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This page was generated on 2021-10-16 15:58:41 -0400 (Sat, 16 Oct 2021).

CHECK results for MetaGxOvarian on malbec2

To the developers/maintainers of the MetaGxOvarian package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 226/406HostnameOS / ArchINSTALLBUILDCHECK
MetaGxOvarian 1.12.0  (landing page)
Michael Zon
Snapshot Date: 2021-10-16 09:30:07 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/MetaGxOvarian
git_branch: RELEASE_3_13
git_last_commit: 83cbe19
git_last_commit_date: 2021-05-19 12:04:15 -0400 (Wed, 19 May 2021)
malbec2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: MetaGxOvarian
Version: 1.12.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MetaGxOvarian.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MetaGxOvarian_1.12.0.tar.gz
StartedAt: 2021-10-16 13:30:49 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 13:36:31 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 342.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MetaGxOvarian.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MetaGxOvarian.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MetaGxOvarian_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/MetaGxOvarian.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaGxOvarian/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaGxOvarian’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase', 'lattice', 'impute', 'AnnotationHub', 'ExperimentHub',
  'SummarizedExperiment'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MetaGxOvarian’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
loadOvarianEsets    72.507  1.385  82.094
loadOvarianDatasets 68.207  1.285  80.386
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘required.R’
 OK
* 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without hyperrefs or index ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/MetaGxOvarian.Rcheck/00check.log’
for details.



Installation output

MetaGxOvarian.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MetaGxOvarian
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘MetaGxOvarian’ ...
** using staged installation
** R
** 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 (MetaGxOvarian)

Tests output

MetaGxOvarian.Rcheck/tests/required.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #
> 
> proc.time()
   user  system elapsed 
  0.143   0.030   0.159 

Example timings

MetaGxOvarian.Rcheck/MetaGxOvarian-Ex.timings

nameusersystemelapsed
loadOvarianDatasets68.207 1.28580.386
loadOvarianEsets72.507 1.38582.094