Mustafa Erhan Ozer
| Snapshot Date: 2026-02-05 13:45 -0500 (Thu, 05 Feb 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 2026-02-09 11:58 -0500 (Mon, 09 Feb 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" | 4888 |
| 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: 2026-02-06 04:40:36 -0500 (Fri, 06 Feb 2026) |
| EndedAt: 2026-02-06 04:45:46 -0500 (Fri, 06 Feb 2026) |
| EllapsedTime: 309.5 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: 25828,6616,3667,7471,5660,10316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7124,10229,642489,6715,7035,81570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,7035,3995,2713,34,212
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5329,3708,389692,51204,3119,81704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,406947,79644,293,92935,5190
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10269,6341,3813,149461,3356,54205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221935,2720,10128,1373,23600,2791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,10379,5328,203,4049,2746
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5054,53335,6476,5445,6445,410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6609,185,10008,79731,355,116085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406947,3562,6319,2647,5369,1591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4700,2641,4668,50674,1394,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,8722,3586,7057,80347,10221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 665,463,5745,729230,23475,10841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 348,5188,6548,10159,6890,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 617,64788,84275,3551,3054,3065
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79661,407010,51608,1807,2591,9104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26119,51660,3101,388372,2786,7391
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2787,7038,776,5617,5962,5190
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1813,54476,3728,8884,1581,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54476,28957,52,5211,2280,55644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7345,2919,1282,55005,2203,6925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4702,80207,5241,9559,54148,57001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5625,48,656,729230,56999,4160
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,150,83733,6356,3708,8743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51204,4537,7352,4855,3949,383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7412,629,9919,8309,54511,5346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123688,51004,23409,5972,212,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1815,7124,84833,2934,4012,4988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,29958,9056,11112,2243,4144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4118,23304,2584,1678,29928,3991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28234,5250,1021,3992,6464,6584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,4853,350,155,293,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 87178,6464,3358,4541,2348,8604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51144,308,10400,5594,1950,29926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51422,212,652,1340,3383,57107
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63892,48,4040,7078,3554,387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5331,51204,3425,8743,90580,9868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29960,1737,3115,1186,9630,3728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23556,7381,729238,3174,55526,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406938,325,4843,706,1345,11096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 351,2063,2790,5160,4988,5592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5443,9021,216,4899,92667,4137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1803,8854,239,686,4256,10965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 479,1769,5327,6602,148979,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,5256,3098,231,9526,23530
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11231,9474,2147,60528,6786,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11136,1355,85446,4719,823,29108
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10000,6897,7097,53335,7040,101180976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2571,3062,5837,2119,80070,3692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6938,54148,186,153,958,27089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407010,124454,5370,57192,5970,1270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5962,351,3065,656,10195,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 147007,4089,132,23054,316,84300
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201305,7098,4709,5970,54600,8567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6341,1892,6517,9927,308,2653
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8564,2161,219,8243,4149,1757
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10316,6352,581,1371,866,6582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,1356,79158,9167,8648,4669
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,29843,51119,79158,5189,112817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3065,8945,2690,4318,2947,4718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,2638,7225,2790,1071,133522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84300,1201,1312,5799,5175,55818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653,10457,9332,842,356,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6890,51608,29928,3717,7381,213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8877,3551,112817,2055,175,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,10102,55937,570,3991,64240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8694,10537,6774,84342,5798,3293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 145264,4654,5507,629,6788,51176
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1757,5369,147007,9927,7421,64087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23304,514,51441,80339,4519,9630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7035,4149,7409,840,6934,463
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,2788,57107,50506,387082,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 350,6602,56999,9479,9919,2678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,5836,29968,64131,25813,4288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4247,811,821,10730,664,5189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7428,3480,3091,7099,1491,51081
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4566,7386,1910,151306,57104,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2587,2683,3875,599,7466,1493
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1593,5789,842,5745,632,10857
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3479,2896,9607,9560,824,79602
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84447,4089,4311,80270,9056,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5830,4654,9374,4853,151,498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27125,26235,376497,5161,60,79572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4539,5372,728,84504,26291,6183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4118,582,1555,632,5330,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158,387,283459,6811,26119,3060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2593,2309,9630,100506658,266,81570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3329,6387,31,26517,1548,81570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,7528,1230,2590,2309,249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2335,5950,51293,1605,79736,492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6794,7297,3489,8471,100128525,161247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51021,157848,4988,4535,64900,6566
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,9365,10841,4247,1351,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79796,1489,23163,54552,7915,199
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 205327,125988,1644,203,9560,1318
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3357,5713,284434,114548,3551,586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,2693,6387,120227,89874,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,347411,1436,27010,4702,54567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1508,795,55572,4153,7274,4702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285126,64116,25821,11132,1232,1789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 821,130589,64788,2948,6564,407004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9365,2289,5009,968,2896,9969
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4760,2762,5367,3598,498,5293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10537,3486,842,23411,6390,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1646,129787,3651,2030,10842,1968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53335,10013,5295,5321,10724,5091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,85569,2308,156,10102,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7372,590,83548,23556,886,1444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113235,350,5467,5256,54205,5551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6890,6182,5740,4502,5445,6439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2746,410,6492,1409,5744,1798
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
62.142 1.368 63.677
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.667 | 0.110 | 0.927 | |