Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:12 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 omicRexposome on nebbiolo2


To the developers/maintainers of the omicRexposome package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/omicRexposome.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 1387/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omicRexposome 1.20.0  (landing page)
Xavier Escribà Montagut
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/omicRexposome
git_branch: RELEASE_3_16
git_last_commit: 351df06
git_last_commit_date: 2022-11-01 11:16:28 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: omicRexposome
Version: 1.20.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:omicRexposome.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings omicRexposome_1.20.0.tar.gz
StartedAt: 2023-04-10 22:27:07 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:41:33 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 866.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: omicRexposome.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:omicRexposome.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings omicRexposome_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/omicRexposome.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 ‘omicRexposome/DESCRIPTION’ ... OK
* this is package ‘omicRexposome’ version ‘1.20.0’
* 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 ‘omicRexposome’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
association-methods 10.362  0.244  10.606
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘exposome_omic_integration.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘exposome_omic_integration.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/omicRexposome.Rcheck/00check.log’
for details.


Installation output

omicRexposome.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘omicRexposome’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (omicRexposome)

Tests output


Example timings

omicRexposome.Rcheck/omicRexposome-Ex.timings

nameusersystemelapsed
add_cls-methods0.1320.0000.135
add_exp-methods0.0350.0040.043
asr0.0310.0000.031
association-methods10.362 0.24410.606
crossomics-methods0.2550.0000.255
crs0.0020.0000.003
getIntegration-methods0.0030.0000.002
mds0.0070.0000.006
plotAssociation-methods0.3340.0120.346
plotHits-methods0.1380.0520.190
plotIntegration-methods0.5900.0920.681
plotLambda-methods0.1650.0040.169
tableHits-methods0.0480.0040.053
tableLambda-methods0.0530.0000.054