Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:01 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 91/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
APL 1.10.2  (landing page)
Clemens Kohl
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/APL
git_branch: RELEASE_3_20
git_last_commit: d71ccae
git_last_commit_date: 2024-11-04 16:23:16 -0500 (Mon, 04 Nov 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for APL on teran2

To the developers/maintainers of the APL package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: APL
Version: 1.10.2
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:APL.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings APL_1.10.2.tar.gz
StartedAt: 2024-11-19 22:52:39 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 22:58:34 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 354.4 seconds
RetCode: 0
Status:   OK  
CheckDir: APL.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:APL.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings APL_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/APL.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘APL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘APL’ version ‘1.10.2’
* 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 code 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 loading without being on the library search path ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

APL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL APL
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘APL’ ...
** using staged installation
** R
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Please consider setting the dimensions to a lower value to speed up the calculation.
Recommended dimensionality: << min(nrows, ncols) * 0.2
Please consider setting the dimensions to a lower value to speed up the calculation.
Recommended dimensionality: << min(nrows, ncols) * 0.2
Please consider setting the dimensions to a lower value to speed up the calculation.
Recommended dimensionality: << min(nrows, ncols) * 0.2
Please consider setting the dimensions to a lower value to speed up the calculation.
Recommended dimensionality: << min(nrows, ncols) * 0.2
Calling cacomp to recompute from matrix.
Please consider setting the dimensions to a lower value to speed up the calculation.
Recommended dimensionality: << min(nrows, ncols) * 0.2
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ]
> 
> proc.time()
   user  system elapsed 
  9.653   0.620  10.276 

Example timings

APL.Rcheck/APL-Ex.timings

nameusersystemelapsed
apl0.9600.0060.966
apl_coords0.0050.0000.005
apl_score0.1690.0240.192
apl_topGO3.5420.1493.693
as.cacomp1.4440.0031.447
as.list-cacomp-method0.010.000.01
ca_3Dplot0.2150.0250.239
ca_biplot0.2240.0470.271
ca_coords0.0040.0020.006
cacomp-class0.0080.0010.009
cacomp0.4000.0040.404
cacomp_names0.0040.0000.004
cacomp_slot0.0040.0000.004
check_cacomp0.0040.0000.004
elbow_method0.3180.0050.323
pick_dims0.6240.0090.633
pipe000
plot_enrichment3.2170.0153.233
runAPL1.6440.0851.730
show.cacomp0.0050.0000.005
subset_dims0.0030.0000.004
var_rows0.0070.0000.008