Bioconductor Package Maintainer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/biocViews |
| Branch: master |
| Last Commit: f0226e2 |
| Last Changed Date: 2019-04-04 11:13:07 -0400 (Thu, 04 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:54:37 -0400 (Tue, 09 Apr 2019).
| Package 153/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biocViews 1.51.15 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: biocViews |
| Version: 1.51.15 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings biocViews_1.51.15.tar.gz |
| StartedAt: 2019-04-09 01:22:14 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:26:21 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 246.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biocViews.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biocViews.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings biocViews_1.51.15.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/biocViews.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.51.15'
* 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:::.get_standard_repository_db_fields'
'tools:::.news_reader_default' '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 ... WARNING
Codoc mismatches from documentation object 'getPackageNEWS':
getPackageNEWS
Code: function(prevRepos = "3.6", currRepos = "3.7", repo = c("bioc",
"data/experiment", "workflows"), srcdir = NULL)
Docs: function(prevRepos = "3.6", currRepos = "3.7", repo = c("bioc",
"data/experiment", "workflows"))
Argument names in code not in docs:
srcdir
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'genReposControlFiles'
'meatPath'
Documented arguments not in \usage in documentation object 'genReposControlFiles':
'meanPath'
Undocumented arguments in documentation object 'write_VIEWS'
'meatPath'
Documented arguments not in \usage in documentation object 'write_VIEWS':
'type' 'meanPath'
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 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 or elapsed time > 5s
user system elapsed
recommendPackages 11.39 11.58 23.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
recommendPackages 8.12 4.89 13.06
* 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 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/biocViews.Rcheck/00check.log'
for details.
biocViews.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/biocViews_1.51.15.tar.gz && rm -rf biocViews.buildbin-libdir && mkdir biocViews.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biocViews.buildbin-libdir biocViews_1.51.15.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL biocViews_1.51.15.zip && rm biocViews_1.51.15.tar.gz biocViews_1.51.15.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 73185 100 73185 0 0 537k 0 --:--:-- --:--:-- --:--:-- 567k
install for i386
* installing *source* package 'biocViews' ...
** 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_1.51.15.zip
* DONE (biocViews)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'biocViews' successfully unpacked and MD5 sums checked
|
biocViews.Rcheck/tests_i386/runTests.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
/cygdrive/c/Rtools/bin/tar: Record size = 10 blocks
WARNING: extractCitations
tarball: C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpuAU85L/testing/testrepos/src/contrib/biocViews_1.51.15.tar.gz
warning: untar(compressed=) is deprecated
/cygdrive/c/Rtools/bin/tar: Record size = 6 blocks
WARNING: extractCitations
tarball: C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpuAU85L/testing/testrepos/src/contrib/biocViews_1.51.15.tar.gz
warning: untar(compressed=) is deprecated
RUNIT TEST PROTOCOL -- Tue Apr 09 01:25:04 2019
***********************************************
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
>
> proc.time()
user system elapsed
52.89 17.56 71.50
|
biocViews.Rcheck/tests_x64/runTests.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
/cygdrive/c/Rtools/bin/tar: Record size = 10 blocks
WARNING: extractCitations
tarball: C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpAjjmQl/testing/testrepos/src/contrib/biocViews_1.51.15.tar.gz
warning: untar(compressed=) is deprecated
/cygdrive/c/Rtools/bin/tar: Record size = 6 blocks
WARNING: extractCitations
tarball: C:\Users\biocbuild\bbs-3.9-bioc\tmpdir\RtmpAjjmQl/testing/testrepos/src/contrib/biocViews_1.51.15.tar.gz
warning: untar(compressed=) is deprecated
RUNIT TEST PROTOCOL -- Tue Apr 09 01:26:12 2019
***********************************************
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
>
> proc.time()
user system elapsed
41.50 25.31 67.85
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biocViews.Rcheck/examples_i386/biocViews-Ex.timings
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biocViews.Rcheck/examples_x64/biocViews-Ex.timings
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