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CHECK report for RITAN on tokay1

This page was generated on 2021-05-06 12:33:17 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RITAN package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1535/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.14.0  (landing page)
Michael Zimmermann
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RITAN
Branch: RELEASE_3_12
Last Commit: 73d26c8
Last Changed Date: 2020-10-27 11:24:14 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RITAN
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RITAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RITAN_1.14.0.tar.gz
StartedAt: 2021-05-06 06:15:09 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:21:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 377.2 seconds
RetCode: 1
Status:   ERROR   
CheckDir: RITAN.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RITAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RITAN_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RITAN.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.14.0'
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'RITAN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.term_enrichment_by_subset
> ### Title: summary.term_enrichment_by_subset
> ### Aliases: summary.term_enrichment_by_subset
> 
> ### ** Examples
> 
> require(RITANdata)
Loading required package: RITANdata
> vac1.de.genes <- list(vac1.day0vs31.de.genes, vac1.day0vs56.de.genes)
> names(vac1.de.genes) <- c("Day0vs31", "Day0vs56")
> e <- term_enrichment_by_subset(vac1.de.genes, "MSigDB_Hallmarks", q_value_threshold = 0.1 )
Loading the requested genesets of "MSigDB_Hallmarks"...

	Loaded 50 genesets.
	Running Enrichment...Warning in file(file, "rt") :
  InternetOpenUrl failed: 'The login request was denied
'
Error in file(file, "rt") : cannot open the connection
Calls: term_enrichment_by_subset ... load_all_protein_coding_symbols -> read.table -> file
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
summary.term_enrichment_by_subset 31.54  14.70   47.83
enrichment_symbols                16.64   9.84   27.38
summary.term_enrichment           17.57   7.58   25.93
plot.term_enrichment              15.61   8.99   25.39
term_enrichment                   14.08   7.48   22.34
* 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 ERROR, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-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://172.29.0.3/BBS/3.12/bioc/src/contrib/RITAN_1.14.0.tar.gz && rm -rf RITAN.buildbin-libdir && mkdir RITAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RITAN.buildbin-libdir RITAN_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RITAN_1.14.0.zip && rm RITAN_1.14.0.tar.gz RITAN_1.14.0.zip
###
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  % 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  121k  100  121k    0     0  1719k      0 --:--:-- --:--:-- --:--:-- 1734k

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_1.14.0.zip
* DONE (RITAN)
* installing to library 'C:/Users/biocbuild/bbs-3.12-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_input1.300.076.48
check_net_input0.030.020.05
enrichment_symbols22.00 6.9832.86
geneset_overlap0.130.000.12
icon_test000
load_geneset_symbols0.000.020.02
network_overlap0.000.010.01
plot.term_enrichment20.98 8.6330.35
plot.term_enrichment_by_subset0.020.000.01
readGMT000
readSIF000
resource_reduce2.360.032.39
show_active_genesets_hist0.020.000.02
summary.term_enrichment22.33 8.5631.65

RITAN.Rcheck/examples_x64/RITAN-Ex.timings

nameusersystemelapsed
as.graph000
check_any_net_input1.500.071.58
check_net_input0.030.020.04
enrichment_symbols16.64 9.8427.38
geneset_overlap0.140.000.14
icon_test000
load_geneset_symbols0.020.000.02
network_overlap0.010.000.01
plot.term_enrichment15.61 8.9925.39
plot.term_enrichment_by_subset0.020.000.02
readGMT000
readSIF000
resource_reduce2.670.002.67
show_active_genesets_hist0.010.000.02
summary.term_enrichment17.57 7.5825.93
summary.term_enrichment_by_subset31.5414.7047.83
term_enrichment14.08 7.4822.34
term_enrichment_by_subset0.020.000.02
vac1.day0vs31.de.genes000
vac1.day0vs56.de.genes000
vac2.day0vs31.de.genes000
vac2.day0vs56.de.genes000
writeGMT000
write_simple_table000