Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-19 11:47 -0400 (Sat, 19 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4474 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4733 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4479 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
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 548/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEqMS 1.23.4 (landing page) Yafeng Zhu
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the DEqMS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEqMS.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: DEqMS |
Version: 1.23.4 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DEqMS_1.23.4.tar.gz |
StartedAt: 2024-10-19 00:50:23 -0400 (Sat, 19 Oct 2024) |
EndedAt: 2024-10-19 00:52:54 -0400 (Sat, 19 Oct 2024) |
EllapsedTime: 150.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DEqMS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DEqMS_1.23.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/DEqMS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘DEqMS/DESCRIPTION’ ... OK * this is package ‘DEqMS’ version ‘1.23.4’ * 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 ‘DEqMS’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... NOTE Package in Depends field not imported from: ‘matrixStats’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Residualplot: no visible global function definition for ‘fitted’ Residualplot: no visible global function definition for ‘residuals’ VarianceScatterplot: no visible global function definition for ‘fitted’ peptideProfilePlot: no visible binding for global variable ‘variable’ peptideProfilePlot: no visible binding for global variable ‘value’ peptideProfilePlot: no visible binding for global variable ‘PSM_id’ peptideProfilePlot: no visible binding for global variable ‘Peptide’ spectraCounteBayes: no visible global function definition for ‘fitted’ Undefined global functions or variables: PSM_id Peptide fitted residuals value variable Consider adding importFrom("stats", "fitted", "residuals") to your NAMESPACE file. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed medpolishSummary 47.170 0.202 47.388 Residualplot 9.497 0.509 10.023 VarianceScatterplot 6.501 0.154 6.658 VarianceBoxplot 5.413 0.132 5.546 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/DEqMS.Rcheck/00check.log’ for details.
DEqMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DEqMS ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘DEqMS’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DEqMS)
DEqMS.Rcheck/DEqMS-Ex.timings
name | user | system | elapsed | |
Residualplot | 9.497 | 0.509 | 10.023 | |
VarianceBoxplot | 5.413 | 0.132 | 5.546 | |
VarianceScatterplot | 6.501 | 0.154 | 6.658 | |
equalMedianNormalization | 4.229 | 0.086 | 4.453 | |
medianSummary | 4.057 | 0.054 | 4.114 | |
medianSweeping | 3.683 | 0.364 | 4.049 | |
medpolishSummary | 47.170 | 0.202 | 47.388 | |
outputResult | 4.635 | 0.075 | 4.726 | |
peptideProfilePlot | 1.485 | 0.035 | 1.520 | |
spectraCounteBayes | 4.856 | 0.110 | 4.990 | |