Mac ARM64 build report for BioC 3.18 - CHECK results for gemma.R on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.2 (2023-10-31) -- "Eye Holes"	4298
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*

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### Running command:
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###   /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_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/gemma.R.Rcheck’
* using R version 4.3.2 (2023-10-31)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘2.0.0’
* 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 ‘gemma.R’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘digest’
A package should be listed in only one of these fields.
* 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 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                           9.396  0.349  16.471
get_dataset_raw_expression                   0.990  0.036   5.581
get_dataset_differential_expression_analyses 0.667  0.047   8.149
get_dataset_expression                       0.546  0.047   7.881
get_datasets                                 0.158  0.016   8.826
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/gemma.R.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gemma.R
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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


R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 1 | SKIP 4 | PASS 111 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On Bioconductor (4): 'testCaches.R:37:3', 'testConvenience.R:14:5',
  'testConvenience.R:36:5', 'testDatasetEndpoints.R:84:5'

[ FAIL 0 | WARN 1 | SKIP 4 | PASS 111 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 27.005   1.137 112.955

Example timings

name	user	system	elapsed
filter_properties	0.039	0.005	0.045
forget_gemma_memoised	0.007	0.004	0.013
gemma_call	0.146	0.017	1.398
get_dataset_annotations	0.081	0.012	0.262
get_dataset_design	0.245	0.020	0.496
get_dataset_differential_expression_analyses	0.667	0.047	8.149
get_dataset_expression	0.546	0.047	7.881
get_dataset_expression_for_genes	0.013	0.002	0.195
get_dataset_object	9.396	0.349	16.471
get_dataset_platforms	0.011	0.001	0.500
get_dataset_processed_expression	0.969	0.038	4.865
get_dataset_quantitation_types	0.009	0.001	0.339
get_dataset_raw_expression	0.990	0.036	5.581
get_dataset_samples	0.061	0.003	0.255
get_datasets	0.158	0.016	8.826
get_datasets_by_ids	0.040	0.004	0.373
get_differential_expression_values	0.007	0.001	0.175
get_gene_go_terms	0.021	0.005	0.360
get_gene_locations	0.010	0.002	0.226
get_gene_probes	0.028	0.004	0.209
get_genes	0.022	0.003	0.352
get_platform_annotations	0.989	0.040	2.318
get_platform_datasets	0.035	0.004	0.315
get_platform_element_genes	0.011	0.001	0.180
get_platforms_by_ids	0.024	0.002	0.368
get_taxa	0.010	0.002	0.173
get_taxa_by_ids	0.009	0.001	0.171
get_taxon_datasets	0.041	0.006	0.396
make_design	0.242	0.026	0.529
search_annotations	0.011	0.002	4.137
search_datasets	0.039	0.007	1.609
search_gemma	0.038	0.007	0.645

CHECK results for gemma.R on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings