Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:41 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1736/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RITAN 1.29.0 (landing page) Michael Zimmermann
| 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 RITAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RITAN.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: RITAN |
Version: 1.29.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RITAN.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RITAN_1.29.0.tar.gz |
StartedAt: 2024-08-16 04:23:15 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 04:28:44 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 329.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: RITAN.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RITAN.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RITAN_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RITAN.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'RITAN/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'RITAN' version '1.29.0' * 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 whether package 'RITAN' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN' Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN' See 'F:/biocbuild/bbs-3.20-bioc/meat/RITAN.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: 'BgeeDB' A package should be listed in only one of these fields. * 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 ... NOTE Namespaces in Imports field not imported from: 'BgeeDB' 'knitr' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE enrichment_symbols: no visible binding for global variable 'active_genesets' icon_dual_between: no visible binding for global variable 'all_symbols' icon_single_within: no visible binding for global variable 'all_symbols' load_geneset_symbols: no visible binding for global variable 'geneset_list' load_geneset_symbols: no visible binding for global variable 'active_genesets' plot.term_enrichment_by_subset: no visible binding for global variable 'Var2' plot.term_enrichment_by_subset: no visible binding for global variable 'Var1' show_active_genesets_hist: no visible binding for global variable 'active_genesets' term_enrichment : process_source: no visible binding for global variable 'active_genesets' Undefined global functions or variables: Var1 Var2 active_genesets all_symbols geneset_list * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... 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, 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/RITAN.Rcheck/00check.log' for details.
RITAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RITAN ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'RITAN' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN' Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN' Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN' ** testing if installed package can be loaded from final location Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN' Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN' ** testing if installed package keeps a record of temporary installation path * DONE (RITAN)
RITAN.Rcheck/RITAN-Ex.timings
name | user | system | elapsed | |
as.graph | 0 | 0 | 0 | |
check_any_net_input | 2.22 | 0.13 | 2.36 | |
check_net_input | 0.04 | 0.00 | 0.05 | |
enrichment_symbols | 0.86 | 0.03 | 0.89 | |
geneset_overlap | 0.10 | 0.01 | 0.11 | |
icon_test | 0 | 0 | 0 | |
load_geneset_symbols | 0.01 | 0.00 | 0.02 | |
network_overlap | 0.03 | 0.00 | 0.03 | |
plot.term_enrichment | 1.97 | 0.66 | 2.80 | |
plot.term_enrichment_by_subset | 0.03 | 0.00 | 0.03 | |
readGMT | 0 | 0 | 0 | |
readSIF | 0 | 0 | 0 | |
resource_reduce | 2.94 | 0.28 | 3.22 | |
show_active_genesets_hist | 0.03 | 0.00 | 0.03 | |
summary.term_enrichment | 0.83 | 0.52 | 1.34 | |
summary.term_enrichment_by_subset | 1.45 | 1.18 | 2.64 | |
term_enrichment | 0.89 | 0.50 | 1.41 | |
term_enrichment_by_subset | 0.02 | 0.00 | 0.01 | |
vac1.day0vs31.de.genes | 0 | 0 | 0 | |
vac1.day0vs56.de.genes | 0 | 0 | 0 | |
vac2.day0vs31.de.genes | 0 | 0 | 0 | |
vac2.day0vs56.de.genes | 0 | 0 | 0 | |
writeGMT | 0 | 0 | 0 | |
write_simple_table | 0 | 0 | 0 | |