Shian Su
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/Glimma |
| git_branch: RELEASE_3_13 |
| git_last_commit: 56d8c66 |
| git_last_commit_date: 2021-05-19 12:19:39 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the Glimma package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Glimma.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 774/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Glimma 2.2.0 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: Glimma |
| Version: 2.2.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Glimma.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Glimma_2.2.0.tar.gz |
| StartedAt: 2021-10-14 23:52:03 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-15 00:03:36 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 692.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Glimma.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Glimma.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Glimma_2.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Glimma.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Glimma/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Glimma' version '2.2.0'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Glimma' can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
data 1.9Mb
htmlwidgets 5.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
glimmaMA.DESeqDataSet 12.82 0.54 17.55
glimmaVolcano.DGEExact 10.91 0.11 11.02
glimmaVolcano.DESeqDataSet 10.17 0.10 11.64
glimmaMA.DGEExact 9.54 0.22 9.77
glMDPlot 5.94 0.26 6.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
glimmaMA.DESeqDataSet 12.84 0.22 21.05
glimmaVolcano.DESeqDataSet 11.69 0.09 13.94
glimmaMA.DGEExact 9.89 0.06 14.31
glimmaVolcano.DGEExact 9.14 0.08 9.22
glMDPlot 6.72 0.15 6.87
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/Glimma.Rcheck/00check.log'
for details.
Glimma.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Glimma_2.2.0.tar.gz && rm -rf Glimma.buildbin-libdir && mkdir Glimma.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Glimma.buildbin-libdir Glimma_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Glimma_2.2.0.zip && rm Glimma_2.2.0.tar.gz Glimma_2.2.0.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
9 6001k 9 578k 0 0 1232k 0 0:00:04 --:--:-- 0:00:04 1231k
50 6001k 50 3028k 0 0 2097k 0 0:00:02 0:00:01 0:00:01 2097k
100 6001k 100 6001k 0 0 2650k 0 0:00:02 0:00:02 --:--:-- 2652k
install for i386
* installing *source* package 'Glimma' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Glimma'
finding HTML links ... done
arraydata html
as.hexcol html
buildXYData html
extractGroups html
glBar html
glBar.default html
glMDPlot.DESeqDataSet html
glMDPlot.DESeqResults html
glMDPlot.DGEExact html
glMDPlot.DGELRT html
glMDPlot.MArrayLM html
glMDPlot html
glMDPlot.default html
glMDRmd html
glMDSPlot.DESeqDataSet html
glMDSPlot.DGEList html
glMDSPlot html
glMDSPlot.default html
glScatter html
glScatter.default html
glTable html
glXYPlot html
glimma html
glimmaMA.DESeqDataSet html
glimmaMA.DGEExact html
glimmaMA.DGELRT html
glimmaMA.MArrayLM html
glimmaMA html
finding level-2 HTML links ... done
glimmaMDS.DESeqDataSet html
glimmaMDS.DGEList html
glimmaMDS html
glimmaMDS.default html
glimmaVolcano.DESeqDataSet html
glimmaVolcano.DGEExact html
glimmaVolcano.DGELRT html
glimmaVolcano.MArrayLM html
glimmaVolcano html
glimmaXY html
glimmaXYWidget html
glimma_plot html
gllink html
gltablink html
is.hex html
lymphomaRNAseq html
makeJson html
makeJson.data.frame html
makeJson.jschart 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 'Glimma' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Glimma' as Glimma_2.2.0.zip
* DONE (Glimma)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Glimma' successfully unpacked and MD5 sums checked
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Glimma.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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)
> test_check("Glimma")
Loading required package: Glimma
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 191 ]
>
> proc.time()
user system elapsed
88.32 3.25 139.60
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Glimma.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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)
> test_check("Glimma")
Loading required package: Glimma
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 191 ]
>
> proc.time()
user system elapsed
88.85 1.85 139.37
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Glimma.Rcheck/examples_i386/Glimma-Ex.timings
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Glimma.Rcheck/examples_x64/Glimma-Ex.timings
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