Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:07 -0400 (Sat, 11 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" | 4586 |
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: SVMDO |
Version: 1.9.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SVMDO_1.9.0.tar.gz |
StartedAt: 2025-10-10 14:24:41 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 14:32:41 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 480.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SVMDO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SVMDO_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 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 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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: 788,7879,8504,7019,29078,51608 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9927,1557,10667,37,2542,1910 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5825,152926,2100,4288,81033,3382 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1277,51181,57048,51004,56259,656 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4598,2475,406934,479,26762,3242 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7424,471,116228,959,10226,406991 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 941,85446,496,858,4285,7220 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2030,432369,55858,10243,4724,6789 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10891,57017,6566,4715,241,3636 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55270,57107,119559,151306,5406,175 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27329,563,8862,629,57107,3290 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10911,54106,9409,2244,2645,10935 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 653,2487,5122,6550,131118,133 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5372,929,100506742,5189,119559,629 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1351,57085,51548,3458,89874,8665 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5837,84300,81034,8862,60528,63931 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6261,3242,54809,2876,2628,10644 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4851,2584,1890,3082,2697,11222 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7515,166785,5175,2064,10724,3598 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3351,5288,551,383,2944,729238 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5228,4144,5590,53632,4967,4552 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7384,25828,4853,64900,4669,7466 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55768,5370,1268,51024,4842,9021 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2740,2590,5654,265,22852,3779 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55753,3101,10195,7289,7287,79087 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1581,2235,10020,255231,3920,5105 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2643,1468,2303,56997,2697,2752 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4700,6786,1281,229,57048,3931 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406934,65993,4125,3684,3293,54915 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 37,54539,7412,7276,100506742,5792 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 80331,2584,5501,5468,151,2632 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2702,2235,4049,55037,11095,221458 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51103,8932,582,26003,10062,406947 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 22933,5618,1585,7099,3952,5925 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 133522,405,5053,60386,4720,1672 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 64131,811,2314,7347,1270,5743 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1340,10524,7391,3373,517,4069 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7528,5970,4855,79736,384,64432 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8743,1277,5345,4846,27329,5445 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4306,2645,5069,836,5194,57128 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 345,26762,85446,100,1352,1353 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51458,6888,4299,3251,10935,5506 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1645,8722,5211,51052,1393,5069 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2697,4879,8945,79736,2786,3554 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 353500,51458,89866,4049,706,2517 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9388,9056,2587,5211,55532,92609 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54106,8842,2952,3692,63892,6897 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 347,7048,2673,1629,1718,650 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23410,2581,79001,6261,5330,150379 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4149,7428,65993,91452,200205,26088 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51144,51300,4758,5727,2587,1347 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 81704,2052,54578,6821,84239,51004 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9572,10891,55034,5167,23654,5291 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55037,4886,2689,8473,23556,2099 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1869,1080,1645,10195,7048,84706 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1072,3293,34,221935,140803,27247 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5189,9759,1201,29960,2890,999 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51083,7284,4760,1329,5193,23753 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 53632,2064,840,350,3779,5644 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 11136,2303,133522,54968,1080,4744 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3375,200539,7248,347,54575,7287 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8473,2591,55937,999,51081,56923 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5617,2119,3251,147007,56623,9663 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5428,6938,2597,26354,5211,55699 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 11255,6389,3339,79144,10159,5406 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1348,7056,3417,53346,50943,10730 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57380,23304,64601,3651,26354,54805 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7384,2147,23054,80207,2539,57001 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3373,8604,518,462,3773,10382 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4069,4149,4118,57085,728,440138 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5444,2056,2335,51103,5286,2834 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27429,3480,100131801,3458,5095,64689 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 492,7220,708,795,6390,27089 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 203859,6868,1906,5728,84889,7325 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 50484,27429,56999,27089,3356,3082 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 356,10159,7025,10229,1734,57192 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6347,79158,10842,1244,26521,2348 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51128,6182,434,3485,54802,3931 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4722,2776,2696,3423,8799,6772 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4547,3958,1232,53345,293,7840 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 100131801,22868,10857,3383,3098,5444 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2992,2303,83439,4852,1956,1769 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4143,8604,6392,197322,1558,3170 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2244,2791,4719,2689,840,60386 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7077,1806,9572,537,79144,2517 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406906,100131801,25821,7389,3988,5295 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6794,6584,2487,55340,55278,344 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3930,8932,5467,10935,1584,10000 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 152926,3952,199,351,201595,22845 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5499,8675,7284,29078,11232,388743 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 148979,51555,32,51103,22933,407045 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 345,51116,1588,54931,3242,285 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5175,388743,3991,5373,56652,7376 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26517,563,158,3557,123,79087 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2791,1373,55163,344,7841,54331 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4153,7412,7351,79944,4502,3600 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 130589,4594,7325,9969,10644,8842 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9409,3479,7942,29960,26175,5595 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9420,3482,55503,1268,9021,4709 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 138050,2108,7355,11232,2835,6571 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57085,1471,3645,5250,129787,7052 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 347,38,7054,7412,1356,5743 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51604,5625,2835,8862,1369,3098 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5369,5214,3795,1027,80201,6721 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 885,5365,11255,92667,391051,498 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 210,2740,2919,1968,3159,6198 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406922,6522,5288,3123,2932,7038 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1363,186,840,3938,1557,6464 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 632,2678,7297,6339,886,6492 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4779,5192,2053,132158,5428,4548 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1019,56259,229,5313,55863,23556 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3440,80224,3101,150,406922,10000 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3980,11136,57620,51083,5498,2647 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84987,60528,142,7100,56997,3356 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23129,6748,6786,7132,8803,92609 --> return NULL... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 74.236 1.857 105.368
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 0.774 | 0.012 | 1.713 | |