Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-14 11:45 -0400 (Thu, 14 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 2139/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SVMDO 1.8.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 1.8.0 |
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_1.8.0.tar.gz |
StartedAt: 2025-08-12 11:37:59 -0400 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 11:49:06 -0400 (Tue, 12 Aug 2025) |
EllapsedTime: 666.9 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SVMDO.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * 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 ‘1.8.0’ * 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 ‘1.8.0’ ** 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 RC (2025-06-05 r88288) -- "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: 5373,84947,2152,10094,6356,1348 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5744,819,85446,79736,5331,5805 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9131,10466,7428,7351,7325,23062 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 551,2697,111,50943,84300,538 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1629,8714,582,199,5538,6720 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 185,116150,54901,6932,5925,2147 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 112817,1812,9104,10466,1641,51144 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4915,55503,7381,10383,5631,6262 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8504,952,7421,1401,2328,3091 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2581,84693,6569,3992,84239,4669 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55768,79934,7386,801,3624,5293 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55283,9365,7252,3293,55858,64689 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1581,5327,2588,3559,5176,7494 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2158,51117,958,407021,51079,4654 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4915,56923,6519,857,8604,5723 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8799,212,4713,1361,11019,28976 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3074,9672,29926,91574,79053,166785 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6521,125988,22797,1347,10229,445 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 790,836,4758,11019,6476,4023 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5274,10195,55630,229,9607,1807 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 200539,84889,54476,6262,3251,64241 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 34,2180,84701,50674,2590,5743 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 643181,4668,593,51085,5595,27235 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54210,1646,3759,1499,156,5507 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55670,5265,249,6531,650,8600 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 516,6198,509,8932,28234,643181 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 338821,63874,50674,11232,2820,7097 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8651,84274,3700,842,4886,54931 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51422,338,175,54567,1607,2990 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 374291,3375,5052,2697,6329,7879 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26060,51094,11131,3157,10102,5372 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5501,7840,9968,2677,6550,5465 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6934,2309,5184,729230,10000,79585 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 121268,4718,1869,7355,5250,406922 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6696,54344,2950,1443,5331,57505 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1621,407006,10616,3440,35,123 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54982,6582,10019,1559,5826,952 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23291,942,4337,4697,8659,55630 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7350,5837,54809,1371,10991,1889 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7124,728294,811,6678,358,50506 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1595,54809,1589,2919,3145,169792 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51206,1435,801,5468,1571,1208 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 341,1757,1583,1281,5594,2936 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3156,8813,9180,551,353,5329 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3479,5727,9370,4688,6794,516 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2937,5580,2710,5365,26354,4594 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1571,79133,84701,388585,359,5631 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4915,2952,351,100,776,4544 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 811,2695,56052,3489,2717,2194 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4853,7319,4282,5730,84572,5830 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 52,152078,4015,79587,57085,51660 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 11213,4887,3308,6387,85479,6579 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 632,9572,2591,149461,2052,5009 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4285,6714,6439,2581,79585,9095 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1893,2034,2305,3418,51611,1672 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2314,5255,5601,3291,6387,5052 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55024,57176,9698,336,253943,9104 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 60684,255231,54915,686,1443,54600 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55572,1373,540,3060,125170,2678 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 129787,8648,80224,7355,65080,81033 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5962,64116,92667,8841,130120,10 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2516,587,1636,563,1910,1524 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2539,1491,1409,6891,51204,23462 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9091,779,3157,51316,200205,685 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 32,3113,131669,4719,3375,1351 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5293,2638,5241,2984,4688,51082 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6387,2760,3920,5743,1909,26517 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7040,6517,8802,407045,3934,2647 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5588,3952,509,4137,84987,10059 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5836,2762,407009,1734,316,3667 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3991,6811,92935,7276,51081,1348 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 491,79944,4069,4049,7385,1737 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 56606,94235,92935,1890,23389,7019 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4000,388,51116,9365,132,6929 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6439,219,131118,153642,18,2581 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1443,26354,7132,64116,132,55858 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10857,3930,6891,2746,8651,1436 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2805,48,84334,7048,6571,84987 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7284,80267,3507,7030,2247,383 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27429,409,130120,340024,6928,64087 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2785,64801,84342,132001,2271,51548 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7057,25839,5901,291,5295,2688 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26003,64801,8841,1401,4000,567 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2348,407024,4233,6774,255308,151306 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26291,2702,6556,3032,7528,6576 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54578,336,6888,2678,5595,7018 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6786,3636,1678,25974,4313,9414 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 729230,3630,9927,2834,11255,6554 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4779,6391,1356,4722,2762,2835 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51293,3158,1234,64801,2266,1650 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51204,847,7084,6352,104,477 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1672,8942,6182,6339,55970,5744 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 80070,5270,3606,9630,4089,5428 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84889,8560,1329,1543,105372280,57176 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7421,338,7287,3351,3425,54210 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 189,221935,2717,5836,90865,30061 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1737,54476,81704,1182,208,4968 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84902,7225,8473,7276,5728,7025 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 374291,513,285,1813,5321,836 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57817,5950,7132,9180,471,1374 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7097,6948,9575,3552,6262,37 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9945,57085,2280,940,549,9559 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1268,100131801,5631,83854,6833,50943 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3551,6347,56729,79053,1644,6898 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54902,27344,1345,364,2099,686 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8877,5962,3939,160287,22820,6319 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 65080,3240,4744,6821,9698,6890 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 31,5241,7038,3489,6199,11019 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2643,4247,64241,79949,197131,1442 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1392,5592,1813,145264,941,1645 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1586,3490,268,124976,490,7841 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2647,84340,572,5789,538,54675 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6891,55024,4049,407010,152926,2628 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1589,53345,55699,3596,563,7052 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5660,6571,407045,819,64805,686 --> return NULL... 2025-08-12 11:48:52.226 R[71625:314281507] XType: com.apple.fonts is not accessible. 2025-08-12 11:48:52.226 R[71625:314281507] XType: XTFontStaticRegistry is enabled. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 176.145 2.347 183.082
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 1.279 | 0.079 | 1.997 | |