Hector Corrada Bravo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/epivizr |
| Branch: RELEASE_3_9 |
| Last Commit: 612e74d |
| Last Changed Date: 2019-05-02 11:53:45 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:28:41 -0400 (Wed, 16 Oct 2019).
| Package 511/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| epivizr 2.14.0 Hector Corrada Bravo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: epivizr |
| Version: 2.14.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epivizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings epivizr_2.14.0.tar.gz |
| StartedAt: 2019-10-16 03:33:13 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:39:19 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 365.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: epivizr.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epivizr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings epivizr_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/epivizr.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'epivizr/DESCRIPTION' ... OK * this is package 'epivizr' version '2.14.0' * 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 'epivizr' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:14: file link 'EpivizServer' in package 'epivizrServer' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:16: file link 'EpivizDataMgr' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:33: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:57: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:58: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:67: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:33: file link 'EpivizServer' in package 'epivizrServer' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:55: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:56: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:60: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:121: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:126: file link 'EpivizMeasurement' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:128: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_blocks.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_blocks.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_curves.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_curves.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_expression.Rd:23: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_expression.Rd:7: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_expression.Rd:20: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/epivizr.Rcheck/00install.out' for details. * 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 ... 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 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' ... OK ** running examples for arch 'x64' ... OK * 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 WARNING See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/epivizr.Rcheck/00check.log' for details.
epivizr.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/epivizr_2.14.0.tar.gz && rm -rf epivizr.buildbin-libdir && mkdir epivizr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epivizr.buildbin-libdir epivizr_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL epivizr_2.14.0.zip && rm epivizr_2.14.0.tar.gz epivizr_2.14.0.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
100 932k 100 932k 0 0 10.9M 0 --:--:-- --:--:-- --:--:-- 11.9M
install for i386
* installing *source* package 'epivizr' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'epivizr'
finding HTML links ... done
EpivizApp-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:14: file link 'EpivizServer' in package 'epivizrServer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:16: file link 'EpivizDataMgr' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:33: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:57: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:58: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizApp-class.Rd:67: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
EpivizChart-class html
EpivizChartMgr-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:33: file link 'EpivizServer' in package 'epivizrServer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:55: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:56: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:60: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:121: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:126: file link 'EpivizMeasurement' in package 'epivizrData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/EpivizChartMgr-class.Rd:128: file link 'EpivizData' in package 'epivizrData' does not exist and so has been treated as a topic
restartEpiviz html
show-EpivizChart-method html
startEpiviz html
tcga_colon_blocks html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_blocks.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_blocks.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
tcga_colon_curves html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_curves.Rd:7: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_curves.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
tcga_colon_expression html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_expression.Rd:23: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_expression.Rd:7: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp4q22GW/R.INSTALL2200426f4700/epivizr/man/tcga_colon_expression.Rd:20: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
** 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 'epivizr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epivizr' as epivizr_2.14.0.zip
* DONE (epivizr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'epivizr' successfully unpacked and MD5 sums checked
|
epivizr.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(epivizr)
>
> test_check("epivizr")
== testthat results ===========================================================
[ OK: 115 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.29 1.15 15.43
|
epivizr.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(epivizr)
>
> test_check("epivizr")
== testthat results ===========================================================
[ OK: 115 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
18.26 0.78 19.03
|
|
epivizr.Rcheck/examples_i386/epivizr-Ex.timings
|
epivizr.Rcheck/examples_x64/epivizr-Ex.timings
|