| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the chipenrich package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chipenrich.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 292/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| chipenrich 2.16.0 (landing page) Raymond G. Cavalcante
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: chipenrich |
| Version: 2.16.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chipenrich_2.16.0.tar.gz |
| StartedAt: 2021-10-14 20:59:09 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:11:13 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 724.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: chipenrich.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chipenrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings chipenrich_2.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/chipenrich.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 'chipenrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chipenrich' version '2.16.0'
* 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 'chipenrich' 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 ... WARNING
Codoc mismatches from documentation object 'hybridenrich':
hybridenrich
Code: function(peaks, out_name = "hybridenrich", out_path = getwd(),
genome = supported_genomes(), genesets = c("GOBP",
"GOCC", "GOMF"), locusdef = "nearest_tss", methods =
c("chipenrich", "polyenrich"), weighting = NULL,
mappability = NULL, qc_plots = TRUE, min_geneset_size
= 15, max_geneset_size = 2000, num_peak_threshold = 1,
randomization = NULL, n_cores = 1)
Docs: function(peaks, out_name = "hybridenrich", out_path = getwd(),
genome = supported_genomes(), genesets = c("GOBP",
"GOCC", "GOMF"), locusdef = "nearest_tss", methods =
c("chipenrich", "polyenrich"), weighting = NULL,
mappability = NULL, qc_plots = TRUE, min_geneset_size
= 15, max_geneset_size = 2000, num_peak_threshold = 1,
randomization = NULL, n_cores = 1, uuid = NULL)
Argument names in docs not in code:
uuid
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'hybridenrich'
'uuid'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
broadenrich 8.83 0.23 9.10
polyenrich 7.29 0.06 7.35
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
broadenrich 8.03 0.08 8.11
polyenrich 7.52 0.03 7.55
* 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 WARNINGs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/chipenrich.Rcheck/00check.log'
for details.
chipenrich.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/chipenrich_2.16.0.tar.gz && rm -rf chipenrich.buildbin-libdir && mkdir chipenrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chipenrich.buildbin-libdir chipenrich_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL chipenrich_2.16.0.zip && rm chipenrich_2.16.0.tar.gz chipenrich_2.16.0.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 115k 100 115k 0 0 605k 0 --:--:-- --:--:-- --:--:-- 610k
install for i386
* installing *source* package 'chipenrich' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'chipenrich'
finding HTML links ... done
assign_peak_segments html
assign_peaks html
broadenrich html
calc_peak_gene_overlap html
chipenrich html
chipenrich_package html
filter_genesets html
genome_to_organism html
genome_to_orgdb html
get_test_method html
hybridenrich html
load_peaks html
num_peaks_per_gene html
peaks2genes html
plot_chipenrich_spline html
plot_dist_to_tss html
plot_gene_coverage html
plot_polyenrich_spline html
polyenrich html
post_process_enrichments html
postprocess_peak_grs html
proxReg html
read_bed html
read_geneset html
read_ldef html
read_mappa html
recode_peaks html
reset_ncores_for_windows html
setup_genesets html
setup_locusdef html
setup_mappa html
supported_genesets html
supported_genomes html
supported_locusdefs html
supported_methods html
supported_read_lengths 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 'chipenrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipenrich' as chipenrich_2.16.0.zip
* DONE (chipenrich)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'chipenrich' successfully unpacked and MD5 sums checked
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chipenrich.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(chipenrich)
>
> test_check("chipenrich")
== Skipped tests ===============================================================
* empty test (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ]
>
> proc.time()
user system elapsed
148.37 3.89 154.65
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chipenrich.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(chipenrich)
>
> test_check("chipenrich")
== Skipped tests ===============================================================
* empty test (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 170 ]
>
> proc.time()
user system elapsed
174.04 2.71 176.81
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chipenrich.Rcheck/examples_i386/chipenrich-Ex.timings
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chipenrich.Rcheck/examples_x64/chipenrich-Ex.timings
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