Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-04 11:37:16 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 2112/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SVMDO 1.4.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SVMDO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SVMDO.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: SVMDO |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SVMDO_1.4.0.tar.gz |
StartedAt: 2024-05-04 04:13:07 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 04:17:58 -0400 (Sat, 04 May 2024) |
EllapsedTime: 290.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SVMDO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SVMDO_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * 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 ‘SVMDO/DESCRIPTION’ ... OK * this is package ‘SVMDO’ version ‘1.4.0’ * 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 ‘SVMDO’ 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 ... OK * 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: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘SVMDO’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading `shiny::dataTableOutput()` is deprecated as of shiny 1.8.1. Please use `DT::DTOutput()` instead. Since you have a suitable version of DT (>= v0.32.1), shiny::dataTableOutput() will automatically use DT::DTOutput() under-the-hood. If this happens to break your app, set `options(shiny.legacy.datatable = TRUE)` to get the legacy datatable implementation (or `FALSE` to squelch this message). See <https://rstudio.github.io/DT/shiny.html> for more information. ** 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 (SVMDO)
SVMDO.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(SVMDO) Loading required package: shiny > > test_check("SVMDO") 'select()' returned 1:1 mapping between keys and columns --> No gene can be mapped.... --> Expected input gene ID: 1629,3569,2222,1200,25801,33 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4668,644096,406938,3932,55970,79191 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3553,148738,57215,6616,1499,117289 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 229,5919,1738,140803,8842,3674 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8455,125988,1392,9451,596,2806 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 43,4726,6928,4276,6714,406906 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6446,100507436,5660,2520,5053,1281 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7345,3290,197322,1052,25828,353 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7409,2260,79602,203,5802,793 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3811,5108,2632,6374,55867,3700 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 79661,4091,162417,91942,3312,5468 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6183,6338,4522,476,4221,3670 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1208,55750,1909,115286,4548,3931 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1497,840,51660,3991,7507,1029 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406938,3640,2889,29851,842,6272 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4319,5295,4744,1509,7274,93587 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1369,27329,2260,2592,3507,773 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10911,9104,57678,6280,9255,3077 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57001,4153,56923,5009,2516,2790 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1316,116519,1757,4724,5781,6535 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5920,5331,1513,2639,3875,4143 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 344,5468,10682,7325,3569,84277 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5071,23753,26503,5806,8398,31 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6531,116228,11266,2992,22796,6505 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4792,3106,151306,4715,1051,6374 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7026,2309,9498,5191,1376,759 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 123099,64772,116519,4129,1636,11254 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 229,4609,55788,8742,1557,3667 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 257313,10666,3033,8799,81034,136259 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6535,2643,686,22845,9241,7350 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6657,3401,8835,3485,3066,7048 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6338,643387,285848,10935,200539,1340 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3815,3598,64102,5830,2776,7385 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 85569,8784,23564,10577,3684,5697 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26088,6183,79934,3638,91869,4854 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 384,9560,7200,2792,3339,6941 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 123,462,1075,7052,55867,3033 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4712,5276,5175,2068,1369,5092 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10165,3690,6550,4886,8854,4288 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 175,5406,94235,18,353500,5967 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4017,3566,37,406938,407021,9095 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5972,1956,5498,706,4069,2954 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3569,344,3292,1208,3557,5590 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3934,186,9518,8228,23365,7507 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4548,406922,3574,50674,3292,256471 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1843,136259,3625,5274,84557,6401 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 100,10116,10886,2152,54414,1030 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2115,2559,5860,5920,563,10102 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4704,8788,1491,2587,2946,1650 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6492,4580,10991,642489,1371,9518 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5599,6351,3385,6535,4285,64220 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 130120,1789,648998,90480,3284,5445 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 275,1806,2791,203,5294,407021 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1968,2896,83985,1270,54575,8813 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4586,2166,5641,5080,55343,200205 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 336,5586,1394,83440,4318,7841 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3356,5726,5565,6535,1565,3990 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 120227,9507,1382,5468,64805,859 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3934,90480,7025,4609,55065,582 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6342,353,10116,821,4852,114884 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2950,5836,265,84868,8471,4889 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6182,959,8202,25974,3119,57061 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8932,200186,5346,6301,6583,410 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2155,1033,7942,4544,3762,643387 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5077,5277,25974,8803,6548,23163 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54806,104909134,516,6584,9722,85476 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4729,1589,5792,9311,3485,10559 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2168,79068,7132,3624,3250,1807 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5255,3426,8462,5071,7325,10599 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5826,2806,6492,111,6392,4709 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6616,8029,100133941,221895,10400,29960 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2697,8462,8609,50639,57085,6401 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 643387,50615,4547,7056,6232,57176 --> return NULL... No gene sets have size between 10 and 500 ... --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 407004,5515,116985,80267,4879,5406 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 89823,23291,4489,4723,1508,54982 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 80224,3242,2791,779,6718,4040 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9575,6620,213,56244,8074,57192 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4914,496,6821,215,10116,8841 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3759,3725,4552,4938,4880,3815 --> return NULL... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 52.063 1.134 53.177
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 0.619 | 0.052 | 0.674 | |