Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:05 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 gemma.R on nebbiolo2


To the developers/maintainers of the gemma.R package:
- Please 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 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 748/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemma.R 1.0.1  (landing page)
Ogan Mancarci
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/gemma.R
git_branch: RELEASE_3_16
git_last_commit: 43adbd5
git_last_commit_date: 2023-01-24 16:44:40 -0400 (Tue, 24 Jan 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gemma.R
Version: 1.0.1
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gemma.R_1.0.1.tar.gz
StartedAt: 2023-04-10 20:50:43 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:55:05 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 262.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gemma.R.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gemma.R_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/gemma.R.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ 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 ‘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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘jsonlite:::simplify’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
processDEA : <anonymous> : <anonymous>: no visible binding for global
  variable ‘experimental.factorValue’
Undefined global functions or variables:
  experimental.factorValue
* 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     6.343  0.385  17.411
get_dataset_expression 0.960  0.111   8.444
search_annotations     0.013  0.000   5.149
* 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 ...
  ‘gemma.R.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/gemma.R.Rcheck/00check.log’
for details.



Installation output

gemma.R.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL gemma.R
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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(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
> options(gemma.API = Sys.getenv('API_PATH','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 7 | SKIP 4 | PASS 111 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (4)

[ FAIL 0 | WARN 7 | SKIP 4 | PASS 111 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 24.479   1.296 128.287 

Example timings

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

nameusersystemelapsed
forget_gemma_memoised0.0210.0000.023
gemma_call0.1180.0040.684
get_dataset_annotations0.0190.0000.103
get_dataset_design0.4470.0280.588
get_dataset_differential_expression_analyses0.3020.0293.650
get_dataset_expression0.9600.1118.444
get_dataset_object 6.343 0.38517.411
get_dataset_platforms0.0120.0000.096
get_dataset_samples0.0760.0120.561
get_datasets_by_ids0.6830.0550.913
get_differential_expression_values0.2980.0113.192
get_gene_go_terms0.0230.0000.193
get_gene_locations0.0120.0000.235
get_gene_probes0.0240.0000.112
get_genes0.0240.0000.180
get_platform_annotations1.0660.0293.871
get_platform_datasets0.0470.0002.538
get_platform_element_genes0.0120.0000.096
get_platforms_by_ids0.0260.0000.186
get_result_sets0.9630.0523.383
get_taxa0.0100.0000.088
get_taxa_by_ids0.0100.0000.088
get_taxon_datasets0.0350.0040.730
search_annotations0.0130.0005.149
search_datasets0.0360.0001.374
search_gemma0.0350.0001.266