Anthony Federico
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/hypeR |
| Branch: RELEASE_3_12 |
| Last Commit: a4fdcb4 |
| Last Changed Date: 2020-10-27 11:43:24 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:47 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the hypeR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 855/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| hypeR 1.6.0 (landing page) Anthony Federico
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: hypeR |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings hypeR_1.6.0.tar.gz |
| StartedAt: 2021-05-06 03:43:14 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:47:47 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 273.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: hypeR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings hypeR_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/hypeR.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 'hypeR/DESCRIPTION' ... OK
* this is package 'hypeR' version '1.6.0'
* 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 'hypeR' 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 ... NOTE
.dots_multi_plot : <anonymous>: no visible binding for global variable
'pval'
.dots_multi_plot : <anonymous>: no visible binding for global variable
'fdr'
.dots_multi_plot : <anonymous>: no visible binding for global variable
'label'
.dots_multi_plot: no visible global function definition for 'head'
.dots_multi_plot: no visible binding for global variable 'significance'
.dots_multi_plot: no visible binding for global variable 'signature'
.dots_multi_plot: no visible binding for global variable 'label'
.dots_multi_plot: no visible binding for global variable 'size'
.dots_plot: no visible binding for global variable 'pval'
.dots_plot: no visible binding for global variable 'fdr'
.dots_plot: no visible binding for global variable 'significance'
.dots_plot: no visible binding for global variable 'size'
.enrichment_map: no visible binding for global variable 'pval'
.enrichment_map: no visible binding for global variable 'fdr'
.find_members: no visible binding for global variable 'from'
.find_members: no visible binding for global variable 'to'
.hiearchy_map: no visible binding for global variable 'pval'
.hiearchy_map: no visible binding for global variable 'fdr'
.hiearchy_map : <anonymous>: no visible binding for global variable
'label'
.hyper_enrichment: no visible global function definition for 'is'
.ks_enrichment: no visible global function definition for 'is'
enrichr_available: no visible binding for global variable '.'
ggvenn: no visible binding for global variable 'x'
ggvenn: no visible binding for global variable 'y'
hyp_dots: no visible global function definition for 'is'
hyp_emap: no visible global function definition for 'is'
hyp_hmap: no visible global function definition for 'is'
hyp_show: no visible global function definition for 'is'
hyp_to_excel: no visible global function definition for 'is'
hyp_to_rmd: no visible global function definition for 'is'
hyp_to_rmd : <anonymous>: no visible global function definition for
'is'
hyp_to_table: no visible global function definition for 'is'
hyp_to_table: no visible global function definition for 'write.table'
hypeR: no visible global function definition for 'is'
hypeR: no visible global function definition for 'packageVersion'
hypeR: no visible global function definition for 'head'
msigdb_available: no visible binding for global variable 'gs_cat'
msigdb_available: no visible binding for global variable 'gs_subcat'
msigdb_download: no visible binding for global variable 'gs_name'
msigdb_download: no visible binding for global variable 'gene_symbol'
msigdb_download: no visible binding for global variable '.'
msigdb_version: no visible global function definition for
'packageVersion'
rctbl_build: no visible global function definition for 'is'
Undefined global functions or variables:
. fdr from gene_symbol gs_cat gs_name gs_subcat head is label
packageVersion pval signature significance size to write.table x y
Consider adding
importFrom("methods", "is", "signature")
importFrom("utils", "head", "packageVersion", "write.table")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'hypeR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichr_available
> ### Title: Get enrichr available genesets
> ### Aliases: enrichr_available
>
> ### ** Examples
>
> enrichr_available()
Error in curl::curl_fetch_memory(url, handle = handle) :
schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake failed).
Calls: enrichr_available ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'hypeR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichr_available
> ### Title: Get enrichr available genesets
> ### Aliases: enrichr_available
>
> ### ** Examples
>
> enrichr_available()
Error in curl::curl_fetch_memory(url, handle = handle) :
schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake failed).
Calls: enrichr_available ... request_fetch -> request_fetch.write_memory -> <Anonymous>
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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/hypeR.Rcheck/00check.log'
for details.
hypeR.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/hypeR_1.6.0.tar.gz && rm -rf hypeR.buildbin-libdir && mkdir hypeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hypeR.buildbin-libdir hypeR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL hypeR_1.6.0.zip && rm hypeR_1.6.0.tar.gz hypeR_1.6.0.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 412k 100 412k 0 0 14.9M 0 --:--:-- --:--:-- --:--:-- 15.4M
install for i386
* installing *source* package 'hypeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'hypeR'
finding HTML links ... done
clean_genesets html
dot-check_overlap html
dot-dots_multi_plot html
dot-dots_plot html
dot-enrichment_map html
dot-find_members html
dot-format_str html
dot-hiearchy_map html
dot-hyper_enrichment html
dot-jaccard_similarity html
dot-ks_enrichment html
dot-kstest html
dot-overlap_similarity html
dot-reverselog_trans html
dot-string_args html
enrichr_available html
enrichr_connect html
enrichr_download html
enrichr_gsets html
enrichr_urls html
genesets_Server html
genesets_UI html
ggempty html
ggeplot html
ggvenn html
gsets html
hyp html
hyp_dots html
hyp_emap html
hyp_hmap html
hyp_show html
hyp_to_excel html
hyp_to_rmd html
hyp_to_table html
hypeR html
hyperdb_info html
hyperdb_rgsets html
limma html
msigdb_available html
msigdb_check_species html
msigdb_download html
msigdb_gsets html
msigdb_info html
msigdb_species html
msigdb_version html
multihyp html
pvector html
rctbl_build html
rctbl_hyp html
rctbl_mhyp html
rgsets html
wgcna 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 'hypeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hypeR' as hypeR_1.6.0.zip
* DONE (hypeR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'hypeR' successfully unpacked and MD5 sums checked
|
hypeR.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(magrittr)
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
> library(hypeR)
>
> test_check("hypeR")
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 409 ]
>
> proc.time()
user system elapsed
42.96 2.67 78.03
|
hypeR.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(magrittr)
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
> library(hypeR)
>
> test_check("hypeR")
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"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS lmultihyp.3.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output lmultihyp.3.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpiypcBM\rmarkdown-str11343aa5dec.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1
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"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS hyp.4.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output hyp.4.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpiypcBM\rmarkdown-str1134662a4d40.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1
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"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS multihyp.4.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output multihyp.4.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpiypcBM\rmarkdown-str1134c105f14.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1
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"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS combo.1.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.1.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpiypcBM\rmarkdown-str11344fbb3c87.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1
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"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS combo.3.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output combo.3.html --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --variable toc_float=1 --variable toc_selectors=h1 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\biocbuild\bbs-3.12-bioc\R\library\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=united --include-in-header "C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpiypcBM\rmarkdown-str113451701628.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --variable code_folding=hide --variable code_menu=1
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 409 ]
>
> proc.time()
user system elapsed
53.18 3.31 77.67
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hypeR.Rcheck/examples_i386/hypeR-Ex.timings
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hypeR.Rcheck/examples_x64/hypeR-Ex.timings
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