Gulden Olgun
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/NoRCE |
| git_branch: RELEASE_3_13 |
| git_last_commit: 1bfbc5e |
| git_last_commit_date: 2021-09-27 16:57:20 -0400 (Mon, 27 Sep 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:14 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the NoRCE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NoRCE.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 1276/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| NoRCE 1.4.0 (landing page) Gulden Olgun
| 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 | OK | OK | | ||||||||
| Package: NoRCE |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NoRCE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NoRCE_1.4.0.tar.gz |
| StartedAt: 2021-10-15 02:46:52 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:53:50 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 418.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: NoRCE.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:NoRCE.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings NoRCE_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/NoRCE.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 'NoRCE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NoRCE' version '1.4.0'
* package encoding: UTF-8
* 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 'NoRCE' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 'NoRCE-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WikiEnrichment
> ### Title: WikiPathways Enrichment
> ### Aliases: WikiEnrichment
>
> ### ** Examples
>
> a <- WikiEnrichment(genes = breastmRNA,org_assembly = "hg19")
Error in function (type, msg, asError = TRUE) :
SSL certificate problem: certificate has expired
Calls: WikiEnrichment ... <Anonymous> -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'NoRCE-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WikiEnrichment
> ### Title: WikiPathways Enrichment
> ### Aliases: WikiEnrichment
>
> ### ** Examples
>
> a <- WikiEnrichment(genes = breastmRNA,org_assembly = "hg19")
Error in function (type, msg, asError = TRUE) :
SSL certificate problem: certificate has expired
Calls: WikiEnrichment ... <Anonymous> -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/NoRCE.Rcheck/00check.log'
for details.
NoRCE.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/NoRCE_1.4.0.tar.gz && rm -rf NoRCE.buildbin-libdir && mkdir NoRCE.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NoRCE.buildbin-libdir NoRCE_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL NoRCE_1.4.0.zip && rm NoRCE_1.4.0.tar.gz NoRCE_1.4.0.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
6 1848k 6 113k 0 0 418k 0 0:00:04 --:--:-- 0:00:04 418k
67 1848k 67 1255k 0 0 988k 0 0:00:01 0:00:01 --:--:-- 989k
100 1848k 100 1848k 0 0 1170k 0 0:00:01 0:00:01 --:--:-- 1169k
install for i386
* installing *source* package 'NoRCE' ...
** 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 'NoRCE'
finding HTML links ... done
KeggEnrichment html
NoRCE-class html
WikiEnrichment html
annGO html
assembly html
brain_disorder_ncRNA html
brain_mirna html
breastmRNA html
calculateCorr html
convertGMT html
convertGeneID html
corrbased html
corrbasedMrna html
createNetwork html
drawDotPlot html
extractBiotype html
filterBiotype html
geneGOEnricher html
genePathwayEnricher html
geneRegionGOEnricher html
geneRegionPathwayEnricher html
getGoDag html
getKeggDiagram html
getNearToExon html
getNearToIntron html
getReactomeDiagram html
getTADOverlap html
getUCSC html
getmiRNACount html
goEnrichment html
listTAD html
mirna html
mirnaGOEnricher html
mirnaPathwayEnricher html
mirnaRegionGOEnricher html
mirnaRegionPathwayEnricher html
mrna html
ncRegion html
packageCheck html
pathwayEnrichment html
predictmiTargets html
reactomeEnrichment html
setParameters html
tad_dmel html
tad_hg19 html
tad_hg38 html
tad_mm10 html
topEnrichment html
writeEnrichment 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 'NoRCE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NoRCE' as NoRCE_1.4.0.zip
* DONE (NoRCE)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'NoRCE' successfully unpacked and MD5 sums checked
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NoRCE.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(NoRCE)
>
> test_check("NoRCE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
10.09 0.65 10.75
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NoRCE.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(NoRCE)
>
> test_check("NoRCE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
>
> proc.time()
user system elapsed
11.87 0.48 12.34
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NoRCE.Rcheck/examples_i386/NoRCE-Ex.timings
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NoRCE.Rcheck/examples_x64/NoRCE-Ex.timings
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