Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:06 -0400 (Sat, 09 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 |
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 | ![]() | ||||||||
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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.9.0.tar.gz |
StartedAt: 2025-08-09 03:21:11 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 03:26:13 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 301.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SVMDO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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: 3157,3934,6834,22868,4654,2683 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6535,308,6182,5306,2559,51608 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3663,2690,3489,2542,811,10102 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7915,3767,56623,6445,153,7919 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3952,5428,3929,229,10875,83548 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1559,1186,162417,3992,11254,406922 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57107,1543,51116,11213,3122,2056 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 463,5406,219,28951,79661,5595 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 55024,7916,7515,23291,53632,51181 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 406,229,10935,64919,2516,111240474 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 255738,8678,5190,6649,2745,7077 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4723,2904,116519,51052,64788,487 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5836,29947,4925,3480,1175,2110 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5214,6648,94235,867,249,1444 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57817,4256,2200,6890,10841,56999 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 653509,3507,4282,212,3425,6439 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 37,2835,51738,6579,9388,10226 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7351,587,4758,54577,9919,7879 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9429,4288,4688,644096,25813,1803 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5295,1543,9374,644096,100130015,1352 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5538,5588,33,653,387787,5257 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 793,2475,5288,3685,2548,859 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10157,2628,8743,91942,54704,10560 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3312,87178,6401,4159,115286,231 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5563,51441,55526,1802,6602,9382 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 432369,10013,50674,2495,7915,7431 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3643,29947,1606,1644,5139,2946 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1558,10379,50814,5468,2784,10753 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23409,2629,51092,124454,2745,694 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2588,9388,92935,3141,5239,84334 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2582,5189,63899,51021,476,170302 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5588,2590,644096,5507,5740,8842 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5346,3948,51092,2184,7879,5095 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 57192,3060,3784,9021,7019,84557 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7284,4069,5551,84275,51128,9759 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 479,5321,26175,137682,8462,5080 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5052,4719,84701,149775,1717,2110 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10165,627,793,6354,4683,149775 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 570,1672,6521,4853,1345,8818 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1813,4854,23395,3158,54106,5092 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10250,6898,5588,4668,1435,101180976 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3170,3416,3425,1185,367,84649 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2588,8942,10730,1956,3425,84889 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 599,4758,83985,79934,5261,1583 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 788,5207,2745,51144,1812,3569 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6535,65993,2303,6794,2247,6339 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6649,4842,2739,4552,2260,156 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 89866,79001,644096,23462,115286,440503 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8648,125988,9388,84701,5743,1890 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 407007,90865,113235,291,2052,8854 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9672,1889,56729,7319,131669,1678 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9868,836,5571,6716,1348,53335 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8517,133396,6564,4779,2169,5409 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4723,3174,2006,79053,55967,2266 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2395,3562,6602,89866,51085,7941 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6339,2890,788,166785,57192,4543 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5195,407024,90624,7386,84557,1027 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4306,116931,151306,4843,5792,5286 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 367,7915,3485,6536,10128,23462 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 1769,4313,22933,629,8879,2305 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 339,112817,60684,4915,8471,4023 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7248,5068,56259,133522,7386,5291 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3700,85365,1812,1718,51316,2688 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2056,1346,5728,1116,3479,7035 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7942,1802,2305,50814,2693,3483 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 25828,2118,4306,2717,1621,4760 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10383,664,64900,359,4314,3651 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 114548,28976,7386,55670,23417,2835 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10383,6565,1056,493,5799,6928 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2936,54205,2786,406934,840,728 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2745,325,6834,1232,57085,1950 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 8639,6714,4780,3558,5096,8195 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 169026,1910,137682,55753,27010,116519 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 51052,2786,5798,116519,627,3170 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3598,3554,1806,875,9868,4713 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 56922,4853,54802,3636,5743,5019 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 26060,57570,4256,2119,4049,4982 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 340024,133522,4968,8202,2729,4852 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 54802,5265,5019,9779,6932,10226 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 80347,8473,3586,8639,7376,7289 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5207,1444,123263,7084,162417,339 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9779,3945,5972,55034,1859,84317 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 491,4256,4704,275,1585,3158 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 376497,56606,55753,858,1080,10157 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 23530,55630,1769,6834,79068,6569 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6339,5654,148738,79633,7386,9663 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 100128525,2932,25828,79731,4306,538 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 79587,1594,63874,80070,162417,4684 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 83884,1769,1468,138050,9997,18 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3598,2646,55902,488,353,55034 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 999,51206,7919,56302,151,4726 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4313,156,2170,3283,5702,1075 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 9445,55186,51079,29929,64432,84061 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5230,100529063,10159,4712,84340,9241 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 56302,491,6720,5551,57678,6550 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 5901,3606,4012,23175,7412,111240474 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 160287,54210,57511,1559,24147,3158 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 942,6908,11213,255738,4702,5095 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84557,574447,79133,7167,2487,8243 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84062,2713,1803,55750,9415,9692 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4726,54344,7840,2949,585,5236 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 7381,4878,5052,779,5621,160428 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6522,4729,2632,23600,656,81704 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 10102,1645,790955,11131,406947,9429 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 6374,26235,55902,3358,26517,1605 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 84447,3304,4982,33,10383,147007 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3091,10226,79736,57570,55818,3606 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 779,8050,7287,81704,6324,6786 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 285362,5799,3113,3283,7056,34 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 2055,4878,7030,5551,52,51604 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 3980,5730,2847,1471,51206,2936 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 4976,1641,50506,5743,27141,4314 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 407040,2030,107075310,7941,51458,10226 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 27089,5009,2689,729238,275,5476 --> return NULL... --> No gene can be mapped.... --> Expected input gene ID: 405,5562,84062,239,4925,513 --> return NULL... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 66.822 1.126 68.070
SVMDO.Rcheck/SVMDO-Ex.timings
name | user | system | elapsed | |
runGUI | 0.643 | 0.032 | 0.811 | |