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This page was generated on 2021-10-13 15:06:05 -0400 (Wed, 13 Oct 2021).

CHECK results for RITAN on machv2

To the developers/maintainers of the RITAN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RITAN.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1588/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.16.0  (landing page)
Michael Zimmermann
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/RITAN
git_branch: RELEASE_3_13
git_last_commit: ded8612
git_last_commit_date: 2021-05-19 12:27:48 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RITAN
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RITAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RITAN_1.16.0.tar.gz
StartedAt: 2021-10-12 23:01:09 -0400 (Tue, 12 Oct 2021)
EndedAt: 2021-10-12 23:03:09 -0400 (Tue, 12 Oct 2021)
EllapsedTime: 119.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RITAN.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RITAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RITAN_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/RITAN.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RITAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RITAN’ version ‘1.16.0’
* 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 ... 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 ‘RITAN’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BgeeDB’ ‘knitr’
  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
icon_test: no visible global function definition for ‘is’
network_overlap: no visible global function definition for ‘is’
network_overlap : map.input.to.STRING: no visible global function
  definition for ‘is’
plot.term_enrichment_by_subset: no visible global function definition
  for ‘is’
plot.term_enrichment_by_subset: no visible binding for global variable
  ‘Var2’
plot.term_enrichment_by_subset: no visible binding for global variable
  ‘Var1’
readSIF: no visible global function definition for ‘is’
term_enrichment_by_subset: no visible global function definition for
  ‘is’
writeGMT: no visible global function definition for ‘is’
Undefined global functions or variables:
  Var1 Var2 is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
enrichment_symbols                2.080  0.082   5.029
summary.term_enrichment_by_subset 1.993  0.107   9.710
summary.term_enrichment           1.109  0.078   8.318
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/RITAN.Rcheck/00check.log’
for details.



Installation output

RITAN.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RITAN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘RITAN’ ...
** 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 (RITAN)

Tests output


Example timings

RITAN.Rcheck/RITAN-Ex.timings

nameusersystemelapsed
as.graph0.0010.0010.001
check_any_net_input1.6510.0571.710
check_net_input0.0550.0070.062
enrichment_symbols2.0800.0825.029
geneset_overlap0.2000.0100.211
icon_test0.0000.0000.001
load_geneset_symbols0.0090.0000.010
network_overlap0.0230.0020.025
plot.term_enrichment1.3710.0694.118
plot.term_enrichment_by_subset0.0240.0010.026
readGMT0.0000.0000.001
readSIF0.0000.0000.001
resource_reduce4.3420.1884.539
show_active_genesets_hist0.0310.0020.033
summary.term_enrichment1.1090.0788.318
summary.term_enrichment_by_subset1.9930.1079.710
term_enrichment0.9670.0554.274
term_enrichment_by_subset0.0180.0020.020
vac1.day0vs31.de.genes000
vac1.day0vs56.de.genes0.0010.0000.000
vac2.day0vs31.de.genes000
vac2.day0vs56.de.genes000
writeGMT000
write_simple_table0.0010.0000.001