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This page was generated on 2023-04-07 11:05:32 -0400 (Fri, 07 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4499
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4279
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4307
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

CHECK results for GmicR on nebbiolo2


To the developers/maintainers of the GmicR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 831/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GmicR 1.12.0  (landing page)
Richard Virgen-Slane
Snapshot Date: 2023-04-05 14:00:05 -0400 (Wed, 05 Apr 2023)
git_url: https://git.bioconductor.org/packages/GmicR
git_branch: RELEASE_3_16
git_last_commit: 729668d
git_last_commit_date: 2022-11-01 11:20:38 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GmicR
Version: 1.12.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:GmicR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings GmicR_1.12.0.tar.gz
StartedAt: 2023-04-05 20:54:02 -0400 (Wed, 05 Apr 2023)
EndedAt: 2023-04-05 21:20:58 -0400 (Wed, 05 Apr 2023)
EllapsedTime: 1615.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GmicR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:GmicR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings GmicR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/GmicR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘GmicR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GmicR’ version ‘1.12.0’
* 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-3.16-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 44.747 10.968 640.738
Auto_WGCNA     13.325  0.301  13.377
InverseARCs     4.965  0.065   5.030
bn_tabu_gen     0.055  0.012 160.604
* 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-3.16-bioc/meat/GmicR.Rcheck/00check.log’
for details.



Installation output

GmicR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL GmicR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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)

Tests output


Example timings

GmicR.Rcheck/GmicR-Ex.timings

nameusersystemelapsed
Auto_WGCNA13.325 0.30113.377
Data_Prep0.1920.0080.200
GO_Module_NameR0.0220.0080.031
GSEAGO_Builder 44.747 10.968640.738
Gmic_viz0.0250.0000.024
InverseARCs4.9650.0655.030
Query_Prep0.4990.0490.246
bn_tabu_gen 0.055 0.012160.604
xCell_loader0.0110.0080.019