| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-04 11:37:42 -0400 (Wed, 04 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 1583/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ptairMS 1.8.0 (landing page) camille Roquencourt
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ptairMS |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.8.0.tar.gz |
| StartedAt: 2023-10-04 05:34:57 -0400 (Wed, 04 Oct 2023) |
| EndedAt: 2023-10-04 05:54:32 -0400 (Wed, 04 Oct 2023) |
| EllapsedTime: 1175.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ptairMS.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ptairMS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.8.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 175.181 2.724 219.462
alignSamples 29.597 1.051 41.205
imputeMat 26.928 0.820 35.510
annotation 25.289 0.606 32.857
writeEset 25.044 0.653 34.714
impute 24.769 0.654 31.487
getPeakList 24.138 0.614 30.474
plot 20.787 0.473 26.293
plotTIC 19.386 0.460 25.136
plotRaw 18.753 0.560 24.847
plotFeatures 18.680 0.489 25.093
plotCalib 17.800 0.420 23.240
rmPeakList 16.869 0.394 23.155
defineKnots 16.804 0.305 20.808
setSampleMetadata 16.395 0.423 23.477
resetSampleMetadata 16.390 0.387 21.356
getFileNames 16.384 0.342 20.564
getDirectory 16.337 0.364 20.544
importSampleMetadata 16.318 0.349 20.090
exportSampleMetada 16.292 0.373 20.725
changeTimeLimits 16.210 0.373 21.190
getSampleMetadata 16.164 0.346 20.023
updatePtrSet 15.886 0.408 22.468
createPtrSet 15.584 0.405 20.713
convert_to_mzML 11.317 0.284 14.821
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/ptairMS.Rcheck/00check.log’
for details.
ptairMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ptairMS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘ptairMS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align.cpp -o align.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findEqualGreaterM.cpp -o findEqualGreaterM.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ptairMS.so RcppExports.o align.o findEqualGreaterM.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 : 5 peaks detected
specie-b2.h5 : 4 peaks detected
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 59 ]
>
> proc.time()
user system elapsed
143.462 3.698 190.528
ptairMS.Rcheck/ptairMS-Ex.timings
| name | user | system | elapsed | |
| LocalMaximaSG | 0.053 | 0.014 | 0.099 | |
| PeakList | 1.335 | 0.163 | 2.098 | |
| alignSamples | 29.597 | 1.051 | 41.205 | |
| annotation | 25.289 | 0.606 | 32.857 | |
| calibration | 1.414 | 0.049 | 1.855 | |
| changeTimeLimits | 16.210 | 0.373 | 21.190 | |
| convert_to_mzML | 11.317 | 0.284 | 14.821 | |
| createPtrSet | 15.584 | 0.405 | 20.713 | |
| defineKnots | 16.804 | 0.305 | 20.808 | |
| detectPeak | 175.181 | 2.724 | 219.462 | |
| exportSampleMetada | 16.292 | 0.373 | 20.725 | |
| formula2mass | 0.005 | 0.001 | 0.007 | |
| getDirectory | 16.337 | 0.364 | 20.544 | |
| getFileNames | 16.384 | 0.342 | 20.564 | |
| getPeakList | 24.138 | 0.614 | 30.474 | |
| getSampleMetadata | 16.164 | 0.346 | 20.023 | |
| importSampleMetadata | 16.318 | 0.349 | 20.090 | |
| impute | 24.769 | 0.654 | 31.487 | |
| imputeMat | 26.928 | 0.820 | 35.510 | |
| plot | 20.787 | 0.473 | 26.293 | |
| plotCalib | 17.80 | 0.42 | 23.24 | |
| plotFeatures | 18.680 | 0.489 | 25.093 | |
| plotRaw | 18.753 | 0.560 | 24.847 | |
| plotTIC | 19.386 | 0.460 | 25.136 | |
| readRaw | 0.169 | 0.025 | 0.251 | |
| resetSampleMetadata | 16.390 | 0.387 | 21.356 | |
| rmPeakList | 16.869 | 0.394 | 23.155 | |
| setSampleMetadata | 16.395 | 0.423 | 23.477 | |
| timeLimits | 2.702 | 0.078 | 3.811 | |
| updatePtrSet | 15.886 | 0.408 | 22.468 | |
| writeEset | 25.044 | 0.653 | 34.714 | |