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This page was generated on 2021-10-13 15:05:37 -0400 (Wed, 13 Oct 2021).

CHECK results for RITAN on tokay2

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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RITAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RITAN_1.16.0.tar.gz
StartedAt: 2021-10-13 04:12:45 -0400 (Wed, 13 Oct 2021)
EndedAt: 2021-10-13 04:20:12 -0400 (Wed, 13 Oct 2021)
EllapsedTime: 447.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RITAN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RITAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RITAN_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/RITAN.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
summary.term_enrichment_by_subset 44.64  15.10   61.46
term_enrichment                   24.88   8.75   34.45
summary.term_enrichment           24.04   8.79   33.64
plot.term_enrichment              21.97   8.27   31.03
enrichment_symbols                22.74   7.36   31.85
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
summary.term_enrichment_by_subset 30.23  18.89   50.86
term_enrichment                   14.24  10.08   25.16
summary.term_enrichment           15.89   8.37   25.16
enrichment_symbols                14.61   7.50   23.11
plot.term_enrichment              14.76   7.34   22.97
* 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: 2 NOTEs
See
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/RITAN_1.16.0.tar.gz && rm -rf RITAN.buildbin-libdir && mkdir RITAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RITAN.buildbin-libdir RITAN_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RITAN_1.16.0.zip && rm RITAN_1.16.0.tar.gz RITAN_1.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  122k  100  122k    0     0   640k      0 --:--:-- --:--:-- --:--:--  644k

install for i386

* 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
  converting help for package 'RITAN'
    finding HTML links ... done
    as.graph                                html  
    check_any_net_input                     html  
    check_net_input                         html  
    cov_undirected                          html  
    enrichment_symbols                      html  
    geneset_overlap                         html  
    icon_single_within                      html  
    icon_test                               html  
    load_all_protein_coding_symbols         html  
    load_geneset_symbols                    html  
    network_overlap                         html  
    plot.term_enrichment                    html  
    plot.term_enrichment_by_subset          html  
    readGMT                                 html  
    readSIF                                 html  
    resource_reduce                         html  
    show_active_genesets_hist               html  
    summary.term_enrichment                 html  
    summary.term_enrichment_by_subset       html  
    term_enrichment                         html  
    term_enrichment_by_subset               html  
    vac1.day0vs31.de.genes                  html  
    vac1.day0vs56.de.genes                  html  
    vac2.day0vs31.de.genes                  html  
    vac2.day0vs56.de.genes                  html  
    writeGMT                                html  
    write_simple_table                      html  
** 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

install for x64

* installing *source* package 'RITAN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RITAN' as RITAN_1.16.0.zip
* DONE (RITAN)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'RITAN' successfully unpacked and MD5 sums checked

Tests output


Example timings

RITAN.Rcheck/examples_i386/RITAN-Ex.timings

nameusersystemelapsed
as.graph000
check_any_net_input1.720.113.67
check_net_input0.080.000.08
enrichment_symbols22.74 7.3631.85
geneset_overlap0.140.000.14
icon_test000
load_geneset_symbols0.010.000.01
network_overlap0.050.010.07
plot.term_enrichment21.97 8.2731.03
plot.term_enrichment_by_subset0.030.000.03
readGMT000
readSIF000
resource_reduce3.000.043.05
show_active_genesets_hist0.030.000.03
summary.term_enrichment24.04 8.7933.64
summary.term_enrichment_by_subset44.6415.1061.46
term_enrichment24.88 8.7534.45
term_enrichment_by_subset0.020.000.01
vac1.day0vs31.de.genes000
vac1.day0vs56.de.genes000
vac2.day0vs31.de.genes000
vac2.day0vs56.de.genes000
writeGMT000
write_simple_table000

RITAN.Rcheck/examples_x64/RITAN-Ex.timings

nameusersystemelapsed
as.graph000
check_any_net_input1.580.061.64
check_net_input0.050.010.06
enrichment_symbols14.61 7.5023.11
geneset_overlap0.120.000.13
icon_test000
load_geneset_symbols000
network_overlap0.020.000.02
plot.term_enrichment14.76 7.3422.97
plot.term_enrichment_by_subset0.020.000.01
readGMT000
readSIF000
resource_reduce2.980.053.03
show_active_genesets_hist0.020.000.02
summary.term_enrichment15.89 8.3725.16
summary.term_enrichment_by_subset30.2318.8950.86
term_enrichment14.2410.0825.16
term_enrichment_by_subset000
vac1.day0vs31.de.genes000
vac1.day0vs56.de.genes000
vac2.day0vs31.de.genes000
vac2.day0vs56.de.genes000
writeGMT000
write_simple_table000