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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 871/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GmicR 1.21.0  (landing page)
Richard Virgen-Slane
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/GmicR
git_branch: devel
git_last_commit: 84bfd05
git_last_commit_date: 2024-10-29 10:40:33 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for GmicR on kjohnson3

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.

raw results


Summary

Package: GmicR
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GmicR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GmicR_1.21.0.tar.gz
StartedAt: 2024-12-23 19:33:38 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 19:39:57 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 378.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GmicR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GmicR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GmicR_1.21.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GmicR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GmicR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GmicR’ version ‘1.21.0’
* 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 ‘/Users/biocbuild/bbs-3.21-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 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
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 17.961  6.257 225.685
Auto_WGCNA      5.159  0.100   5.235
bn_tabu_gen     0.017  0.004  76.286
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/GmicR.Rcheck/00check.log’
for details.


Installation output

GmicR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GmicR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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)

Tests output


Example timings

GmicR.Rcheck/GmicR-Ex.timings

nameusersystemelapsed
Auto_WGCNA5.1590.1005.235
Data_Prep0.1010.0110.113
GO_Module_NameR0.0130.0010.015
GSEAGO_Builder 17.961 6.257225.685
Gmic_viz0.0120.0000.013
InverseARCs1.7300.0281.760
Query_Prep0.0930.0240.099
bn_tabu_gen 0.017 0.00476.286
xCell_loader0.0060.0010.007