| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:39 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 1558/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ptairMS 1.9.0 (landing page) camille Roquencourt
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: ptairMS |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ptairMS_1.9.0.tar.gz |
| StartedAt: 2023-06-06 04:33:45 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 04:49:09 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 924.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ptairMS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ptairMS_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ptairMS.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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++ (GCC) 10.3.1’
* 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 loading without being on the library search path ... 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 118.560 0.467 119.244
alignSamples 24.890 0.195 25.192
imputeMat 23.786 0.068 23.898
writeEset 22.584 0.048 22.675
impute 21.904 0.052 21.998
getPeakList 21.439 0.091 21.570
annotation 21.147 0.084 21.271
plotTIC 17.026 0.056 17.116
plot 16.938 0.032 17.002
plotRaw 16.872 0.048 16.954
plotFeatures 16.005 0.048 16.084
plotCalib 15.369 0.031 15.429
resetSampleMetadata 15.132 0.032 15.194
defineKnots 14.855 0.168 15.045
getDirectory 14.886 0.016 14.930
importSampleMetadata 14.789 0.056 14.872
updatePtrSet 14.717 0.028 14.773
getSampleMetadata 14.702 0.028 14.756
setSampleMetadata 14.640 0.048 14.718
rmPeakList 14.505 0.044 14.577
exportSampleMetada 14.512 0.032 14.571
getFileNames 14.341 0.044 14.412
changeTimeLimits 14.318 0.016 14.356
createPtrSet 12.325 0.041 12.442
convert_to_mzML 7.415 0.077 7.504
* 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-3.18-bioc/meat/ptairMS.Rcheck/00check.log’
for details.
ptairMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL ptairMS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘ptairMS’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c align.cpp -o align.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c findEqualGreaterM.cpp -o findEqualGreaterM.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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 version 4.3.0 (2023-04-21) -- "Already Tomorrow"
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
110.118 0.811 111.123
ptairMS.Rcheck/ptairMS-Ex.timings
| name | user | system | elapsed | |
| LocalMaximaSG | 0.027 | 0.004 | 0.032 | |
| PeakList | 1.203 | 0.032 | 1.254 | |
| alignSamples | 24.890 | 0.195 | 25.192 | |
| annotation | 21.147 | 0.084 | 21.271 | |
| calibration | 1.194 | 0.020 | 1.217 | |
| changeTimeLimits | 14.318 | 0.016 | 14.356 | |
| convert_to_mzML | 7.415 | 0.077 | 7.504 | |
| createPtrSet | 12.325 | 0.041 | 12.442 | |
| defineKnots | 14.855 | 0.168 | 15.045 | |
| detectPeak | 118.560 | 0.467 | 119.244 | |
| exportSampleMetada | 14.512 | 0.032 | 14.571 | |
| formula2mass | 0.000 | 0.003 | 0.004 | |
| getDirectory | 14.886 | 0.016 | 14.930 | |
| getFileNames | 14.341 | 0.044 | 14.412 | |
| getPeakList | 21.439 | 0.091 | 21.570 | |
| getSampleMetadata | 14.702 | 0.028 | 14.756 | |
| importSampleMetadata | 14.789 | 0.056 | 14.872 | |
| impute | 21.904 | 0.052 | 21.998 | |
| imputeMat | 23.786 | 0.068 | 23.898 | |
| plot | 16.938 | 0.032 | 17.002 | |
| plotCalib | 15.369 | 0.031 | 15.429 | |
| plotFeatures | 16.005 | 0.048 | 16.084 | |
| plotRaw | 16.872 | 0.048 | 16.954 | |
| plotTIC | 17.026 | 0.056 | 17.116 | |
| readRaw | 0.156 | 0.000 | 0.156 | |
| resetSampleMetadata | 15.132 | 0.032 | 15.194 | |
| rmPeakList | 14.505 | 0.044 | 14.577 | |
| setSampleMetadata | 14.640 | 0.048 | 14.718 | |
| timeLimits | 1.737 | 0.004 | 1.745 | |
| updatePtrSet | 14.717 | 0.028 | 14.773 | |
| writeEset | 22.584 | 0.048 | 22.675 | |