Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1345/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstatsBig 1.5.0 (landing page) Mateusz Staniak
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the MSstatsBig package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsBig.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MSstatsBig |
Version: 1.5.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MSstatsBig.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MSstatsBig_1.5.0.tar.gz |
StartedAt: 2024-12-24 09:03:10 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 09:04:38 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 88.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSstatsBig.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MSstatsBig.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MSstatsBig_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MSstatsBig.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSstatsBig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsBig’ version ‘1.5.0’ * 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 ‘MSstatsBig’ can be installed ... OK * 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE MSstatsPreprocessBig: no visible binding for global variable ‘input’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘PeptideSequence’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘PrecursorCharge’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘FragmentIon’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘ProductCharge’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘ProteinName’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘Feature’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘Intensity’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘MeanAbundance’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘feature_rank’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘NumProteins’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘IsotopeLabelType’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘Run’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘Condition’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘BioReplicate’ MSstatsPreprocessBigArrow: no visible binding for global variable ‘NumObs’ MSstatsPreprocessBigSparklyr: no visible global function definition for ‘%>%’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘Condition’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘BioReplicate’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘PeptideSequence’ MSstatsPreprocessBigSparklyr: no visible global function definition for ‘n_distinct’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘ProteinName’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘NumProteins’ MSstatsPreprocessBigSparklyr: no visible global function definition for ‘tbl’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘PrecursorCharge’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘FragmentIon’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘ProductCharge’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘IsotopeLabelType’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘Run’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘Intensity’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘NumObs’ MSstatsPreprocessBigSparklyr: no visible global function definition for ‘min_rank’ MSstatsPreprocessBigSparklyr: no visible binding for global variable ‘Rank’ cleanSpectronautChunk: no visible global function definition for ‘all_of’ cleanSpectronautChunk: no visible binding for global variable ‘Intensity’ cleanSpectronautChunk: no visible binding for global variable ‘Excluded’ cleanSpectronautChunk: no visible binding for global variable ‘Identified’ cleanSpectronautChunk: no visible binding for global variable ‘EGQvalue’ cleanSpectronautChunk: no visible binding for global variable ‘PGQvalue’ cleanSpectronautChunk: no visible binding for global variable ‘FFrgLossType’ cleanSpectronautChunk: no visible binding for global variable ‘LabeledSequence’ cleanSpectronautChunk: no visible global function definition for ‘:=’ cleanSpectronautChunk: no visible binding for global variable ‘IsotopeLabelType’ cleanSpectronautChunk: no visible binding for global variable ‘IsLabeled’ cleanSpectronautChunk: no visible binding for global variable ‘ProteinName’ cleanSpectronautChunk: no visible binding for global variable ‘PeptideSequence’ cleanSpectronautChunk: no visible binding for global variable ‘PrecursorCharge’ cleanSpectronautChunk: no visible binding for global variable ‘FragmentIon’ cleanSpectronautChunk: no visible binding for global variable ‘ProductCharge’ cleanSpectronautChunk: no visible binding for global variable ‘Run’ cleanSpectronautChunk: no visible binding for global variable ‘BioReplicate’ cleanSpectronautChunk: no visible binding for global variable ‘Condition’ Undefined global functions or variables: %>% := BioReplicate Condition EGQvalue Excluded FFrgLossType Feature FragmentIon Identified Intensity IsLabeled IsotopeLabelType LabeledSequence MeanAbundance NumObs NumProteins PGQvalue PeptideSequence PrecursorCharge ProductCharge ProteinName Rank Run all_of feature_rank input min_rank n_distinct tbl * 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 bigSpectronauttoMSstatsFormat 6.211 0.305 6.562 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/MSstatsBig.Rcheck/00check.log’ for details.
MSstatsBig.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MSstatsBig ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘MSstatsBig’ ... ** 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 (MSstatsBig)
MSstatsBig.Rcheck/MSstatsBig-Ex.timings
name | user | system | elapsed | |
MSstatsAddAnnotationBig | 1.194 | 0.052 | 1.291 | |
MSstatsPreprocessBig | 0.454 | 0.063 | 0.518 | |
bigFragPipetoMSstatsFormat | 0.276 | 0.012 | 0.288 | |
bigSpectronauttoMSstatsFormat | 6.211 | 0.305 | 6.562 | |