcheck’
* using R Under development (unstable) (2023-03-12 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 ‘1.9.0’
* 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 118.449 0.464 118.915
alignSamples 24.042 0.403 24.515
imputeMat 23.128 0.184 23.313
getPeakList 22.091 0.184 22.275
impute 21.859 0.116 21.975
writeEset 21.644 0.160 21.806
annotation 21.393 0.259 21.656
plot 17.307 0.020 17.331
plotTIC 16.895 0.068 16.964
plotRaw 16.835 0.124 16.960
plotFeatures 15.922 0.144 16.067
defineKnots 15.435 0.116 15.551
plotCalib 14.961 0.076 15.038
setSampleMetadata 14.892 0.082 14.975
getSampleMetadata 14.850 0.068 14.919
exportSampleMetada 14.786 0.056 14.842
rmPeakList 14.612 0.116 14.729
getFileNames 14.519 0.116 14.636
updatePtrSet 14.565 0.012 14.578
importSampleMetadata 14.342 0.048 14.390
getDirectory 14.270 0.080 14.350
changeTimeLimits 14.101 0.104 14.205
resetSampleMetadata 14.030 0.078 14.109
createPtrSet 11.661 0.084 11.791
convert_to_mzML 7.381 0.048 7.430
* 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
107.770 1.236 108.996
ptairMS.Rcheck/ptairMS-Ex.timings
| name | user | system | elapsed | |
| LocalMaximaSG | 0.028 | 0.004 | 0.032 | |
| PeakList | 1.18 | 0.04 | 1.24 | |
| alignSamples | 24.042 | 0.403 | 24.515 | |
| annotation | 21.393 | 0.259 | 21.656 | |
| calibration | 1.205 | 0.011 | 1.216 | |
| changeTimeLimits | 14.101 | 0.104 | 14.205 | |
| convert_to_mzML | 7.381 | 0.048 | 7.430 | |
| createPtrSet | 11.661 | 0.084 | 11.791 | |
| defineKnots | 15.435 | 0.116 | 15.551 | |
| detectPeak | 118.449 | 0.464 | 118.915 | |
| exportSampleMetada | 14.786 | 0.056 | 14.842 | |
| formula2mass | 0.004 | 0.000 | 0.005 | |
| getDirectory | 14.27 | 0.08 | 14.35 | |
| getFileNames | 14.519 | 0.116 | 14.636 | |
| getPeakList | 22.091 | 0.184 | 22.275 | |
| getSampleMetadata | 14.850 | 0.068 | 14.919 | |
| importSampleMetadata | 14.342 | 0.048 | 14.390 | |
| impute | 21.859 | 0.116 | 21.975 | |
| imputeMat | 23.128 | 0.184 | 23.313 | |
| plot | 17.307 | 0.020 | 17.331 | |
| plotCalib | 14.961 | 0.076 | 15.038 | |
| plotFeatures | 15.922 | 0.144 | 16.067 | |
| plotRaw | 16.835 | 0.124 | 16.960 | |
| plotTIC | 16.895 | 0.068 | 16.964 | |
| readRaw | 0.150 | 0.004 | 0.154 | |
| resetSampleMetadata | 14.030 | 0.078 | 14.109 | |
| rmPeakList | 14.612 | 0.116 | 14.729 | |
| setSampleMetadata | 14.892 | 0.082 | 14.975 | |
| timeLimits | 1.646 | 0.000 | 1.646 | |
| updatePtrSet | 14.565 | 0.012 | 14.578 | |
| writeEset | 21.644 | 0.160 | 21.806 | |