Sean Davis
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/BiocPkgTools |
| Branch: RELEASE_3_12 |
| Last Commit: f427c50 |
| Last Changed Date: 2021-04-13 15:30:49 -0400 (Tue, 13 Apr 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:30:01 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the BiocPkgTools package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 167/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocPkgTools 1.8.2 (landing page) Sean Davis
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: BiocPkgTools |
| Version: 1.8.2 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocPkgTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocPkgTools_1.8.2.tar.gz |
| StartedAt: 2021-05-06 00:51:27 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:02:45 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 677.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocPkgTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocPkgTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocPkgTools_1.8.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocPkgTools.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 'BiocPkgTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiocPkgTools' version '1.8.2'
* 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 'BiocPkgTools' 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
Namespace in Imports field not imported from: 'rappdirs'
All declared Imports should be used.
Unexported object imported by a ':::' call: 'BiocManager:::.repositories'
See the note in ?`:::` about the use of this operator.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_bioc_data 40.51 0.21 40.83
firstInBioc 23.99 0.17 24.20
biocDownloadStats 23.45 0.15 23.75
pkgCombDependencyGain 18.10 0.61 18.89
pkgDepMetrics 15.16 0.65 15.91
buildPkgDependencyDataFrame 13.05 0.06 13.17
biocBuildReport 10.22 0.11 22.00
inducedSubgraphByPkgs 8.81 0.06 8.91
githubURLParts 7.75 0.07 7.87
subgraphByDegree 6.98 0.02 7.01
githubDetails 6.64 0.08 52.86
getBiocVignette 6.58 0.07 6.80
buildPkgDependencyIgraph 6.56 0.06 6.64
biocPkgList 6.28 0.10 10.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_bioc_data 27.74 0.44 28.25
firstInBioc 22.95 0.31 23.34
biocDownloadStats 20.04 0.32 20.45
pkgCombDependencyGain 15.09 0.54 15.79
pkgDepMetrics 13.17 0.57 13.81
biocBuildReport 12.46 0.12 12.88
buildPkgDependencyDataFrame 10.41 0.22 10.71
githubDetails 7.14 0.08 21.25
inducedSubgraphByPkgs 6.32 0.03 6.36
githubURLParts 6.23 0.06 6.33
subgraphByDegree 5.67 0.02 5.75
buildPkgDependencyIgraph 5.50 0.11 5.63
biocPkgList 5.28 0.06 5.36
getBiocVignette 5.17 0.01 5.27
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocPkgTools.Rcheck/00check.log'
for details.
BiocPkgTools.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/BiocPkgTools_1.8.2.tar.gz && rm -rf BiocPkgTools.buildbin-libdir && mkdir BiocPkgTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocPkgTools.buildbin-libdir BiocPkgTools_1.8.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BiocPkgTools_1.8.2.zip && rm BiocPkgTools_1.8.2.tar.gz BiocPkgTools_1.8.2.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 272k 100 272k 0 0 2336k 0 --:--:-- --:--:-- --:--:-- 2348k
install for i386
* installing *source* package 'BiocPkgTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BiocPkgTools'
finding HTML links ... done
BiocPkgTools-cache html
BiocPkgTools html
CRANstatus html
biocBuildEmail html
biocBuildReport html
biocDownloadStats html
biocExplore html
biocPkgList html
buildPkgDependencyDataFrame html
buildPkgDependencyIgraph html
dataciteXMLGenerate html
dot-getDepGain html
firstInBioc html
generateBiocPkgDOI html
getBiocVignette html
getPackageInfo html
get_bioc_data html
githubDetails html
githubURLParts html
inducedSubgraphByPkgs html
pkgCombDependencyGain html
pkgDepImports html
pkgDepMetrics html
problemPage html
subgraphByDegree 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 'BiocPkgTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocPkgTools' as BiocPkgTools_1.8.2.zip
* DONE (BiocPkgTools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BiocPkgTools' successfully unpacked and MD5 sums checked
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BiocPkgTools.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(BiocPkgTools)
Loading required package: htmlwidgets
>
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.12/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1312841 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 21 ]
>
> proc.time()
user system elapsed
32.48 0.68 47.56
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BiocPkgTools.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(BiocPkgTools)
Loading required package: htmlwidgets
>
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.12/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1312841 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 21 ]
>
> proc.time()
user system elapsed
24.87 0.56 26.90
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BiocPkgTools.Rcheck/examples_i386/BiocPkgTools-Ex.timings
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BiocPkgTools.Rcheck/examples_x64/BiocPkgTools-Ex.timings
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