Back to Build/check report for BioC 3.15
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-06-27 11:09:56 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 nebbiolo1


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 818/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GmicR 1.10.0  (landing page)
Richard Virgen-Slane
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/GmicR
git_branch: RELEASE_3_15
git_last_commit: e27e644
git_last_commit_date: 2022-04-26 11:59:44 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: GmicR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GmicR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GmicR_1.10.0.tar.gz
StartedAt: 2022-06-26 20:06:22 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:21:58 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 936.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GmicR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GmicR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GmicR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GmicR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GmicR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GmicR’ version ‘1.10.0’
* 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 ... 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-3.15-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 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 45.849 12.661 591.302
Auto_WGCNA     13.188  1.107  14.014
InverseARCs     5.657  0.086   5.745
bn_tabu_gen     0.066  0.000 172.087
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/GmicR.Rcheck/00check.log’
for details.



Installation output

GmicR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GmicR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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_WGCNA13.188 1.10714.014
Data_Prep0.1960.0480.244
GO_Module_NameR0.0270.0040.033
GSEAGO_Builder 45.849 12.661591.302
Gmic_viz0.0240.0010.027
InverseARCs5.6570.0865.745
Query_Prep0.2720.1190.257
bn_tabu_gen 0.066 0.000172.087
xCell_loader0.0160.0040.019