Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:39 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 1517/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PAST 1.20.0 (landing page) Thrash Adam
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the PAST package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PAST.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: PAST |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PAST.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PAST_1.20.0.tar.gz |
StartedAt: 2024-08-12 02:16:20 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 02:26:21 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 600.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: PAST.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PAST.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PAST_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PAST.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘PAST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PAST’ version ‘1.20.0’ * 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 ‘PAST’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::findMatches’ by ‘utils::findMatches’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’ See ‘/home/biocbuild/bbs-3.19-bioc/meat/PAST.Rcheck/00install.out’ for details. * 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 assign_SNPs_to_genes: no visible binding for global variable ‘position’ assign_SNPs_to_genes: no visible binding for global variable ‘Marker_original’ assign_SNPs_to_genes: no visible binding for global variable ‘effect’ assign_SNPs_to_genes: no visible binding for global variable ‘p.value’ assign_SNPs_to_genes: no visible binding for global variable ‘linked_snp_count’ assign_SNPs_to_genes: no visible binding for global variable ‘name’ assign_SNPs_to_genes: no visible binding for global variable ‘marker’ assign_chunk: no visible binding for global variable ‘chromosome’ assign_chunk: no visible global function definition for ‘IRanges’ assign_chunk: no visible binding for global variable ‘position’ assign_chunk: no visible binding for global variable ‘seqid’ assign_chunk: no visible binding for global variable ‘Name’ find_pathway_significance: no visible binding for global variable ‘gene_id’ plot_pathways: no visible binding for global variable ‘running_enrichment_score’ Undefined global functions or variables: IRanges Marker_original Name chromosome effect gene_id linked_snp_count marker name p.value position running_enrichment_score seqid * 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 ... WARNING Undocumented arguments in Rd file 'assign_SNPs_to_genes.Rd' ‘filter_type’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 plot_pathways 6.096 1.038 98.994 find_pathway_significance 4.434 0.599 92.249 assign_SNPs_to_genes 4.484 0.496 60.293 * 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: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/PAST.Rcheck/00check.log’ for details.
PAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL PAST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘PAST’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::findMatches’ by ‘utils::findMatches’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::findMatches’ by ‘utils::findMatches’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::findMatches’ by ‘utils::findMatches’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’ ** testing if installed package keeps a record of temporary installation path * DONE (PAST)
PAST.Rcheck/PAST-Ex.timings
name | user | system | elapsed | |
assign_SNPs_to_genes | 4.484 | 0.496 | 60.293 | |
find_pathway_significance | 4.434 | 0.599 | 92.249 | |
load_GWAS_data | 0.135 | 0.028 | 0.162 | |
load_LD | 0.489 | 0.028 | 0.517 | |
plot_pathways | 6.096 | 1.038 | 98.994 | |