Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-27 12:30 -0400 (Fri, 27 Sep 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" | 4451 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
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 1572/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
primirTSS 1.23.0 (landing page) Pumin Li
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the primirTSS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/primirTSS.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: primirTSS |
Version: 1.23.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings primirTSS_1.23.0.tar.gz |
StartedAt: 2024-09-26 22:59:15 -0400 (Thu, 26 Sep 2024) |
EndedAt: 2024-09-26 23:04:19 -0400 (Thu, 26 Sep 2024) |
EllapsedTime: 303.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: primirTSS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings primirTSS_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/primirTSS.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘primirTSS/DESCRIPTION’ ... OK * this is package ‘primirTSS’ version ‘1.23.0’ * 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 ‘primirTSS’ 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 dependencies in R code ... WARNING '::' or ':::' import not declared from: 'magrittr' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE check_DHS_df: no visible binding for global variable ‘can_tss’ check_DHS_df: no visible binding for global variable ‘new_info’ check_DHS_s: no visible binding for global variable ‘dhs_p1’ check_DHS_s: no visible binding for global variable ‘dhs_p2’ eponine_score: no visible binding for global variable ‘previous’ eponine_score: no visible binding for global variable ‘histone_p1_flank’ eponine_score: no visible binding for global variable ‘histone_p2_flank’ eponine_score: no visible binding for global variable ‘tss_p1’ eponine_score: no visible binding for global variable ‘tss_p2’ find_nearest_peak: no visible binding for global variable ‘mir_name’ find_nearest_peak: no visible binding for global variable ‘start1’ find_nearest_peak: no visible binding for global variable ‘end1’ mir_tf: no visible binding for global variable ‘arrow’ mir_tf: no visible binding for global variable ‘seqname’ mir_tf: no visible binding for global variable ‘TF’ mir_tf: no visible binding for global variable ‘TF_class’ phast_score: no visible binding for global variable ‘loci’ phast_score: no visible binding for global variable ‘eponine_rank’ phast_score: no visible binding for global variable ‘phast_rank’ phast_score: no visible binding for global variable ‘e_p_rank’ phast_score_plot: no visible binding for global variable ‘loci’ plot_primiRNA_track: no visible binding for global variable ‘predicted_tss’ plot_primiRNA_track: no visible binding for global variable ‘symbol_name’ plot_primiRNA_track: no visible binding for global variable ‘stem_loop_p1’ plot_primiRNA_track: no visible binding for global variable ‘stem_loop_p2’ plot_primiRNA_track: no visible binding for global variable ‘gene_id’ plot_primiRNA_track: no visible binding for global variable ‘gene_p1’ plot_primiRNA_track: no visible binding for global variable ‘gene_p2’ plot_primiRNA_track: no visible binding for global variable ‘tss_p1’ plot_primiRNA_track: no visible binding for global variable ‘tss_p2’ require_fa: no visible binding for global variable ‘arrow’ tss_filter: no visible binding for global variable ‘gene_id’ tss_filter: no visible binding for global variable ‘new_info’ tss_filter: no visible binding for global variable ‘predicted_tss’ tss_filter: no visible binding for global variable ‘tss_type’ Undefined global functions or variables: TF TF_class arrow can_tss dhs_p1 dhs_p2 e_p_rank end1 eponine_rank gene_id gene_p1 gene_p2 histone_p1_flank histone_p2_flank loci mir_name new_info phast_rank predicted_tss previous seqname start1 stem_loop_p1 stem_loop_p2 symbol_name tss_p1 tss_p2 tss_type * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/primirTSS.Rcheck/00check.log’ for details.
primirTSS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL primirTSS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘primirTSS’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’ ** testing if installed package keeps a record of temporary installation path * DONE (primirTSS)
primirTSS.Rcheck/primirTSS-Ex.timings
name | user | system | elapsed | |
find_tss | 0.051 | 0.003 | 0.056 | |
peak_join | 0.372 | 0.008 | 0.382 | |
peak_merge | 0.058 | 0.001 | 0.059 | |
plot_primiRNA | 0.011 | 0.000 | 0.011 | |
run_primirTSSapp | 0.000 | 0.000 | 0.001 | |
trans_cor | 0.253 | 0.016 | 0.272 | |