Sara Aibar
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/AUCell |
| Branch: RELEASE_3_10 |
| Last Commit: b1f460c |
| Last Changed Date: 2019-10-29 13:10:44 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:29:04 -0400 (Wed, 15 Apr 2020).
| Package 98/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AUCell 1.8.0 Sara Aibar
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: AUCell |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AUCell.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings AUCell_1.8.0.tar.gz |
| StartedAt: 2020-04-15 01:22:42 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:27:46 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 303.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: AUCell.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AUCell.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings AUCell_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/AUCell.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AUCell/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AUCell' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'AUCell' 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 ... NOTE
'library' or 'require' call to 'rbokeh' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'BiocGenerics'
All declared Imports should be used.
Unexported object imported by a ':::' call: 'S4Vectors:::disableValidity'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AUCell_createViewerApp : <anonymous>: no visible global function
definition for '%>%'
AUCell_createViewerApp : <anonymous>: no visible binding for global
variable 'tsne1'
AUCell_createViewerApp : <anonymous>: no visible binding for global
variable 'tsne2'
AUCell_createViewerApp : <anonymous>: no visible binding for global
variable 'cell'
Undefined global functions or variables:
%>% cell tsne1 tsne2
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'cbind' and siglist 'aucellResults'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'aucellResults-class':
'\S4method{cbind}{aucellResults}'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
AUCell_exploreThresholds 6.49 1.36 7.6
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
AUCell_exploreThresholds 4.53 1.22 5.32
* 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 ... NOTE
'::' or ':::' import not declared from: 'reshape2'
* 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, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/AUCell.Rcheck/00check.log'
for details.
AUCell.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/AUCell_1.8.0.tar.gz && rm -rf AUCell.buildbin-libdir && mkdir AUCell.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AUCell.buildbin-libdir AUCell_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL AUCell_1.8.0.zip && rm AUCell_1.8.0.tar.gz AUCell_1.8.0.zip
###
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install for i386
* installing *source* package 'AUCell' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'cbind' in package 'AUCell'
** help
*** installing help indices
converting help for package 'AUCell'
finding HTML links ... done
AUCell_buildRankings html
finding level-2 HTML links ... done
AUCell_calcAUC html
AUCell_createViewerApp html
AUCell_exploreThresholds html
AUCell_plotHist html
AUCell_plotTSNE html
GeneSet-methods html
aucellResults-class html
orderAUC html
plotGeneCount html
plotTsne_cellProps html
updateAucellResults html
** building package indices
** installing vignettes
'AUCell.Rmd' using 'UTF-8'
** 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 'AUCell' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AUCell' as AUCell_1.8.0.zip
* DONE (AUCell)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'AUCell' successfully unpacked and MD5 sums checked
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AUCell.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(AUCell)
Attaching package: 'AUCell'
The following object is masked from 'package:base':
cbind
>
> test_check("AUCell")
min 1% 5% 10% 50% 100%
3 5 6 7 10 16
min 1% 5% 10% 50% 100%
3 5 6 7 10 16
== testthat results ===========================================================
[ OK: 41 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
22.03 6.56 25.01
|
AUCell.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(AUCell)
Attaching package: 'AUCell'
The following object is masked from 'package:base':
cbind
>
> test_check("AUCell")
min 1% 5% 10% 50% 100%
3 5 6 7 10 16
min 1% 5% 10% 50% 100%
3 5 6 7 10 16
== testthat results ===========================================================
[ OK: 41 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
28.71 4.85 29.76
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AUCell.Rcheck/examples_i386/AUCell-Ex.timings
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AUCell.Rcheck/examples_x64/AUCell-Ex.timings
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