Back to Build/check report for BioC 3.20 experimental data |
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This page was generated on 2024-08-22 14:51 -0400 (Thu, 22 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
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 107/425 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
easierData 1.11.0 (landing page) Oscar Lapuente-Santana
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||
To the developers/maintainers of the easierData package: - 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. |
Package: easierData |
Version: 1.11.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:easierData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings easierData_1.11.0.tar.gz |
StartedAt: 2024-08-22 11:27:31 -0400 (Thu, 22 Aug 2024) |
EndedAt: 2024-08-22 11:41:15 -0400 (Thu, 22 Aug 2024) |
EllapsedTime: 823.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: easierData.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:easierData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings easierData_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/easierData.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘easierData/DESCRIPTION’ ... OK * this is package ‘easierData’ version ‘1.11.0’ * 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 ‘easierData’ 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 ... ERROR Running examples in ‘easierData-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: list_easierData > ### Title: List the datasets > ### Aliases: list_easierData > > ### ** Examples > > df <- list_easierData() Error in value[[3L]](cond) : failed to connect reason: Timeout was reached: [bioconductor.org] SSL connection timeout Consider rerunning with 'localHub=TRUE' Calls: list_easierData ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted * 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: 1 ERROR See ‘/home/biocbuild/bbs-3.20-data-experiment/meat/easierData.Rcheck/00check.log’ for details.
easierData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL easierData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘easierData’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (easierData)
easierData.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: 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(easierData) > > test_check("easierData") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 26.770 1.357 32.278
easierData.Rcheck/easierData-Ex.timings
name | user | system | elapsed | |
get_HGNC_annotation | 0.000 | 0.000 | 0.001 | |
get_Mariathasan2018_PDL1_treatment | 0 | 0 | 0 | |
get_TCGA_mean_pancancer | 0 | 0 | 0 | |
get_TCGA_sd_pancancer | 0.001 | 0.000 | 0.000 | |
get_cor_scores_genes | 0 | 0 | 0 | |
get_group_lrpairs | 0 | 0 | 0 | |
get_intercell_networks | 0 | 0 | 0 | |
get_lr_frequency_TCGA | 0 | 0 | 0 | |
get_opt_models | 0.001 | 0.000 | 0.000 | |
get_opt_xtrain_stats | 0 | 0 | 0 | |
get_scores_signature_genes | 0 | 0 | 0 | |