Malgorzata Nowicka
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/DRIMSeq |
| Branch: RELEASE_3_11 |
| Last Commit: 7225753 |
| Last Changed Date: 2020-08-05 08:21:37 -0400 (Wed, 05 Aug 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:29 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE DRIMSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 504/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DRIMSeq 1.16.1 Malgorzata Nowicka
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: DRIMSeq |
| Version: 1.16.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DRIMSeq_1.16.1.tar.gz |
| StartedAt: 2020-10-17 03:32:59 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:41:54 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 534.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DRIMSeq.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DRIMSeq_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DRIMSeq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DRIMSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DRIMSeq' version '1.16.1'
* 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 'DRIMSeq' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpusFIQt/R.INSTALL21dc1e7c472e/DRIMSeq/man/dmTest.Rd:93: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpusFIQt/R.INSTALL21dc1e7c472e/DRIMSeq/man/dmTest.Rd:193: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DRIMSeq.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 ... WARNING
Documented arguments not in \usage in documentation object 'dmSQTLtest-class':
'...'
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dmSQTLtest-class 168.61 0.30 168.96
dmDStest-class 10.34 0.11 10.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dmSQTLtest-class 171.60 0.19 171.80
dmDStest-class 12.38 0.08 12.46
* 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: 2 WARNINGs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/DRIMSeq.Rcheck/00check.log'
for details.
DRIMSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DRIMSeq_1.16.1.tar.gz && rm -rf DRIMSeq.buildbin-libdir && mkdir DRIMSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DRIMSeq.buildbin-libdir DRIMSeq_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DRIMSeq_1.16.1.zip && rm DRIMSeq_1.16.1.tar.gz DRIMSeq_1.16.1.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 83962 100 83962 0 0 1455k 0 --:--:-- --:--:-- --:--:-- 1673k
install for i386
* installing *source* package 'DRIMSeq' ...
** using staged installation
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'proportions' in package 'DRIMSeq'
** help
*** installing help indices
converting help for package 'DRIMSeq'
finding HTML links ... done
MatrixList-class html
dmDSdata-class html
dmDSdata html
dmDSfit-class html
dmDSprecision-class html
dmDStest-class html
dmFilter html
dmFit html
finding level-2 HTML links ... done
dmPrecision html
dmSQTLdata-class html
dmSQTLdata html
dmSQTLfit-class html
dmSQTLprecision-class html
dmSQTLtest-class html
dmTest html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpusFIQt/R.INSTALL21dc1e7c472e/DRIMSeq/man/dmTest.Rd:93: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpusFIQt/R.INSTALL21dc1e7c472e/DRIMSeq/man/dmTest.Rd:193: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
dm_plotDataDSInfo html
dm_plotProportions html
plotData html
plotPValues html
plotPrecision html
plotProportions 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 'DRIMSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DRIMSeq' as DRIMSeq_1.16.1.zip
* DONE (DRIMSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DRIMSeq' successfully unpacked and MD5 sums checked
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DRIMSeq.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(DRIMSeq)
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
>
> test_check("DRIMSeq")
== testthat results ===========================================================
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
11.73 0.42 12.14
|
DRIMSeq.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(DRIMSeq)
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
>
> test_check("DRIMSeq")
== testthat results ===========================================================
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
8.92 0.32 9.23
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DRIMSeq.Rcheck/examples_i386/DRIMSeq-Ex.timings
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DRIMSeq.Rcheck/examples_x64/DRIMSeq-Ex.timings
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