* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/TrustVDJ.Rcheck’ * using R Under development (unstable) (2023-07-22 r84734) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2) GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2) * running under: Fedora 34 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘TrustVDJ/DESCRIPTION’ ... OK * this is package ‘TrustVDJ’ version ‘0.1.0’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘TrustVDJ’ can be installed ... [20s/20s] OK * checking package 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [25s/25s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 examples ... OK * checking examples with --run-donttest ...Warning: elapsed-time limit of 45 minutes reached for sub-process [0m/45m] ERROR Running examples in ‘TrustVDJ-Ex.R’ failed The error most likely occurred in: > ### Name: Download > ### Title: Download files retryable > ### Aliases: Download > > ### ** Examples > > URLs = paste0('http://www.imgt.org//download/', c('V-QUEST/IMGT_V-QUEST_reference_directory', + 'GENE-DB/IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP')) > ## No test: > Download(URLs, c('vdj_species.html', 'IMGT_download.fa')) --> 2023-07-23 17:31:12.308349 1 : downloading for vdj_species.html <-- Warning in download.file(URL, paste0(outdir, "/", name), method, TRUE) : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:32:12.317524 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:33:12.419542 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:34:14.515928 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:35:16.608371 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:36:18.707735 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:37:20.800233 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:38:22.890231 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:39:24.983956 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:40:27.086831 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:41:29.17889 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:42:31.272691 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:43:33.369499 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:44:35.469473 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:45:37.566954 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:46:39.659788 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:47:41.755537 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:48:43.847321 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:49:45.941149 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:50:48.034782 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:51:50.129882 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:52:52.220591 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:53:54.307031 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:54:56.396903 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:55:58.498976 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:57:00.597229 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:58:02.685033 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 17:59:04.783336 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:00:06.869899 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:01:08.96581 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:02:11.069073 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:03:13.172982 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:04:15.262476 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:05:17.350901 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:06:19.44201 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:07:21.531538 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:08:23.626982 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:09:25.717093 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:10:27.806409 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:11:29.898122 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:12:31.999966 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:13:34.092599 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:14:36.188384 1: download fail for vdj_species.html !-- Warning in download.file(URL, destfile = paste0(outdir, "/", name), method, : URL 'http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory': Timeout of 60 seconds was reached Warning in value[[3L]](cond) : --! 2023-07-23 18:15:38.27891 1: download fail for vdj_species.html !-- Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘vdj_species.html’ * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/blackswan/ripley/R/packages/tests-devel/TrustVDJ.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 47:30.96, 140.10 + 15.52