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This page was generated on 2021-10-15 15:06:16 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the primirTSS package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1430/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
primirTSS 1.10.0 (landing page) Pumin Li
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: primirTSS |
Version: 1.10.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:primirTSS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings primirTSS_1.10.0.tar.gz |
StartedAt: 2021-10-15 03:40:15 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 03:45:48 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 333.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: primirTSS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:primirTSS.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings primirTSS_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/primirTSS.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'primirTSS/DESCRIPTION' ... OK * this is package 'primirTSS' version '1.10.0' * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... 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 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 ... 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 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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/primirTSS.Rcheck/00check.log' for details.
primirTSS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch primirTSS ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' * installing *source* package 'primirTSS' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'primirTSS' finding HTML links ... done find_tss html peak_join html peak_merge html plot_primiRNA html primirTSS html run_primirTSSapp html trans_cor html ** 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 (primirTSS) Making 'packages.html' ... done
primirTSS.Rcheck/primirTSS-Ex.timings
name | user | system | elapsed | |
find_tss | 0.07 | 0.00 | 0.08 | |
peak_join | 0.58 | 0.00 | 0.58 | |
peak_merge | 0.08 | 0.00 | 0.08 | |
plot_primiRNA | 0.03 | 0.00 | 0.03 | |
run_primirTSSapp | 0 | 0 | 0 | |
trans_cor | 0.47 | 0.02 | 1.22 | |