Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
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 787/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemma.R 3.2.0  (landing page)
Ogan Mancarci
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/gemma.R
git_branch: RELEASE_3_20
git_last_commit: cf32d0a
git_last_commit_date: 2024-10-29 11:14:34 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for gemma.R on kjohnson3

To the developers/maintainers of the gemma.R package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemma.R.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: gemma.R
Version: 3.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemma.R_3.2.0.tar.gz
StartedAt: 2024-11-09 02:55:55 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 03:05:04 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 549.4 seconds
RetCode: 0
Status:   OK  
CheckDir: gemma.R.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemma.R_3.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gemma.R.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘3.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘gemma.R’ 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 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
get_dataset_object                           2.677  0.084   7.778
get_dataset_raw_expression                   0.366  0.020   5.752
get_dataset_expression                       0.248  0.021   7.971
get_dataset_differential_expression_analyses 0.136  0.011   5.723
* 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: OK


Installation output

gemma.R.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gemma.R
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘gemma.R’ ...
** 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 (gemma.R)

Tests output

gemma.R.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(dplyr)

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> # Prevent certificate issues for GitHub actions
> options(gemma.SSL = FALSE)
> # get gemma api path if it's set in the environment
> gemma.R:::setGemmaPath('prod')
[1] "https://gemma.msl.ubc.ca/rest/v2/"
> print(gemma.R:::gemmaPath())
[1] "https://gemma.msl.ubc.ca/rest/v2/"
> test_check("gemma.R")
Loading required package: gemma.R
[ FAIL 0 | WARN 1 | SKIP 4 | PASS 193 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On Bioconductor (4): 'testCaches.R:37:3', 'testConvenience.R:15:5',
  'testConvenience.R:37:5', 'testDatasetEndpoints.R:86:5'

[ FAIL 0 | WARN 1 | SKIP 4 | PASS 193 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 20.161   1.043 258.324 

Example timings

gemma.R.Rcheck/gemma.R-Ex.timings

nameusersystemelapsed
dot-getResultSets000
filter_properties0.0260.0020.029
forget_gemma_memoised0.0050.0110.021
gemma_call0.0440.0050.817
get_child_terms0.0940.0060.198
get_dataset_annotations0.0030.0010.102
get_dataset_design0.0740.0040.197
get_dataset_differential_expression_analyses0.1360.0115.723
get_dataset_expression0.2480.0217.971
get_dataset_expression_for_genes0.0660.0060.340
get_dataset_object2.6770.0847.778
get_dataset_platforms0.0030.0000.089
get_dataset_processed_expression0.3980.0194.320
get_dataset_quantitation_types0.0030.0010.191
get_dataset_raw_expression0.3660.0205.752
get_dataset_samples0.0450.0040.223
get_datasets0.0530.0064.123
get_datasets_by_ids0.0130.0010.178
get_differential_expression_values0.0740.0133.044
get_gene_differential_expression_values0.2190.0133.951
get_gene_go_terms0.0110.0010.182
get_gene_locations0.0070.0000.239
get_gene_probes0.0090.0020.249
get_genes0.0070.0000.183
get_platform_annotations0.2570.0152.467
get_platform_datasets0.0130.0010.290
get_platform_element_genes0.0040.0000.101
get_platforms_by_ids0.0090.0000.193
get_result_sets0.0110.0010.187
get_taxa0.0030.0000.078
get_taxa_by_ids0.0030.0010.077
get_taxon_datasets0.0130.0010.255
make_design0.1510.0050.353
search_annotations0.0030.0010.079
search_datasets0.0110.0010.342
search_gemma0.0340.0050.309
update_result0.1590.0083.121