Mustafa Erhan Ozer
| Snapshot Date: 2026-04-07 13:45 -0400 (Tue, 07 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 2026-04-08 11:58 -0400 (Wed, 08 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: 2026-04-08 04:40:51 -0400 (Wed, 08 Apr 2026) |
| EndedAt: 2026-04-08 04:45:51 -0400 (Wed, 08 Apr 2026) |
| EllapsedTime: 300.4 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: 3636,64240,54552,7428,2646,5741
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 410,4922,388585,2064,9526,6352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9104,5799,54806,8642,23389,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6794,84557,5646,11255,4760,3554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1346,479,4967,57017,5091,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5743,6492,7297,1789,7052,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255027,353500,100,6811,3077,26003
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27249,26175,1345,1149,27232,5740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3948,1348,3293,642489,8710,4722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,27232,38,1028,22868,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8665,25821,5373,5825,5176,401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 498,795,83854,7292,490,211
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8884,53346,3418,60386,2303,132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 517,100506742,7388,6774,128486,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6999,11093,407045,4842,51004,5195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6248,3251,2006,7352,241,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51204,26119,407004,6199,5176,56848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23590,9409,2584,5275,2159,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8564,79158,4338,364,255738,2159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4609,123099,84334,2548,1329,9474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5571,4286,6891,2695,51116,55788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26191,7297,2303,5370,2280,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56945,2180,952,3065,1608,1559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,23062,788,3598,84987,2099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5068,8639,5162,7248,4137,3250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 340024,506,572,29968,857,8517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7220,5590,60,3291,586,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5053,389,55863,4825,2695,5445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 629,2987,7098,5214,3692,6445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7386,4539,201305,8202,407010,84557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5562,80331,1208,89874,8243,4035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 435,338821,1559,51649,79783,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1029,4688,175,1869,2952,6387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54539,51293,6329,4012,10269,6341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 859,10165,5241,54675,64131,4718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7167,111,6183,5442,958,56919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10841,26227,3570,407009,821,1351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,514,2582,83884,4312,79133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 155,43,2713,1393,2539,28234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6602,4137,4723,4713,2542,2693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9409,824,5175,3728,10580,6198
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2835,255308,5364,3995,27429,51167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4548,2247,836,7099,9167,4313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2739,196385,3708,3576,5744,201595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4878,151,1230,4669,2690,11019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 150,4126,3645,860,3356,60
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4887,1312,5105,4543,6324,10682
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5901,3795,5962,23274,79796,9474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80347,4852,2113,84275,2108,8942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,656,84504,4627,1201,2203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50507,56938,6317,7082,1232,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,56999,3658,6199,5792,27125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28951,23409,463,2063,10,1956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55034,5787,952,3759,1355,5644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285,7384,84701,29880,2542,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80331,5286,6392,7347,1543,114548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9779,6584,4337,4744,2056,3507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51477,1489,3486,824,586,203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54552,941,3141,55343,4712,4512
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3958,81034,1363,8087,2266,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1356,118,7289,5306,56945,6514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51548,84239,6770,7347,8854,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4942,1071,6248,2113,5919,7096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132001,6569,114548,5473,57104,2697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60386,57085,2677,51478,6811,3329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5631,4314,1859,2992,64788,4056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,2835,4015,6718,80331,54205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1374,9560,4716,6357,4149,79001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,10423,5192,9054,9971,229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5473,5243,201305,1646,406991,3995
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8243,1645,2639,255738,6720,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,100506742,200205,2109,5967,1268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6550,51604,8884,23590,479,178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2710,150,4700,4306,3250,2334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,56997,1497,1813,1806,1716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,1019,54798,55486,9779,2119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124626,131118,22933,7248,4056,84947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27247,7084,5571,3158,654,8942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5594,51293,4318,3034,2934,860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644096,4123,2762,9513,790955,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4049,2791,91647,4726,23304,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,285126,5476,326625,64131,4547
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4716,55005,1890,5727,1347,52
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,2034,4715,28958,5590,51128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3627,293,2194,2517,5241,9382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4126,57761,7319,4982,56997,7388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1641,2739,4160,3552,406991,2702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201595,1557,51021,857,26354,2159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,2063,6523,3938,3934,1185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2542,9507,3899,4609,2235,4887
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10891,2678,79934,7078,9559,5443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113235,11254,6248,84769,10999,5588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3559,116150,84275,1716,283459,8659
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,3479,6535,54896,8050,7275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5327,6324,355,3159,249,5096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 999,2099,10577,57048,79087,56923
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,80267,1471,2260,170302,6261
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 150,2746,54549,6387,4695,2588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9498,2712,2235,54476,768239,1557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7320,5571,9971,181,3159,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 941,2693,593,7386,51081,3329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,55644,27329,5346,84239,4143
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133396,1843,2752,3558,7840,51293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2720,9365,847,10842,407006,652
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1621,2947,84557,27125,5901,2328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56606,7388,2690,959,587,5646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3952,79944,6925,80201,7289,572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6696,23654,2790,3554,2697,632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116085,7424,2896,1027,1738,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57104,28958,4318,958,344,2948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 358,5214,64131,7350,8743,55037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2030,3658,6556,23062,1374,1909
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
61.207 1.845 63.188
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.705 | 0.032 | 2.023 | |