Federico Marini
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/pcaExplorer |
| Branch: RELEASE_3_12 |
| Last Commit: d1867b5 |
| Last Changed Date: 2020-10-27 11:13:51 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:42 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the pcaExplorer package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1313/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pcaExplorer 2.16.0 (landing page) Federico Marini
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: pcaExplorer |
| Version: 2.16.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings pcaExplorer_2.16.0.tar.gz |
| StartedAt: 2021-05-06 05:24:04 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:36:02 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 718.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pcaExplorer.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaExplorer.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings pcaExplorer_2.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/pcaExplorer.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 'pcaExplorer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pcaExplorer' version '2.16.0'
* 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:
.github
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 'pcaExplorer' 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
pcaExplorer: no visible binding for '<<-' assignment to
'pcaexplorer_env'
pcaExplorer : <anonymous>: no visible binding for global variable
'airway'
pcaExplorer : <anonymous>: no visible binding for global variable
'pcaexplorer_env'
Undefined global functions or variables:
airway pcaexplorer_env
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_annotation 4.76 0.37 5.16
** 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/pcaExplorer.Rcheck/00check.log'
for details.
pcaExplorer.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/pcaExplorer_2.16.0.tar.gz && rm -rf pcaExplorer.buildbin-libdir && mkdir pcaExplorer.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaExplorer.buildbin-libdir pcaExplorer_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL pcaExplorer_2.16.0.zip && rm pcaExplorer_2.16.0.tar.gz pcaExplorer_2.16.0.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 22.3M 100 22.3M 0 0 91.4M 0 --:--:-- --:--:-- --:--:-- 91.7M
install for i386
* installing *source* package 'pcaExplorer' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'pcaExplorer'
finding HTML links ... done
correlatePCs html
distro_expr html
finding level-2 HTML links ... done
geneprofiler html
genespca html
get_annotation html
get_annotation_orgdb html
hi_loadings html
limmaquickpca2go html
makeExampleDESeqDataSet_multifac html
pair_corr html
pca2go html
pcaExplorer-pkg html
pcaExplorer html
pcaplot html
pcaplot3d html
pcascree html
plotPCcorrs html
topGOtable 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 'pcaExplorer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaExplorer' as pcaExplorer_2.16.0.zip
* DONE (pcaExplorer)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'pcaExplorer' successfully unpacked and MD5 sums checked
|
pcaExplorer.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(pcaExplorer)
Welcome to pcaExplorer v2.16.0
If you use pcaExplorer in your work, please cite:
Federico Marini, Harald Binder
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
BMC Bioinformatics, 2019 - https://doi.org/10.1186/s12859-019-2879-1
>
> test_check("pcaExplorer")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 17 ]
>
> proc.time()
user system elapsed
79.60 3.71 84.93
|
pcaExplorer.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(pcaExplorer)
Welcome to pcaExplorer v2.16.0
If you use pcaExplorer in your work, please cite:
Federico Marini, Harald Binder
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
BMC Bioinformatics, 2019 - https://doi.org/10.1186/s12859-019-2879-1
>
> test_check("pcaExplorer")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 17 ]
>
> proc.time()
user system elapsed
79.42 1.57 83.46
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pcaExplorer.Rcheck/examples_i386/pcaExplorer-Ex.timings
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pcaExplorer.Rcheck/examples_x64/pcaExplorer-Ex.timings
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