Zheng Wei
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/enrichTF |
| git_branch: RELEASE_3_13 |
| git_last_commit: 956c94b |
| git_last_commit_date: 2021-05-19 12:43:30 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the enrichTF package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/enrichTF.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 575/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| enrichTF 1.8.0 (landing page) Zheng Wei
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: enrichTF |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:enrichTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings enrichTF_1.8.0.tar.gz |
| StartedAt: 2021-10-14 22:44:40 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:56:17 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 697.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: enrichTF.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:enrichTF.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings enrichTF_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.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 'enrichTF/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'enrichTF' version '1.8.0'
* 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 'enrichTF' 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 ... NOTE
Warning in options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning in options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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
processing,TissueOpennessConserve: no visible binding for global
variable 'X2'
Undefined global functions or variables:
X2
* 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GeneOntology 19.18 2.09 21.35
TissueOpennessSpecificity 16.96 0.08 17.15
GenBackground 5.73 1.58 24.66
Pipelines 1.84 0.20 18.33
MotifsInRegions 1.72 0.10 19.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TissueOpennessSpecificity 21.31 0.05 21.38
GeneOntology 15.12 0.95 16.10
GenBackground 5.59 1.29 13.50
Pipelines 1.72 0.17 18.16
MotifsInRegions 1.36 0.11 19.48
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.Rcheck/00check.log'
for details.
enrichTF.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/enrichTF_1.8.0.tar.gz && rm -rf enrichTF.buildbin-libdir && mkdir enrichTF.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=enrichTF.buildbin-libdir enrichTF_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL enrichTF_1.8.0.zip && rm enrichTF_1.8.0.tar.gz enrichTF_1.8.0.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
28 1005k 28 290k 0 0 907k 0 0:00:01 --:--:-- 0:00:01 909k
100 1005k 100 1005k 0 0 1461k 0 --:--:-- --:--:-- --:--:-- 1461k
install for i386
* installing *source* package 'enrichTF' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'enrichTF'
finding HTML links ... done
EnrichStep-class html
GenBackground html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/genBackground.html
finding level-2 HTML links ... done
GeneOntology html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/geneOntology.html
MotifsInRegions html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/motifsInRegions.html
Pipelines html
RegionConnectTargetGene html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/regionConnectTargetGene.html
SingleSampleReport html
TFsEnrichInRegions html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/tfsEnrichInRegions.html
TissueOpennessConserve html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/tissueOpennessConserve.html
TissueOpennessSpecificity html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/tissueOpennessSpecificity.html
UnzipAndMergeBed html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/enrichTF.buildbin-libdir/00LOCK-enrichTF/00new/enrichTF/help/unzipAndMergeBed.html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package can be loaded from final location
Warning in options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'enrichTF' ...
** testing if installed package can be loaded
Warning in options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
* MD5 sums
packaged installation of 'enrichTF' as enrichTF_1.8.0.zip
* DONE (enrichTF)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'enrichTF' successfully unpacked and MD5 sums checked
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enrichTF.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(enrichTF)
Loading required package: pipeFrame
Warning message:
In options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
>
> test_check("enrichTF")
[1] "2021-10-14 22:55:01 EDT"
[1] "2021-10-14 22:55:01 EDT"
[1] "2021-10-14 22:55:01 EDT"
[1] "2021-10-14 22:55:01 EDT"
[1] "2021-10-14 22:55:01 EDT"
[1] "2021-10-14 22:55:01 EDT"
[1] "2021-10-14 22:55:03 EDT"
[1] "2021-10-14 22:55:03 EDT"
[1] "2021-10-14 22:55:03 EDT"
[1] "2021-10-14 22:55:03 EDT"
[1] "2021-10-14 22:55:03 EDT"
[1] "2021-10-14 22:55:03 EDT"
[1] "2021-10-14 22:55:19 EDT"
[1] "2021-10-14 22:55:19 EDT"
[1] "2021-10-14 22:55:19 EDT"
[1] "2021-10-14 22:55:19 EDT"
[1] "2021-10-14 22:55:19 EDT"
[1] "2021-10-14 22:55:19 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
>
> proc.time()
user system elapsed
22.06 3.25 72.53
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enrichTF.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(enrichTF)
Loading required package: pipeFrame
Warning message:
In options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
>
> test_check("enrichTF")
[1] "2021-10-14 22:55:48 EDT"
[1] "2021-10-14 22:55:48 EDT"
[1] "2021-10-14 22:55:48 EDT"
[1] "2021-10-14 22:55:48 EDT"
[1] "2021-10-14 22:55:48 EDT"
[1] "2021-10-14 22:55:48 EDT"
[1] "2021-10-14 22:55:50 EDT"
[1] "2021-10-14 22:55:50 EDT"
[1] "2021-10-14 22:55:50 EDT"
[1] "2021-10-14 22:55:50 EDT"
[1] "2021-10-14 22:55:50 EDT"
[1] "2021-10-14 22:55:50 EDT"
[1] "2021-10-14 22:56:10 EDT"
[1] "2021-10-14 22:56:10 EDT"
[1] "2021-10-14 22:56:10 EDT"
[1] "2021-10-14 22:56:10 EDT"
[1] "2021-10-14 22:56:10 EDT"
[1] "2021-10-14 22:56:10 EDT"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
>
> proc.time()
user system elapsed
22.01 2.03 50.12
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enrichTF.Rcheck/examples_i386/enrichTF-Ex.timings
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enrichTF.Rcheck/examples_x64/enrichTF-Ex.timings
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