Malgorzata Nowicka
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/DRIMSeq |
| Branch: RELEASE_3_12 |
| Last Commit: 3b9c0e8 |
| Last Changed Date: 2020-10-27 11:12:40 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:30:59 -0400 (Thu, 06 May 2021).
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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 509/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DRIMSeq 1.18.0 (landing page) Malgorzata Nowicka
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: DRIMSeq |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DRIMSeq_1.18.0.tar.gz |
| StartedAt: 2021-05-06 02:23:25 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:35:04 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 698.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DRIMSeq.Rcheck |
| Warnings: 2 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DRIMSeq_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DRIMSeq.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.18.0'
* 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 'DRIMSeq' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpygCeOL/R.INSTALL193c1dd45473/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-3.12-bioc/tmpdir/RtmpygCeOL/R.INSTALL193c1dd45473/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-3.12-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 219.80 0.38 220.29
dmDStest-class 25.68 0.08 26.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dmSQTLtest-class 240.49 0.19 241.20
dmDStest-class 27.37 0.04 27.42
* 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-3.12-bioc/meat/DRIMSeq.Rcheck/00check.log'
for details.
DRIMSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/DRIMSeq_1.18.0.tar.gz && rm -rf DRIMSeq.buildbin-libdir && mkdir DRIMSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DRIMSeq.buildbin-libdir DRIMSeq_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DRIMSeq_1.18.0.zip && rm DRIMSeq_1.18.0.tar.gz DRIMSeq_1.18.0.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
100 83581 100 83581 0 0 4574k 0 --:--:-- --:--:-- --:--:-- 4801k
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-3.12-bioc/tmpdir/RtmpygCeOL/R.INSTALL193c1dd45473/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-3.12-bioc/tmpdir/RtmpygCeOL/R.INSTALL193c1dd45473/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_1.18.0.zip
* DONE (DRIMSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DRIMSeq' successfully unpacked and MD5 sums checked
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DRIMSeq.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
> library(DRIMSeq)
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
>
> test_check("DRIMSeq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
>
> proc.time()
user system elapsed
14.73 0.42 15.15
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DRIMSeq.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
> library(DRIMSeq)
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
>
> test_check("DRIMSeq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
>
> proc.time()
user system elapsed
15.10 0.67 15.76
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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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