Kaur Alasoo
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/wiggleplotr |
| Branch: RELEASE_3_8 |
| Last Commit: 2fe7de2 |
| Last Changed Date: 2019-01-04 13:53:23 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:27:42 -0400 (Sat, 13 Apr 2019).
| Package 1634/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| wiggleplotr 1.6.1 Kaur Alasoo
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: wiggleplotr |
| Version: 1.6.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:wiggleplotr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings wiggleplotr_1.6.1.tar.gz |
| StartedAt: 2019-04-13 06:12:33 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 06:15:12 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 159.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: wiggleplotr.Rcheck |
| Warnings: 3 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:wiggleplotr.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings wiggleplotr_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/wiggleplotr.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'wiggleplotr/DESCRIPTION' ... OK
* this is package 'wiggleplotr' version '1.6.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'wiggleplotr' 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 ... NOTE
plotCoverage: no visible global function definition for 'is'
plotTranscripts: no visible global function definition for 'is'
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 'getGenotypePalette':
getGenotypePalette
Code: function(old = FALSE)
Docs: function()
Argument names in code not in docs:
old
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
Warning: 'AnnotationFilter::GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
plotCoverageFromEnsembldb 7.32 0.51 7.83
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: 'AnnotationFilter::GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
plotCoverageFromEnsembldb 8.15 0.39 8.53
* 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 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/wiggleplotr.Rcheck/00check.log'
for details.
wiggleplotr.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/wiggleplotr_1.6.1.tar.gz && rm -rf wiggleplotr.buildbin-libdir && mkdir wiggleplotr.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=wiggleplotr.buildbin-libdir wiggleplotr_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL wiggleplotr_1.6.1.zip && rm wiggleplotr_1.6.1.tar.gz wiggleplotr_1.6.1.zip
###
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install for i386
* installing *source* package 'wiggleplotr' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'wiggleplotr'
finding HTML links ... done
getGenotypePalette html
makeManhattanPlot html
ncoa7_cdss html
ncoa7_exons html
ncoa7_metadata html
pasteFactors html
plotCoverage html
plotCoverageFromEnsembldb html
plotCoverageFromUCSC html
plotTranscripts html
plotTranscriptsFromEnsembldb html
plotTranscriptsFromUCSC html
wiggleplotr html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'wiggleplotr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'wiggleplotr' as wiggleplotr_1.6.1.zip
* DONE (wiggleplotr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'wiggleplotr' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
wiggleplotr.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> library(testthat)
> library(wiggleplotr)
>
> test_check("wiggleplotr")
== testthat results ===========================================================
OK: 6 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.15 0.32 4.48
|
wiggleplotr.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> library(testthat)
> library(wiggleplotr)
>
> test_check("wiggleplotr")
== testthat results ===========================================================
OK: 6 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.95 0.17 5.12
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wiggleplotr.Rcheck/examples_i386/wiggleplotr-Ex.timings
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wiggleplotr.Rcheck/examples_x64/wiggleplotr-Ex.timings
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