Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:35:24 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 853/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GmicR 1.14.0 (landing page) Richard Virgen-Slane
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the GmicR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GmicR.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: GmicR |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GmicR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GmicR_1.14.0.tar.gz |
StartedAt: 2023-10-15 21:44:21 -0400 (Sun, 15 Oct 2023) |
EndedAt: 2023-10-15 22:08:49 -0400 (Sun, 15 Oct 2023) |
EllapsedTime: 1467.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GmicR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GmicR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GmicR_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GmicR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘GmicR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GmicR’ 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 ‘GmicR’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ape::degree’ by ‘bnlearn::degree’ when loading ‘GmicR’ See ‘/home/biocbuild/bbs-3.17-bioc/meat/GmicR.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components with restrictions not permitted: GPL-2 + file LICENSE * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘data.table’ 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 GSEAGO_Builder: no visible binding for global variable ‘ex’ Undefined global functions or variables: ex * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed GSEAGO_Builder 45.815 11.673 541.353 Auto_WGCNA 11.487 0.276 11.689 bn_tabu_gen 0.039 0.005 179.059 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GmicR_vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/GmicR.Rcheck/00check.log’ for details.
GmicR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GmicR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘GmicR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘ape::degree’ by ‘bnlearn::degree’ when loading ‘GmicR’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘ape::degree’ by ‘bnlearn::degree’ when loading ‘GmicR’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘ape::degree’ by ‘bnlearn::degree’ when loading ‘GmicR’ ** testing if installed package keeps a record of temporary installation path * DONE (GmicR)
GmicR.Rcheck/GmicR-Ex.timings
name | user | system | elapsed | |
Auto_WGCNA | 11.487 | 0.276 | 11.689 | |
Data_Prep | 0.184 | 0.052 | 0.237 | |
GO_Module_NameR | 0.032 | 0.000 | 0.033 | |
GSEAGO_Builder | 45.815 | 11.673 | 541.353 | |
Gmic_viz | 0.026 | 0.000 | 0.028 | |
InverseARCs | 4.669 | 0.060 | 4.730 | |
Query_Prep | 0.342 | 0.041 | 0.281 | |
bn_tabu_gen | 0.039 | 0.005 | 179.059 | |
xCell_loader | 0.02 | 0.00 | 0.02 | |