Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-14 12:06 -0400 (Tue, 14 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 2148/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SVMDO 1.9.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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: 1.9.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.9.0.tar.gz |
StartedAt: 2025-10-13 22:04:51 -0400 (Mon, 13 Oct 2025) |
EndedAt: 2025-10-13 22:06:48 -0400 (Mon, 13 Oct 2025) |
EllapsedTime: 116.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SVMDO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SVMDO/DESCRIPTION’ ... OK * this is package ‘SVMDO’ version ‘1.9.0’ * 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 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.9.0’ ** 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 (SVMDO)
SVMDO.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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: 154,5250,79776,9919,7386,434 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10935,120227,650,6925,1734,27235 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1798,10379,1992,28958,4702,336 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8877,5971,145264,6448,7038,9919 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2475,26088,23411,644096,3087,6901 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6354,728,476,186,844,3717 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7035,1203,2309,9945,8462,54704 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 129787,5860,132,2064,435,23062 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 685,54982,3283,8818,27010,4726 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2683,2572,10753,50814,3170,7078 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 160428,587,51548,84447,265,3703 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3440,1339,8818,9131,123099,1080 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6774,81704,55037,488,2697,3598 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 149461,6198,6387,2820,8195,27247 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1376,1815,4669,11093,57128,4925 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7287,2950,2588,7528,344,11222 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8050,27235,10643,5331,55503,1339 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 463,55186,5571,8722,8942,200810 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6579,7097,27429,2169,79602,4878 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 885,7287,6522,4702,51079,148979 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57570,7942,56938,57017,27089,4125 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3596,2310,2638,80207,1436,3293 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54915,2888,361,81704,5467,5078 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6382,79587,4705,3559,4852,5193 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5211,80347,6890,153642,5230,5139 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1345,9377,2932,4069,132158,116228 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3489,824,8678,516,56652,3157 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 25828,158,3034,2643,52,599 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5270,123,518,3172,5350,105372280 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2950,3586,9607,7345,91452,55753 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3119,11231,3552,2694,5346,9414 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51204,3636,506,2878,6383,1374 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 64689,3712,1672,5019,5053,5799 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5925,84275,4712,8473,7099,64240 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9409,1444,2792,339,22820,8504 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26227,65993,3293,3145,5264,538 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 158,7320,7325,81704,593,121268 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2847,56938,6714,4842,4942,2591 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3948,10316,842,1734,1409,5054 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7098,4126,1312,2653,64801,1581 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9091,3576,3636,1339,5562,7431 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406934,221935,383,1543,5236,5592 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7132,55343,1312,1589,22845,160287 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51099,8504,55034,55902,4012,4843 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4852,4715,2646,54806,3156,18 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2118,57017,9692,5713,4159,729238 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1593,9692,3995,255231,3784,959 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2643,3600,1468,406,57001,1029 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5195,3759,11095,2990,4729,26235 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1601,7038,3373,23129,129787,8722 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1277,790,4744,197322,644096,1789 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5276,6901,6928,407040,3479,79661 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5350,9479,60386,316,537,10165 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9507,2793,55788,875,8050,2776 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 355,5967,1175,361,6602,162417 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 50674,54809,6535,55750,26354,10537 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 22796,29078,10094,3159,1435,79776 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4143,54576,1116,55967,5563,7515 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3481,120227,345,133522,3158,219 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 35,5967,341,54931,23417,5590 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 407045,3356,7376,1337,80224,4358 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1524,6339,285848,80070,9507,2280 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 627,2710,51119,3485,7466,6402 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 292,7157,1401,1595,92935,10062 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4718,104909134,1029,790955,54148,4285 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 105372280,100128525,3988,4713,10116,6351 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10857,80331,56997,6392,6720,10128 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 407011,55902,5126,18,463,353 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3295,3992,847,9415,11035,686 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 858,596,60386,2639,57128,859 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3784,90624,405,4846,284958,1393 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57176,116931,316,56606,199,54576 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6948,5313,2271,338,4285,64919 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10135,266,55768,9479,55331,221935 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3460,5329,26521,7431,7026,513 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4705,3710,2729,221458,3703,6897 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5194,55186,54896,8462,84706,2110 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2690,6833,30061,23400,23474,1636 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 574447,2820,148738,266,114548,6556 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6718,54802,29880,6341,10269,493 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10250,4695,1559,640,5730,498 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 56259,4357,844,10382,133522,4035 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1186,133,5293,26762,9560,26517 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3158,7428,2155,81704,5345,2908 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5176,7325,256471,57085,55526,7352 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10891,5730,1584,249,5447,5264 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2169,11095,100128525,492,1116,1369 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3670,7319,2932,8799,23054,4695 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 551,149461,84987,563,153,132001 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5092,2653,266,27247,11254,255738 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 148738,1268,407021,4143,686,56997 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 486,4967,29880,6794,9380,50674 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1716,1363,10221,2948,11131,63899 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6262,7941,5369,56938,1376,3710 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6564,8694,92935,7879,169792,10423 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406938,1200,79731,55644,3557,10999 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4695,54675,1348,84572,6448,5592 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4547,7347,57511,6948,4306,197 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2712,8567,9868,4683,265,7054 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1636,4232,153,2638,9968,10000 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10874,4669,8604,22852,2305,407024 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27125,3304,948,80331,6262,4552 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1493,4684,25915,4023,2820,563 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84572,1080,819,406937,56923,7295 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6821,1606,388753,1629,6648,83884 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54968,6391,84902,10875,51181,55486 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 18,63892,116228,51167,1672,200539 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406922,2157,6492,590,1392,5105 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2628,1559,6927,2950,9526,9630 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 79633,1992,549,10965,15,5702 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51441,3308,1374,5331,2695,1606 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 112817,10195,353,493,8473,4312 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1806,7352,1029,1182,216,1116 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 283120,7480,2944,1489,3949,506 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 821,2673,5250,655,2752,5654 --> return NULL... 2025-10-13 22:06:44.867 R[30346:456068586] XType: Using static font registry. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 24.169 0.407 24.973
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 0.304 | 0.012 | 0.528 | |