Mustafa Erhan Ozer
| Snapshot Date: 2026-02-18 13:45 -0500 (Wed, 18 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 2026-02-19 11:57 -0500 (Thu, 19 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" | 4890 |
| 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: 2026-02-19 06:40:50 -0500 (Thu, 19 Feb 2026) |
| EndedAt: 2026-02-19 06:46:42 -0500 (Thu, 19 Feb 2026) |
| EllapsedTime: 352.4 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runGUI 0.739 0.153 5.21
* 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: 121268,632,7407,8639,231,81027
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79661,101180976,9630,5654,2158,2332
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89866,2591,5618,160287,1636,10102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23543,84833,65080,3293,210,3101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100130015,5506,2593,4318,2056,2119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 655,4889,2260,3117,51021,2950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27239,79783,5091,1371,1149,7345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,55967,3119,55818,330,6462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6324,9388,19,3115,7018,239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79944,847,5723,3358,7424,80222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2161,3062,1581,3383,79602,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,5329,1859,23475,203,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5330,5350,1234,9414,844,2678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2673,585,5257,9512,140803,33
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4803,5096,148738,8462,37,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6716,1390,8564,23417,1890,51
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3939,23654,867,886,3486,958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,200186,7054,2767,2309,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9365,5444,1585,3483,5621,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7412,493,9607,1352,8932,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4288,51441,8743,23417,1234,285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132,55278,6445,2146,5563,253559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23291,7388,498,844,4790,11231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1499,5054,81793,1346,84706,7077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51548,54805,64601,283459,7054,819
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3643,2158,948,9575,2949,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2118,2161,5189,64788,5447,2559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64432,1028,2266,434,221935,51660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 846,2592,410,539,407010,1890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2170,1910,3293,51085,114814,4712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7919,2158,217,293,64601,130589
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26521,84447,153642,55340,208,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1493,3507,55331,120227,593,9131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728,3569,3312,596,125170,4719
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6774,265,23530,2582,54809,57128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 186,2745,125988,5264,5194,1277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9056,54901,1337,56923,6833,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3553,23129,7385,5713,9332,7048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6439,3813,5236,3558,51119,5191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5054,8243,203859,6890,1601,347687
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 688,1544,6391,89866,6999,79796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,407011,506,5971,23753,3700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3295,492,2987,80070,64805,8567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3312,8884,79944,23395,7384,27125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57192,5919,558,1802,1803,56848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 811,2289,84649,140803,3929,80224
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84987,2760,2309,92935,124976,150379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388,1027,104,5654,514,9054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 256394,54344,5444,5594,406982,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3992,4358,1910,885,3174,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9559,126328,51085,407006,6775,51083
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5331,3773,87178,4540,6928,8710
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23389,2055,5828,57620,84706,1889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6236,64805,23516,54539,3418,1072
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29947,6804,5901,5660,84987,3065
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81033,23163,84239,3458,11231,54567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,406991,5328,53346,3899,6891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5730,54578,3995,860,147968,10935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7220,2798,147968,7124,3172,8710
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6890,406938,1182,3948,26003,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,1444,10991,55699,10533,6948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7030,5834,6347,57570,1589,3553
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388372,51477,2538,25821,7422,200539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4925,410,4700,3939,1789,1524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,8803,6901,9054,7292,5054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,1591,54896,28976,3783,128486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 175,3174,51604,8642,10560,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10682,5830,4790,123099,1340,4853
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,2158,84274,9969,2950,23062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11131,5239,10560,374291,3158,55937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6932,353,4541,3099,54915,10999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5571,1636,9420,51099,10269,1346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57215,3375,1394,7056,6550,2645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29843,2712,79783,1373,4288,4860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7098,5162,10616,3606,1557,6834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8517,8772,2695,5476,8195,2559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79736,4716,4023,688,153,84769
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4853,5052,2647,824,2063,7355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3156,84334,4724,5228,5255,12
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64900,183,3479,64240,54567,2303
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,353500,8517,4548,65993,5268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5860,2100,1544,706,6696,23474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6556,151306,6261,6531,29968,23753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9056,6897,124454,91949,116150,3638
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5409,3645,7078,3791,22845,6354
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 292,84317,57678,5373,6564,4855
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,91949,5832,268,4709,60
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1559,471,91949,6928,8471,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100130015,57215,79133,5744,7412,5257
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79776,81689,10008,7019,4697,9091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56652,100,26003,23062,4715,2786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,435,3034,3991,3329,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5832,405,3358,6927,6748,5071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2581,1508,10753,811,51099,574447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,51300,1581,2998,4314,201595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84557,5330,9076,255027,28234,142
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388753,11231,5345,3558,50507,2064
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 384,406934,23411,1543,406922,6356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113263,30061,79587,10533,23475,255231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,57107,4537,551,4654,1807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6317,6891,81027,3779,846,706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1650,3651,8202,3115,284434,55005
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2987,27249,2696,5092,9429,3115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84504,256471,1634,56945,6583,5825
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26003,790955,57128,1345,407009,1491
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27249,3559,1649,28234,10842,22797
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 405,147968,54798,51204,348,8694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1208,10102,27010,6550,7352,23411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5515,1490,999,1890,124454,1444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1361,9091,4922,2767,407010,56938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,5372,3117,5625,10157,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644974,5192,5095,32,55340,115286
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
109.595 3.657 113.442
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.739 | 0.153 | 5.210 | |