Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:19 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 PAST package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1439/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PAST 1.14.0 (landing page) Thrash Adam
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: PAST |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PAST_1.14.0.tar.gz |
StartedAt: 2023-04-10 21:46:18 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 21:53:20 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 422.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: PAST.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PAST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PAST_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/PAST.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PAST/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PAST’ version ‘1.14.0’ * 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::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ 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::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 ‘/Users/biocbuild/bbs-3.16-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 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 ... 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 documentation object 'assign_SNPs_to_genes' ‘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 5.388 0.287 85.630 assign_SNPs_to_genes 5.052 0.256 58.330 find_pathway_significance 4.820 0.254 86.355 * 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.16-bioc/meat/PAST.Rcheck/00check.log’ for details.
PAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PAST ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘PAST’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ 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::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::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ 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::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::union’ by ‘dplyr::union’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’ Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’ 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::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 | 5.052 | 0.256 | 58.330 | |
find_pathway_significance | 4.820 | 0.254 | 86.355 | |
load_GWAS_data | 0.156 | 0.006 | 0.162 | |
load_LD | 0.515 | 0.014 | 0.529 | |
plot_pathways | 5.388 | 0.287 | 85.630 | |