Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:19:58 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for APL on nebbiolo1


To the developers/maintainers of the APL package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/APL.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 73/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
APL 1.0.1  (landing page)
Elzbieta Gralinska
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/APL
git_branch: RELEASE_3_15
git_last_commit: 88cc955
git_last_commit_date: 2022-10-14 19:07:16 -0400 (Fri, 14 Oct 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: APL
Version: 1.0.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:APL.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings APL_1.0.1.tar.gz
StartedAt: 2022-10-18 18:34:21 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:38:51 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 270.4 seconds
RetCode: 0
Status:   OK  
CheckDir: APL.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:APL.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings APL_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/APL.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘APL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘APL’ version ‘1.0.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘APL’ 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
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
apl_topGO       6.363  0.159   6.524
plot_enrichment 5.286  0.057   5.342
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: OK


Installation output

APL.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL APL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘APL’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* DONE (APL)

Tests output

APL.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(APL)



> test_check("APL")
Calling cacomp to recompute from matrix.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 14.411   1.312  16.284 

Example timings

APL.Rcheck/APL-Ex.timings

nameusersystemelapsed
apl0.1750.0000.175
apl_coords0.0060.0000.006
apl_score1.2530.0071.261
apl_topGO6.3630.1596.524
as.cacomp1.0450.0441.089
as.list-cacomp-method0.0150.0010.015
ca_3Dplot0.1770.0110.189
ca_biplot0.0840.0080.092
ca_coords0.0020.0030.006
cacomp-class0.0110.0000.011
cacomp0.7360.0110.748
cacomp_names0.0050.0000.005
cacomp_slot0.0010.0030.005
check_cacomp0.0050.0000.005
elbow_method0.5080.0160.524
pick_dims1.1310.0081.139
pipe000
plot_enrichment5.2860.0575.342
runAPL1.7270.0131.739
show.cacomp0.0050.0000.005
subset_dims0.0010.0030.004
var_rows0.0100.0010.010