Mustafa Erhan Ozer
| Snapshot Date: 2026-04-03 13:45 -0400 (Fri, 03 Apr 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-04 11:58 -0400 (Sat, 04 Apr 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" | 4897 |
| 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: 2026-04-04 04:35:41 -0400 (Sat, 04 Apr 2026) |
| EndedAt: 2026-04-04 04:40:45 -0400 (Sat, 04 Apr 2026) |
| EllapsedTime: 303.4 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 24.04.4 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: 2524,8884,2645,60,4256,149461
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1353,123263,4922,1717,26275,7350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51293,53632,2788,1571,123283,2157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,9919,6898,64805,5629,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,6901,116085,3440,4118,1621
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6472,84062,10911,64805,3692,2767
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 811,4541,406922,3636,3117,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3155,4318,3382,5350,5971,9507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1803,406913,100506742,51144,51477,479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5950,440138,1571,6888,79949,3115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23400,10165,9370,11131,407021,347411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84706,23543,3945,11222,29108,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51004,4539,5515,8202,7157,3598
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3586,4656,5213,1621,644974,3156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,5409,570,197322,6582,326625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5770,5644,4760,29958,1893,9420
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 94235,718,7941,5329,3929,388753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,3945,57192,221458,4723,5265
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3030,10000,3174,10753,409,1345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4976,2645,358,201305,694,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29108,6938,3784,10157,4744,5369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2100,8659,284654,2113,201305,4654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1892,100128525,3481,10580,463,7515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8431,3113,3920,4000,3283,34
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56848,51079,6401,1374,145264,50943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9526,2184,10269,5190,137994,11112
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81034,27125,788,26275,4684,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,4536,6554,57505,8802,2266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 941,6356,6317,4654,2689,81033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56923,54901,3949,22796,84572,10841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104909134,587,29843,54704,2475,477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,65018,6470,867,23516,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4899,57215,5787,1992,57570,4889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2101,1757,255308,85479,2597,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1509,4502,7424,5321,4519,57511
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,10116,4609,4358,2332,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54106,115286,4697,1769,56999,26003
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6351,94235,2908,4842,9512,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63931,90865,4319,3692,7025,56259
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51176,5191,1956,4160,8877,5836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54511,8309,6678,22820,3949,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 292,585,55343,1514,11136,5256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3172,3645,5599,5264,1585,115286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51181,4137,6522,5467,3242,1028
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5122,6948,2820,1339,5579,10116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,3663,3357,5592,9512,2593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153642,1910,2936,2641,6928,3692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4233,2584,1394,10935,51024,3062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7352,23556,7096,4232,200539,3115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,1203,388,5962,6554,3948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 384,162417,22820,9066,7284,840
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131669,2052,1075,22852,2118,388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3170,496,3934,2739,51241,11232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1021,2720,7381,11019,2235,8877
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4853,3162,9365,32,79585,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9560,9365,6898,5053,79949,216
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,147007,9051,1557,3357,345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,5009,5468,50507,2247,407004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10379,407004,2936,4899,410,23129
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8678,9498,471,5194,875,23475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4724,8604,6584,694,4719,2110
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,123099,1027,10229,6582,6505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 293,64689,5799,5286,81570,6347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6445,4702,9409,4598,54915,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23654,7038,6402,5580,407009,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 860,6536,4713,4594,89778,1544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 122961,1644,54205,55670,137682,5213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100506742,9927,23530,5092,3952,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,1356,7099,4540,51478,5621
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8408,201305,4318,8050,54577,5053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9095,1621,3630,191,4338,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6354,642489,388962,285126,2739,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5579,6927,84693,54931,10000,285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91942,3162,2115,55818,3552,27232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2647,836,5617,2992,27249,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5621,2063,4720,5595,1186,790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 462,54567,60,51085,2118,2309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2056,2305,51241,1340,6571,5243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81793,4846,5370,3596,109,7916
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54106,7350,81027,5346,387082,51441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,3598,2006,3098,5161,551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,5236,2683,7388,6324,3952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51167,3992,6183,7284,3954,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55902,9104,90865,4566,79661,4598
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6934,2878,6906,1203,4023,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,9091,1270,4967,60386,347687
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51422,860,4282,57001,4126,9779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169792,539,79001,5255,4314,186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7275,3087,1327,6342,4143,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,125988,55486,406,84889,6811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4319,1497,4864,9969,4728,1401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113220,3759,152926,7498,10128,2475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7386,5330,80224,2056,8517,1906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5625,406906,23474,5052,5291,5728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6678,51181,654,56623,2712,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 801,6356,338,151,574447,1443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2987,80222,6582,55858,50943,1601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54896,9370,6929,6390,256471,10991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81034,3692,64900,8678,57570,11132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5159,53346,4143,1588,3552,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,3992,3600,5228,434,54331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10524,3767,1442,116150,1409,123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1392,1072,1869,51204,284654,253559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,100303755,2629,5330,821,4973
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10537,4842,26521,563,4547,84340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 551,1629,11096,574447,3980,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,55343,114814,517,6329,7025
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5625,54802,728294,406906,55526,38
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2760,23411,55037,8408,9507,79736
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6609,387787,5571,81704,5563,51206
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4780,1589,3980,3382,1629,152078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3586,2538,63899,89874,55970,57505
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
63.271 2.000 65.403
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.652 | 0.022 | 3.718 | |