Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-12 12:10 -0400 (Tue, 12 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 2119/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SVMDO 1.9.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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: 2025-08-12 00:37:43 -0400 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 00:43:16 -0400 (Tue, 12 Aug 2025) |
EllapsedTime: 333.3 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 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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-x86_64/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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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: 55753,285,23590,4286,729238,51081 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3948,56999,22933,7879,8665,2731 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51176,2713,788,26762,2729,3156 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1586,7412,5618,4704,181,1678 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 11254,406,122961,2693,2888,6403 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406991,2720,1803,2328,7350,23400 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1376,6576,1589,948,959,2539 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 407021,203859,63874,3482,166785,217 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 514,7372,8799,367,60,7276 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2516,5176,596,4915,3875,5265 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1028,29928,952,10157,643181,63892 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4976,2760,1584,2632,5264,685 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5270,2992,6833,2334,5571,3899 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3673,116228,1757,56999,6868,776 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1355,6476,3122,5313,316,65985 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7157,4128,2695,2194,5193,56652 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5830,10165,91942,10524,23274,6898 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5660,10753,4688,11232,10466,6934 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1801,3703,5595,4842,65985,4023 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 125170,7036,1672,10891,210,54576 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3091,1629,101180976,23417,4843,26003 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1186,2203,6571,6938,140803,2908 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5365,338,4719,477,1641,3081 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1186,4544,8504,4153,5256,29947 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9759,2572,6445,4319,6834,517 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8854,87178,2110,388753,53346,4286 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55630,11132,1361,2683,63892,664 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5189,54982,2108,9451,347411,10013 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7325,1786,10559,409,1585,364 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5078,796,858,54658,593,6888 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5781,4684,5071,189,6531,4144 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 22901,4286,2109,79587,2677,7297 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 685,221935,6566,5444,6774,1859 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 948,6715,1544,5126,5837,5091 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1601,518,2641,2056,54968,3990 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3141,7097,1071,79731,107075310,2949 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 122961,407040,84274,231,1909,58528 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4982,2688,1312,387787,885,23054 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 56919,2542,63931,4357,51082,3382 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2752,6932,8799,189,5331,3098 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 596,6198,3606,1282,3123,26003 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4233,5331,51293,90865,284184,5828 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9945,201305,6906,1728,858,23411 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6696,2690,9630,3899,407011,10229 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 64919,4695,2244,55788,1182,5588 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6576,54968,686,84889,5584,5139 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2243,2992,3988,7320,91869,4879 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 488,3284,941,2632,2495,175 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1591,7292,116228,26235,125170,3077 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 427,344,665,1537,493,51458 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4233,1675,1585,6354,5364,10524 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2146,10965,8560,407011,79053,64131 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 664,3309,6821,80222,10159,7916 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27010,55902,790955,10466,23389,1022 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1149,10642,6897,1786,7289,6616 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1813,60684,6716,221935,2548,255308 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 63931,958,940,694,54931,27141 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5054,2395,3033,183,389,79796 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 345,51548,26235,5595,2303,3562 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 652,181,488,2582,56729,79133 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 64432,84649,51116,1798,728294,23274 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3875,340024,4855,125988,729238,941 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5592,4247,5792,84833,8722,2888 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9095,64900,5329,81704,5211,3157 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55572,2161,3489,1028,79736,2642 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 169026,4137,4627,9056,50674,517 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7347,8504,3284,3358,411,54600 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 101180976,207,627,5250,6929,3651 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5621,10577,2646,3489,3569,6565 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 80347,1737,64801,22978,57176,1646 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5243,5370,132,1175,8567,3483 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 596,93587,56945,410,1072,79585 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4724,7407,231,6786,6720,51052 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1363,407040,492,80347,1393,181 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1583,3356,9429,84275,1471,9382 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 388962,51181,79585,776,326625,8243 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 65985,6609,4688,1807,358,5161 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1910,5228,8660,2052,6374,3155 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7026,6382,137994,5972,1028,6554 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9429,6521,52,8694,325,1675 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 629,79944,5255,29947,10667,2778 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6389,1801,5445,116519,1339,867 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 388962,130589,5654,4311,4854,2729 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 410,94235,3159,652,51649,54549 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2804,6340,4288,5590,1595,1634 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 15,513,132158,84889,23038,9021 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2034,1443,3507,5126,10559,5228 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5241,1893,170302,80201,5618,84902 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1075,3358,22845,57128,158,3062 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54205,1393,84705,2184,2947,55331 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5276,7372,9076,81704,9559,81570 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55034,3712,7167,4988,3953,256471 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 60684,5805,3684,10724,4299,79602 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2834,3703,7466,27232,26521,91869 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51604,5617,2147,6715,2695,1645 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2395,2006,38,4311,9415,2118 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 795,6401,27344,3945,4852,1373 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 34,2731,514,4702,90624,51024 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2271,26227,1813,124976,2834,3073 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 338821,551,5236,23474,51081,2271 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2990,3728,790955,7879,4654,10250 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1812,104,1116,23274,1586,51608 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23654,509,285848,1621,3293,155 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1369,51085,7276,81704,644096,55532 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84342,549,643181,10379,5373,18 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 60684,91452,10094,7916,2944,23516 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27429,3479,50507,1889,2937,6584 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2717,5428,28976,4855,3440,389692 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1586,79661,5350,2805,1352,212 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 486,80201,9663,728,10845,27329 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 940,55670,2030,4718,538,875 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5825,84701,54552,5925,137682,3170 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7275,5306,5901,5798,1409,55283 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3483,3375,221935,2643,2328,9559 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 867,9927,694,153642,858,114548 --> return NULL... 2025-08-12 00:43:07.641 R[36324:439894213] XType: com.apple.fonts is not accessible. 2025-08-12 00:43:07.641 R[36324:439894213] XType: XTFontStaticRegistry is enabled. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 65.244 1.496 67.464
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 0.758 | 0.050 | 1.392 | |