Mustafa Erhan Ozer
| Snapshot Date: 2026-02-19 13:45 -0500 (Thu, 19 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 2026-02-20 11:58 -0500 (Fri, 20 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: 2026-02-20 05:57:52 -0500 (Fri, 20 Feb 2026) |
| EndedAt: 2026-02-20 06:02:53 -0500 (Fri, 20 Feb 2026) |
| EllapsedTime: 301.4 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: 3490,1340,407009,5257,64689,55278
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 157848,27247,1543,84701,706,55270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6901,411,388372,55768,51458,410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4508,2475,109,80222,6402,5727
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 761,5096,493,3423,7252,387787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 155,64689,8879,1075,6616,5315
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4688,345,22868,5644,8932,821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6609,113235,587,4668,5306,10062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8772,7025,1327,509,2890,291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2788,7018,90624,479,5373,5970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84869,2063,9076,29881,2835,7295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5728,10935,80339,2878,104,7428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,1807,51021,1636,1869,6556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55278,3483,4967,2845,685,255738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6403,3945,4718,5257,23395,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9409,999,207,6906,29078,15
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4149,7026,8879,6775,8710,7494
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,8694,4700,596,4502,406937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6774,2591,84902,6649,38,229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2752,316,388743,23556,2702,1718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,23175,4697,1491,959,1361
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5243,5629,6536,2948,64116,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1390,1607,3638,8799,353,27089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51092,51441,359,6616,2668,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 627,200186,5621,55902,3082,23054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 24147,2593,518,2034,116085,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3667,292,84869,85446,51422,56259
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,104909134,51293,6929,51555,6391
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5594,4319,1906,10250,5367,1803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85476,6382,22852,3596,10059,4744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92667,9429,1548,1801,5834,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5824,8722,7391,10667,123688,2693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2940,3357,5428,8862,6522,65080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 147007,8431,51082,51052,596,9927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5139,4160,26060,653,3600,2109
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 836,5901,5447,7038,1646,5159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113263,54205,160428,4688,3645,5078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,7124,3308,29947,1909,55343
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7284,1499,388753,11254,4855,51477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3948,1968,10991,6248,6329,5741
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6898,3479,80331,91452,4684,10559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2950,351,80331,866,3283,7084
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6515,7325,2760,3783,54106,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,2243,6649,29947,6582,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8567,8932,2524,9021,284434,1649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4232,351,1786,7407,1806,4846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2639,64116,3990,93587,26503,255231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4519,79633,48,23291,8722,4125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1352,1548,83439,55526,7276,4846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3122,26517,79158,291,25915,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11112,3074,3813,7025,54982,6834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3357,6522,2791,493753,5161,4688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7077,2271,51649,9513,7052,64900
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 886,4684,3060,388962,6522,387082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84769,116519,5860,2056,80222,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2944,4128,1028,124454,3480,5331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29968,64116,79731,728294,10379,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3931,2184,51555,2745,2987,9779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 538,23556,4760,145264,2395,440138
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10457,169026,5792,10250,23236,2876
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2542,6602,55902,6392,2169,486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1716,50674,292,26517,131118,35
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3480,92609,2572,241,169026,1444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2303,7078,6927,2159,462,1649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30061,53346,2588,55340,37,2593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,9672,3054,3553,2584,1737
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,268,22933,4351,10379,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54205,6199,6505,6833,79144,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22933,1583,1345,5350,4089,5499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6584,1282,4668,153642,5330,65080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63899,6775,1893,868,5190,1737
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2746,2303,5190,2940,116085,2731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7172,6352,5702,2108,2903,2334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5538,1645,23753,5096,2146,125988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,6868,347411,229,65993,388585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,2335,9498,462,57107,90580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4123,5372,5621,4153,407021,2940
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54511,5053,388753,5092,4729,3423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,5618,5313,23208,3283,2157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,38,7276,3091,84062,8564
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 156,3953,3606,4049,1649,3795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57817,81033,284184,6868,3312,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7289,1802,4695,866,150379,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5588,1351,4285,761,79087,9429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4718,253559,29960,376497,7386,3440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5644,2702,92667,54931,8471,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8659,3174,2159,84557,84833,64801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 846,23590,8567,2629,29926,471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4123,498,6317,3440,4713,3980
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5730,283459,5590,6821,4552,7436
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2055,54982,3980,1675,409,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81689,3978,6387,3717,10195,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 509,283459,56729,31,4540,4700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 664,857,37,3417,10991,4311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151306,2785,83884,10533,148979,1072
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3082,7390,2689,1815,2166,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653509,255231,388,7030,1186,374291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8567,590,79783,64900,27232,5105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4247,376497,284958,5406,819,364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5189,2314,7385,10062,3123,686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 249,6354,54809,55699,7515,51116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 706,55526,5286,6890,15,617
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 585,55699,7389,5194,160287,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7919,51,197322,643181,10166,391051
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 840,123688,5293,389692,1909,51117
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,3486,2588,54511,80201,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50674,79776,5727,138050,1734,1728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79585,3663,1201,9377,91869,2677
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 593,3692,487,23590,5799,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,6448,54567,656,100303755,292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54902,635,4729,3953,4256,7386
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2804,344905,8195,1409,7252,79602
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
61.776 1.286 63.196
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.666 | 0.039 | 2.016 | |