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).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (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 |
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. |
Package 748/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemma.R 1.0.1 (landing page) Ogan Mancarci
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
gemma.R.Rcheck/gemma.R-Ex.timings
name | user | system | elapsed | |
forget_gemma_memoised | 0.021 | 0.000 | 0.023 | |
gemma_call | 0.118 | 0.004 | 0.684 | |
get_dataset_annotations | 0.019 | 0.000 | 0.103 | |
get_dataset_design | 0.447 | 0.028 | 0.588 | |
get_dataset_differential_expression_analyses | 0.302 | 0.029 | 3.650 | |
get_dataset_expression | 0.960 | 0.111 | 8.444 | |
get_dataset_object | 6.343 | 0.385 | 17.411 | |
get_dataset_platforms | 0.012 | 0.000 | 0.096 | |
get_dataset_samples | 0.076 | 0.012 | 0.561 | |
get_datasets_by_ids | 0.683 | 0.055 | 0.913 | |
get_differential_expression_values | 0.298 | 0.011 | 3.192 | |
get_gene_go_terms | 0.023 | 0.000 | 0.193 | |
get_gene_locations | 0.012 | 0.000 | 0.235 | |
get_gene_probes | 0.024 | 0.000 | 0.112 | |
get_genes | 0.024 | 0.000 | 0.180 | |
get_platform_annotations | 1.066 | 0.029 | 3.871 | |
get_platform_datasets | 0.047 | 0.000 | 2.538 | |
get_platform_element_genes | 0.012 | 0.000 | 0.096 | |
get_platforms_by_ids | 0.026 | 0.000 | 0.186 | |
get_result_sets | 0.963 | 0.052 | 3.383 | |
get_taxa | 0.010 | 0.000 | 0.088 | |
get_taxa_by_ids | 0.010 | 0.000 | 0.088 | |
get_taxon_datasets | 0.035 | 0.004 | 0.730 | |
search_annotations | 0.013 | 0.000 | 5.149 | |
search_datasets | 0.036 | 0.000 | 1.374 | |
search_gemma | 0.035 | 0.000 | 1.266 | |