Mustafa Erhan Ozer
| Snapshot Date: 2026-03-04 13:45 -0500 (Wed, 04 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: RELEASE_3_22 |
| git_last_commit: 86871da |
| git_last_commit_date: 2025-10-29 11:23:08 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-05 11:57 -0500 (Thu, 05 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4894 |
| 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 2163/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.10.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for SVMDO in R Universe. | ||||||||||||||
|
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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2026-03-05 04:52:27 -0500 (Thu, 05 Mar 2026) |
| EndedAt: 2026-03-05 04:57:32 -0500 (Thu, 05 Mar 2026) |
| EllapsedTime: 304.4 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.10.0’
* 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 ‘1.10.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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: 1869,384,2314,57505,84701,6352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6788,5743,5919,89778,4536,7325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1544,1080,2100,656,9180,84947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6721,5372,130589,4056,2597,100128525
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29926,3638,55863,2235,5293,10316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30061,7388,29881,949,3938,10250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5501,3938,8504,291,7284,1843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10400,4513,5167,8660,4543,30061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10116,8462,407045,54575,1471,5162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2799,57128,6928,10295,54476,10991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,2990,84342,5646,3483,54968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3673,129787,2247,4726,4669,10643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5595,517,1641,1355,664,1557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3954,51458,84300,125170,3791,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84649,6925,1028,6938,2064,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 256394,7057,6357,3899,5972,1583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2169,1394,3308,1409,2591,7471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5631,1491,10965,84947,81027,57107
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2739,407004,84649,6402,407007,154
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 293,5409,23411,4720,83854,2645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 593,4723,54931,1409,4540,358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2745,57085,5579,124454,10400,116150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4524,2309,5306,1650,4233,5328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4654,2950,166785,885,1589,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83884,55818,4719,29881,64801,405
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6392,7220,186,1601,100,80207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3949,3030,5592,27329,2987,4056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406937,4683,4123,133522,1348,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8309,216,3162,4855,4544,6908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1185,57380,3440,2243,5139,7320
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3692,7385,3054,1318,3684,1807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6342,2597,4780,3482,5230,8567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5350,3312,256394,3417,5860,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8818,1910,6383,6236,8942,140803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 249,80267,130589,2108,4089,11222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8243,4519,54806,3795,11132,1636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2056,2260,5213,6908,157848,5191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81027,2690,5551,5830,3948,6236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 361,2645,3304,123283,84275,4123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,347411,90480,6505,60,4089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5581,3418,1649,3309,7220,388585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1071,2271,2571,5465,4719,5189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790,79731,463,56302,266,5345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1393,563,1585,51604,85365,160287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 492,54552,3795,4720,291,100130015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64240,4118,6890,3284,201595,5629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84869,221458,1636,5592,54549,3295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6402,64689,7919,4536,4312,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493753,64116,445,51293,3482,7040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51099,3598,1444,181,7428,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,64601,10643,22796,5080,2194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9663,1080,5291,5579,347411,4128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8431,4878,7172,2668,7942,3953
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 411,3651,2639,1650,5193,1728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6948,4256,80339,2678,8841,56259
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,477,516,4760,487,64240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,116519,6199,2101,87178,3813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,4338,2280,156,275,12
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 376497,113235,3162,708,11231,181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3122,38,486,55768,3141,84701
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 210,284434,8471,2152,9945,476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 635,5176,3240,846,10682,3991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130120,5261,9241,169792,90580,3958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6714,54476,9692,551,80201,4012
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 656,1185,463,5370,6788,462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91869,1489,113235,1649,51167,6476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3170,3356,4508,844,6648,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10333,3483,5139,2888,10135,4288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83733,4702,5189,81793,2118,5188
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3417,4299,6908,5236,2161,54549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79585,120227,3170,4704,326625,2646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54675,11254,7391,85365,4594,347687
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2641,2559,51021,83884,6519,23475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149775,147968,590,55970,212,10580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11222,55858,5792,6929,4049,406982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5447,285362,2524,5465,7325,6934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3995,255738,120227,2834,196385,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4123,498,23175,4149,54915,5824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1019,4519,156,1056,201305,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,407007,12,4695,101180976,23304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1200,5409,3673,239,55526,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83439,197322,10938,2628,9332,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,51601,347411,2642,1737,5473
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5091,6248,54552,6515,23462,6804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3145,1071,80267,156,1149,3507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51079,55750,3417,2791,19,10845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1345,1543,213,4543,3486,3490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 664,476,4851,5828,4357,5728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55644,9526,50484,29108,1392,84275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27010,6602,112817,9919,4697,25821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1757,5370,241,5798,26354,7124
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,55024,886,2309,1186,2949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1813,6569,656,6584,26191,4049
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,3945,54576,7124,11019,1116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3485,137994,387082,435,51441,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55699,9512,2787,4846,3995,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388753,3813,4779,358,2745,157848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2987,85479,2875,4288,51206,435
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,1116,7084,12,4288,205327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55037,8678,2647,2593,9054,7025
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132158,5345,4314,5230,1346,819
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,85569,2572,427,27249,3600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,124626,2785,6357,35,6932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3554,4351,3929,85569,84649,55037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,5629,7167,60386,51094,51241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1514,4700,1650,56997,2638,824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1728,2805,128486,10269,5950,6523
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,3172,2641,3643,406913,55503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4887,2590,3586,344905,2952,3624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3667,2475,3598,79944,2875,27125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 268,7030,7082,1514,79934,2289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2710,89866,1717,90865,51555,7025
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
63.775 1.259 65.210
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.689 | 0.024 | 0.873 | |