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This page was generated on 2024-12-12 11:40 -0500 (Thu, 12 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4752
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4464
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4415
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4370
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4279
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 781/2273HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemma.R 3.3.0  (landing page)
Ogan Mancarci
Snapshot Date: 2024-12-11 13:40 -0500 (Wed, 11 Dec 2024)
git_url: https://git.bioconductor.org/packages/gemma.R
git_branch: devel
git_last_commit: 890574d
git_last_commit_date: 2024-11-26 15:33:49 -0500 (Tue, 26 Nov 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  ERROR    ERROR  skipped


CHECK results for gemma.R on nebbiolo1

To the developers/maintainers of the gemma.R package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]: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: 3.3.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gemma.R_3.3.0.tar.gz
StartedAt: 2024-12-12 00:00:20 -0500 (Thu, 12 Dec 2024)
EndedAt: 2024-12-12 00:16:21 -0500 (Thu, 12 Dec 2024)
EllapsedTime: 960.9 seconds
RetCode: 0
Status:   OK  
CheckDir: gemma.R.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gemma.R_3.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gemma.R.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘3.3.0’
* 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'
 INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                                              user system elapsed
get_dataset_object                           6.728  0.388  11.054
get_dataset_processed_expression             1.187  0.376   6.158
get_dataset_raw_expression                   1.200  0.146   6.769
get_dataset_expression                       0.773  0.152   8.322
get_dataset_differential_expression_analyses 0.436  0.039   6.409
* 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

gemma.R.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL gemma.R
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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(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 0 | SKIP 4 | PASS 197 ]

══ 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 0 | SKIP 4 | PASS 197 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
101.088   3.602 371.651 

Example timings

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

nameusersystemelapsed
dot-getResultSets0.0000.0000.001
filter_properties0.0570.0100.069
forget_gemma_memoised0.0130.0140.028
gemma_call0.1580.0200.884
get_child_terms0.2680.0700.433
get_dataset_annotations0.0090.0010.098
get_dataset_design0.2360.0060.359
get_dataset_differential_expression_analyses0.4360.0396.409
get_dataset_expression0.7730.1528.322
get_dataset_expression_for_genes0.2780.0080.551
get_dataset_object 6.728 0.38811.054
get_dataset_platforms0.0510.0020.252
get_dataset_processed_expression1.1870.3766.158
get_dataset_quantitation_types0.0100.0020.299
get_dataset_raw_expression1.2000.1466.769
get_dataset_samples0.2000.0360.482
get_datasets0.1650.0772.157
get_datasets_by_ids0.0550.0090.235
get_differential_expression_values0.2250.0313.293
get_gene_differential_expression_values0.7560.1373.951
get_gene_go_terms0.0380.0090.361
get_gene_locations0.0220.0020.240
get_gene_probes0.0220.0050.190
get_genes0.0230.0030.207
get_platform_annotations0.7500.0542.986
get_platform_datasets0.0350.0020.215
get_platform_element_genes0.0120.0020.111
get_platforms_by_ids0.0250.0030.215
get_result_sets0.0360.0080.226
get_taxa0.0090.0010.087
get_taxa_by_ids0.0090.0000.086
get_taxon_datasets0.0330.0070.308
make_design0.5290.0150.816
search_annotations0.0110.0000.090
search_datasets0.0340.0110.459
search_gemma0.0910.0330.463
update_result0.7370.2964.312