Mustafa Erhan Ozer
| Snapshot Date: 2026-02-27 13:45 -0500 (Fri, 27 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 2026-02-28 11:58 -0500 (Sat, 28 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" | 4891 |
| 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: 2026-02-28 04:46:52 -0500 (Sat, 28 Feb 2026) |
| EndedAt: 2026-02-28 04:51:51 -0500 (Sat, 28 Feb 2026) |
| EllapsedTime: 299.4 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: 11213,1071,2303,8818,175,84557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5828,2147,2776,60684,5293,5601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1606,344,5571,376497,84889,1352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1029,54802,10135,7084,7345,55283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3358,3082,4547,55863,201595,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,3158,84334,3030,8087,79587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84947,1956,10116,4598,4537,1608
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7915,5970,4627,7407,7345,2593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4123,9370,255308,4144,538,3123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6548,11096,160428,8945,55902,509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 291,11093,3481,4705,84701,149461
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7025,1508,3670,6403,55858,1601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114814,885,432369,1356,4889,1392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2289,5257,1401,284654,7292,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26119,23175,23129,1329,191,25813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6548,5442,6569,942,2713,27239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4668,121268,55503,514,79944,3172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4502,6925,3099,10020,7036,1734
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56302,9066,1798,4886,2266,3339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,191,325,6198,5095,2582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4887,9054,92483,54344,1992,9180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83884,3065,665,5580,57001,113220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3101,2334,125988,153642,5970,885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197,2099,55937,2113,1353,63892
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,3598,3117,3099,685,50674
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8842,80267,5579,5506,2314,1409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55024,6775,140803,5406,131118,8710
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10250,26503,3290,5468,3373,54931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,51548,4143,7026,23062,406982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5327,4846,2791,3991,7376,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4288,3709,3065,55065,3358,5723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4358,9672,100128525,7840,84987,1442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255027,513,5967,440503,5192,1606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7054,7124,2694,101180976,8945,84239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50814,2932,266,2835,4700,1022
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,1586,4313,5919,3606,64689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 488,5837,255738,8802,326625,4160
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5515,4976,3700,952,4609,4860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26227,2760,8471,5236,29929,7172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55630,10157,5837,347,4712,11136
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5315,8517,4842,256394,84902,5261
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7412,8564,487,79783,170302,8431
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 284958,4540,50506,64116,3293,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1340,100506742,653,10559,5660,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4668,3586,3284,1268,2876,58528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 942,11213,3606,26354,1149,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3773,599,130120,5515,2690,5126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9575,6354,80070,516,22901,56302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 32,4547,4149,200205,3074,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113235,9056,2745,7390,7097,54331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2289,63892,216,7077,26291,590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10128,6351,65018,58528,326625,4338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5139,7941,590,9091,3953,4539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407011,2786,3099,7352,199,1327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,1557,5313,10935,4123,10642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5834,476,1757,6445,4015,1056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7030,83693,8195,2308,51079,4547
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,140803,9388,3980,6464,27010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84334,291,688,7292,2785,6338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4922,4915,54575,132001,3598,10013
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3141,5538,6716,6932,9021,5328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6584,6770,83733,1786,1859,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55005,25813,112817,6347,5967,4899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 574447,3489,64801,8799,221935,9095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 959,89866,4552,407006,842,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 266,57620,9332,4915,84274,55163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6715,5256,1557,91452,55186,5321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 367,6317,91869,4609,2864,476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1581,11132,84902,55818,7054,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 514,2147,4853,9415,54704,285362
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407010,100128525,4688,3759,3931,2495
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493753,5617,3570,5551,706,10019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2904,10250,6183,1369,79944,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,2712,153642,3073,10128,574447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1270,57678,123283,2785,1555,596
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,2903,6775,23395,642489,1401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6888,1859,824,231,5195,656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,5590,10911,199,6715,1968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6236,10243,203859,387,4879,4519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79934,84061,29881,23304,2668,3570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3030,3643,2159,1281,79087,338821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116085,9370,6932,8879,2632,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7372,2632,6505,51082,265,654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64131,2693,5507,1586,4790,34
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1401,116228,5805,5834,64087,132158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89866,463,6514,26003,492,56938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,221935,2101,23163,55278,5972
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23304,2984,4143,104909134,391051,1548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,2056,54148,968,572,2170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4744,2762,5971,123,9382,824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,11112,4123,6571,4012,5443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 585,1027,56999,3030,9607,3482
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 346171,57176,2702,9945,205327,5160
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9575,1490,81027,10466,6183,498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6513,1277,3479,9759,1893,7040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23054,7384,137682,54915,1806,81704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55503,4728,406938,1071,51601,3458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3351,1650,338821,293,1329,4744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 253559,8604,162417,434,6347,6584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,3119,617,5288,54902,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 842,506,2729,29928,10269,359
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6183,5595,351,1175,2834,1329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2597,593,212,498,4153,105372280
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29843,2677,5506,629,7528,79736
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 650,55937,3119,2767,3423,55268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4233,4726,388,55065,4744,599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4306,4118,7345,3630,5825,5713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3440,23410,2303,3783,84693,3570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 551,9180,4942,8462,6464,181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79053,6356,2712,5078,6199,8678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,958,406947,9054,10724,476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407006,123099,6934,55065,10644,6774
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
62.028 1.258 63.422
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.714 | 0.036 | 4.515 | |