Michael Zimmermann
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 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) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:19 -0400 (Fri, 15 Oct 2021).
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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. |
| Package 1588/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RITAN 1.16.0 (landing page) Michael Zimmermann
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| 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: 2021-10-15 04:37:34 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:39:28 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 113.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: RITAN.Rcheck |
| Warnings: NA |
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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
###
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* 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' ... 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
> 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
> 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
* 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-3.13-bioc/meat/RITAN.Rcheck/00check.log'
for details.
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
###
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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 122k 100 122k 0 0 641k 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
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RITAN.Rcheck/examples_i386/RITAN-Ex.timings
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RITAN.Rcheck/examples_x64/RITAN-Ex.timings
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