Mustafa Erhan Ozer
| Snapshot Date: 2026-01-19 13:45 -0500 (Mon, 19 Jan 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 2026-01-22 11:58 -0500 (Thu, 22 Jan 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" | 4886 |
| 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 | | ||||||||
|
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: 2026-01-20 04:45:39 -0500 (Tue, 20 Jan 2026) |
| EndedAt: 2026-01-20 04:50:38 -0500 (Tue, 20 Jan 2026) |
| EllapsedTime: 299.5 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: 585,10857,11095,54915,1718,3638
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7384,4282,2034,5095,1499,3703
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197322,55005,8675,959,5625,10135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64805,7389,4233,3700,5468,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 445,4723,3312,4790,4828,5727
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2944,7172,2572,9779,285848,5581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,79776,1444,51079,10730,5919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2936,56919,3570,23129,3145,79736
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2720,6535,9479,51422,150379,6775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5184,23417,24147,9382,3784,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23462,10243,154,7386,6318,4513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10857,2787,5972,728294,1584,57586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7515,3113,56623,2740,2729,5230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,3291,3358,10560,114814,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10560,55034,6492,3978,5588,708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4306,151306,123,7082,22796,4502
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 268,3692,63931,4282,6554,1337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 330,9415,5162,875,549,2778
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90580,150379,6678,51167,2678,29958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1675,1347,1559,1363,391051,2784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5581,196385,5194,6720,4714,5501
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,2944,6678,92483,26191,2475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6390,4718,64241,79587,1028,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27089,6521,199,93587,6716,4779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55753,6932,4319,5925,57586,4889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4299,27235,4149,7428,64788,1028
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3958,51083,8659,26521,1353,29947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2702,3939,5789,137994,3157,6834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2006,4729,388753,10524,2289,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 134,949,1869,640,3416,65018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3988,1234,93587,5625,57085,5367
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,5740,7167,6523,2864,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406934,2834,5646,1738,3123,1843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 145264,4318,514,212,56606,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221935,5236,4726,156,253943,55486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7428,5501,89778,5230,7528,491
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1543,330,518,265,283120,885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51021,54476,1798,1468,5255,406913
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1022,4654,2646,2309,57215,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116228,5501,1361,2395,1559,5740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54931,2632,7350,8665,4656,6891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11231,6464,388585,9526,1718,15
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,6390,124976,3953,1641,9414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1601,6788,5646,11232,5071,134
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9663,868,1890,3375,506,221458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,6718,325,6357,427,3759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2200,2689,1889,409,10730,2100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2632,4143,85446,338,2799,8743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9241,56729,4547,347687,124976,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5834,148738,2147,5588,1471,1646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55526,5330,2847,131669,2934,9512
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,1182,4153,268,7040,6648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3636,7345,5805,5617,23389,8862
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7054,3685,285,57511,5562,9507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 801,3980,6403,5826,9076,3485
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4668,153,54658,640,94235,11095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,3304,1339,23556,3291,4594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 208,7428,6868,23400,4790,151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2936,57192,6748,1029,151,90865
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3242,3551,134,2806,55343,23236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1950,22845,201305,5660,1175,4669
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6860,207,255738,7284,55037,169026
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64788,463,3553,113220,123099,1374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353500,196385,5447,2243,2159,63892
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84317,6317,3673,866,1361,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,23163,8772,5579,27249,114548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158,477,4723,6932,229,4357
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3291,405,83884,5162,1116,3553
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23129,87178,5617,3382,89778,10965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 796,203,491,241,356,4720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,5406,2998,15,11231,5162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4537,26175,51167,5243,4825,183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2593,32,255308,9572,6470,3117
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53905,51082,5967,133,27429,57085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1910,3383,4760,12,109,9575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 570,434,432369,388585,1355,57620
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9479,3141,3482,129787,5189,6554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,7345,5860,10845,3658,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1374,1508,4126,51092,51094,6356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2689,2597,4502,8648,5189,84572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10116,5824,105372280,5498,23530,3627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 156,131118,2539,9409,5592,3290
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5743,1524,10019,123099,92609,6472
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55753,1329,407006,1282,155,4889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4967,2109,166785,5925,5580,7018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1718,8648,2788,84869,5409,4700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 189,6356,406913,7916,3113,6715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6748,1072,3382,131669,29926,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6748,2158,4712,790955,2517,1910
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4512,84062,857,3929,2335,2646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11095,5406,1906,3170,7436,4123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10295,2720,55037,8803,51083,10102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 940,27089,384,567,122961,186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 819,3636,28976,3559,5189,26060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,3779,57817,54968,4654,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4719,9969,4137,491,688,5211
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 440503,6472,593,7498,2888,150379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493,51021,2932,51611,409,5579
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3600,3251,2790,26235,3423,4720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8818,23236,8710,181,51206,55863
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3710,19,29881,9056,89874,4720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3934,844,2113,6403,4860,3290
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,776,3630,338821,23038,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131118,2645,6786,654,54658,9054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 768239,275,2590,3156,493753,1312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3784,4519,640,2952,1028,4780
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3033,79144,6324,4851,2752,54575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132,825,406922,7388,130120,391051
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,6464,8504,10226,549,25813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1798,23038,406982,325,2806,1075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79783,3638,1201,255738,8309,51116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6198,844,9241,157848,28951,51241
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
61.228 2.000 63.384
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.646 | 0.026 | 0.832 | |