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This page was generated on 2022-01-24 13:06:53 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 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 1614/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.18.0  (landing page)
Michael Zimmermann
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/RITAN
git_branch: RELEASE_3_14
git_last_commit: e2ef1ac
git_last_commit_date: 2021-10-26 12:35:18 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RITAN
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RITAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RITAN_1.18.0.tar.gz
StartedAt: 2022-01-24 01:18:34 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 01:21:56 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 202.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: RITAN.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RITAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RITAN_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RITAN.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.18.0'
* 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' ... ERROR
Running examples in 'RITAN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichment_symbols
> ### Title: enrichment_symbols
> ### Aliases: enrichment_symbols
> 
> ### ** Examples
> 
> require(RITANdata)
Loading required package: RITANdata
Warning: Package 'RITANdata' is deprecated and will be removed from Bioconductor
  version 3.15
> myGeneSet <- c('BRCA1','RAD51C','VAV1','HRAS','ABCC1','CYP1B1','CYP3A5')
> 
> ## Not run: 
> ##D ## We suggest using term_enrichment() instead. E.g.:
> ##D e <- enrichment_symbols(myGeneSet, 'GO')
> ## End(Not run)
> 
> ## But, you may use enrichment_symbols() directly for an individual term:
> load_geneset_symbols('GO')
Loading the requested genesets of "GO"...

	Loaded 15831 genesets.
> e <- enrichment_symbols(myGeneSet, 'DNA_repair')
Warning in file(file, "rt") :
  the 'wininet' method of url() is deprecated for ftp:// URLs
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'A connection with the server could not be established
'
Error in file(file, "rt") : cannot open the connection
Calls: enrichment_symbols ... load_all_protein_coding_symbols -> read.table -> file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'RITAN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichment_symbols
> ### Title: enrichment_symbols
> ### Aliases: enrichment_symbols
> 
> ### ** Examples
> 
> require(RITANdata)
Loading required package: RITANdata
Warning: Package 'RITANdata' is deprecated and will be removed from Bioconductor
  version 3.15
> myGeneSet <- c('BRCA1','RAD51C','VAV1','HRAS','ABCC1','CYP1B1','CYP3A5')
> 
> ## Not run: 
> ##D ## We suggest using term_enrichment() instead. E.g.:
> ##D e <- enrichment_symbols(myGeneSet, 'GO')
> ## End(Not run)
> 
> ## But, you may use enrichment_symbols() directly for an individual term:
> load_geneset_symbols('GO')
Loading the requested genesets of "GO"...

	Loaded 15831 genesets.
> e <- enrichment_symbols(myGeneSet, 'DNA_repair')
Warning in file(file, "rt") :
  the 'wininet' method of url() is deprecated for ftp:// URLs
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'The connection with the server was reset
'
Error in file(file, "rt") : cannot open the connection
Calls: enrichment_symbols ... load_all_protein_coding_symbols -> read.table -> file
Execution halted
* 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 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RITAN.Rcheck/00check.log'
for details.


Installation output

RITAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RITAN_1.18.0.tar.gz && rm -rf RITAN.buildbin-libdir && mkdir RITAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RITAN.buildbin-libdir RITAN_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RITAN_1.18.0.zip && rm RITAN_1.18.0.tar.gz RITAN_1.18.0.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
  3  121k    3  3837    0     0  47875      0  0:00:02 --:--:--  0:00:02 47962
100  121k  100  121k    0     0   649k      0 --:--:-- --:--:-- --:--:--  650k

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_1.18.0.zip
* DONE (RITAN)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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_input1.540.061.76
check_net_input0.050.010.06

RITAN.Rcheck/examples_x64/RITAN-Ex.timings

nameusersystemelapsed
as.graph000
check_any_net_input1.700.051.75
check_net_input0.060.000.06