| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:14 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the biocViews package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biocViews.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 173/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biocViews 1.62.1 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: biocViews |
| Version: 1.62.1 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings biocViews_1.62.1.tar.gz |
| StartedAt: 2022-04-12 16:20:22 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:24:49 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 267.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biocViews.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings biocViews_1.62.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/biocViews.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biocViews/DESCRIPTION' ... OK
* this is package 'biocViews' version '1.62.1'
* 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 'biocViews' 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
':::' call which should be '::': 'tools:::vignetteInfo'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'tools:::.build_news_db_from_package_NEWS_Rd'
'tools:::.build_news_db_from_package_NEWS_md'
'tools:::.build_repository_package_db'
'tools:::.expand_package_description_db_R_fields'
'tools:::.get_standard_repository_db_fields'
'tools:::.news_reader_default' 'tools:::.read_description'
'tools:::.split_dependencies'
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 ... NOTE
getPackageNEWS : getNews: no visible binding for global variable
'Version'
getReverseDepends : <anonymous>: no visible binding for global variable
'Package'
Undefined global functions or variables:
Package Version
* 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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... 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
recommendPackages 12.31 4.58 17.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
recommendPackages 7.86 5.88 13.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/biocViews.Rcheck/00check.log'
for details.
biocViews.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/biocViews_1.62.1.tar.gz && rm -rf biocViews.buildbin-libdir && mkdir biocViews.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biocViews.buildbin-libdir biocViews_1.62.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL biocViews_1.62.1.zip && rm biocViews_1.62.1.tar.gz biocViews_1.62.1.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
58 75503 58 44362 0 0 281k 0 --:--:-- --:--:-- --:--:-- 281k
100 75503 100 75503 0 0 146k 0 --:--:-- --:--:-- --:--:-- 146k
install for i386
* installing *source* package 'biocViews' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'biocViews'
finding HTML links ... done
BiocView-class html
Htmlized-class html
PackageDetail-class html
RepositoryDetail-class html
biocViews-package html
biocViewsVocab html
extractManuals html
extractNEWS html
extractTopLevelFiles html
extractVignettes html
genReposControlFiles html
getBiocSubViews html
getBiocViews html
getCurrentbiocViews html
getPackageNEWS html
getPackageTitles html
getPacksAndViews html
getSubTerms html
guessPackageType html
htmlDoc html
htmlFilename html
htmlValue html
recommendBiocViews html
recommendPackages html
validation_tests html
writeBiocViews html
writeHtmlDoc html
writePackageDetailHtml html
writeRFilesFromVignettes html
writeRepositoryHtml html
writeTopLevelView html
write_REPOSITORY html
write_SYMBOLS html
write_VIEWS html
** building package indices
** installing vignettes
'HOWTO-BCV.Rnw'
'createReposHtml.Rnw'
** 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 'biocViews' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biocViews' as biocViews_1.62.1.zip
* DONE (biocViews)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'biocViews' successfully unpacked and MD5 sums checked
|
biocViews.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> BiocGenerics:::testPackage("biocViews")
Generate citation for C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp4UmBqb/testing/testrepos/src/contrib/biocViews2_1.62.1.tar.gz ... (try to process CITATION file) OK
Generate citation for C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp4UmBqb/testing/testrepos/src/contrib/biocViews_1.62.1.tar.gz ... /usr/bin/tar: biocViews/inst/CITATION: Not found in archive
/usr/bin/tar: Exiting with failure status due to previous errors
(auto-generate from DESCRIPTION file) OK
RUNIT TEST PROTOCOL -- Tue Apr 12 16:23:41 2022
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
biocViews RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
Warning messages:
1: In untar(tarball, tpaths, exdir = tmpdir) :
'tar.exe -xf "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp4UmBqb/testing/testrepos/src/contrib/biocViews_1.62.1.tar.gz" -C "C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4UmBqb" "biocViews/DESCRIPTION" "biocViews/inst/CITATION"' returned error code 2
2: In citation(pkgname, lib.loc = tmpdir, auto = description) :
no date field in DESCRIPTION file of package 'biocViews'
3: In citation(pkgname, lib.loc = tmpdir, auto = description) :
could not determine year for 'biocViews' from package DESCRIPTION file
>
> proc.time()
user system elapsed
60.87 14.12 76.09
|
biocViews.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> BiocGenerics:::testPackage("biocViews")
Generate citation for C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpsNg7la/testing/testrepos/src/contrib/biocViews2_1.62.1.tar.gz ... (try to process CITATION file) OK
Generate citation for C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpsNg7la/testing/testrepos/src/contrib/biocViews_1.62.1.tar.gz ... /usr/bin/tar: biocViews/inst/CITATION: Not found in archive
/usr/bin/tar: Exiting with failure status due to previous errors
(auto-generate from DESCRIPTION file) OK
RUNIT TEST PROTOCOL -- Tue Apr 12 16:24:38 2022
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
biocViews RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5
Number of errors: 0
Number of failures: 0
Warning messages:
1: In untar(tarball, tpaths, exdir = tmpdir) :
'tar.exe -xf "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpsNg7la/testing/testrepos/src/contrib/biocViews_1.62.1.tar.gz" -C "C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpsNg7la" "biocViews/DESCRIPTION" "biocViews/inst/CITATION"' returned error code 2
2: In citation(pkgname, lib.loc = tmpdir, auto = description) :
no date field in DESCRIPTION file of package 'biocViews'
3: In citation(pkgname, lib.loc = tmpdir, auto = description) :
could not determine year for 'biocViews' from package DESCRIPTION file
>
> proc.time()
user system elapsed
41.42 14.06 56.62
|
|
biocViews.Rcheck/examples_i386/biocViews-Ex.timings
|
biocViews.Rcheck/examples_x64/biocViews-Ex.timings
|