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This page was generated on 2024-12-09 11:46 -0500 (Mon, 09 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4749
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4461
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4411
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4366
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4241
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 911/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSgalgoR 1.17.0  (landing page)
Carlos Catania
Snapshot Date: 2024-12-08 13:40 -0500 (Sun, 08 Dec 2024)
git_url: https://git.bioconductor.org/packages/GSgalgoR
git_branch: devel
git_last_commit: 5111e23
git_last_commit_date: 2024-10-29 10:53:20 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for GSgalgoR on kunpeng2

To the developers/maintainers of the GSgalgoR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/GSgalgoR.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GSgalgoR
Version: 1.17.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GSgalgoR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GSgalgoR_1.17.0.tar.gz
StartedAt: 2024-12-09 06:24:05 -0000 (Mon, 09 Dec 2024)
EndedAt: 2024-12-09 06:27:04 -0000 (Mon, 09 Dec 2024)
EllapsedTime: 179.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GSgalgoR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GSgalgoR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GSgalgoR_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GSgalgoR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (conda-forge gcc 14.2.0-1) 14.2.0
    GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSgalgoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSgalgoR’ version ‘1.17.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSgalgoR’ 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  galgo.Rd: survival
  non_dominated_summary.Rd: survival
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
plot_pareto              3.473  0.229   8.432
classify_multiple        3.463  0.146   8.162
callback_base_report     2.770  0.439   8.245
create_centroids         2.833  0.077   7.132
non_dominated_summary    2.646  0.234   6.870
galgo                    2.196  0.336   7.035
to_dataframe             2.281  0.108   6.982
to_list                  2.292  0.083   6.977
callback_base_return_pop 2.005  0.190   7.419
callback_default         2.036  0.113   6.982
callback_no_report       2.035  0.096   7.121
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GSgalgoR.Rcheck/00check.log’
for details.


Installation output

GSgalgoR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GSgalgoR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘GSgalgoR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (GSgalgoR)

Tests output

GSgalgoR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(GSgalgoR)
> 
> test_check("GSgalgoR")
..........         k                      rnkIndex   CrowD
result.1 8 0.02212350 201.10126        1     Inf
result.3 9 0.02402496 160.41638        1 1.37352
result.4 8 0.03651880  48.37265        1     Inf
         k                      rnkIndex    CrowD
result.1 8 0.02212350 201.10126        1      Inf
result.3 2 0.11803624  30.01863        1      Inf
result.4 4 0.04509859 173.43985        1 1.798893
......[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 20.273   1.337  70.902 

Example timings

GSgalgoR.Rcheck/GSgalgoR-Ex.timings

nameusersystemelapsed
calculate_distance1.9690.1151.904
callback_base_report2.7700.4398.245
callback_base_return_pop2.0050.1907.419
callback_default2.0360.1136.982
callback_no_report2.0350.0967.121
classify_multiple3.4630.1468.162
cluster_algorithm0.5820.0480.444
cluster_classify2.5880.1051.960
cosine_similarity0.0000.0000.001
create_centroids2.8330.0777.132
galgo2.1960.3367.035
k_centroids0.6220.0360.471
non_dominated_summary2.6460.2346.870
plot_pareto3.4730.2298.432
surv_fitness0.6440.0320.679
to_dataframe2.2810.1086.982
to_list2.2920.0836.977