Mustafa Erhan Ozer
| Snapshot Date: 2026-02-09 13:45 -0500 (Mon, 09 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 2026-02-12 11:58 -0500 (Thu, 12 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" | 4889 |
| 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: 2026-02-10 05:09:49 -0500 (Tue, 10 Feb 2026) |
| EndedAt: 2026-02-10 05:14:46 -0500 (Tue, 10 Feb 2026) |
| EllapsedTime: 297.4 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: 2559,265,101180976,4723,10166,10020
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90480,79053,1337,5009,60,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 266,8803,4704,54805,2052,2875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 811,1346,3099,65993,54549,326625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2034,27235,685,22978,10094,50484
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 486,5191,1537,113263,3795,5184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116931,9630,7295,1595,1524,3242
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79602,268,191,10019,55970,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5445,2948,2348,10457,4669,388743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1807,3930,339,249,132158,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55532,2805,7480,6319,5551,48
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200205,3553,4668,407024,1351,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84317,2395,6772,2475,170302,231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84869,4627,4089,3373,5781,6775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,64801,9409,64689,5236,3949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 125170,3700,5830,55486,3284,2875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 958,200186,4968,5167,760,1203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51082,3565,54539,2101,2950,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 432369,55037,208,728,4760,57128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1717,84869,1509,1071,149461,5919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1644,83548,3651,958,1889,686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3077,212,6505,5268,51604,4779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23409,10250,10991,3250,3952,5702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9414,25813,5105,23516,1672,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60,79144,11213,582,3033,3312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7471,2516,6535,2572,51144,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1281,55532,51021,653,1312,653509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6821,23411,54896,56848,6536,2784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 376497,599,5277,5702,56923,3101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4864,3663,3157,4886,2949,463
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6716,2314,11231,197322,23236,4654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 617,4684,4233,325,3284,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,124976,116931,3978,1282,51085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,10250,1594,388372,3293,5595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,2834,200205,3554,6382,344905
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6908,6833,79572,5192,5009,5781
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3710,51085,91942,23389,50507,5370
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4714,89866,3032,1815,940,487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 181,3638,7084,1200,6513,4976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5230,23530,56919,27247,1393,5350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6519,5476,1859,7428,22820,1392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5617,779,10116,4688,4282,5370
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,2790,2729,406937,2788,83548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,4694,9414,3791,5330,1859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2266,7078,1537,6554,84447,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 339,116150,5660,10,9479,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5646,325,30061,81793,3813,128486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6774,1537,249,55343,2647,10333
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53346,5306,11019,5211,391051,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,875,2653,9414,7390,84889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3290,5444,8431,8202,3091,9630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1734,5473,2908,3552,10243,100130015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2678,1641,6696,3636,3663,3383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,2475,205327,22796,79144,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4724,665,60386,7372,2161,142
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,2998,7078,54809,4000,23395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406906,640,4566,57586,54576,131669
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,3598,8803,79736,490,6938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6357,10243,4598,3958,5644,1757
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2235,81689,125170,3992,477,2113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8802,875,57048,57192,5162,1371
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,391051,205327,2158,255231,2243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54968,57085,844,788,1738,6009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5346,212,664,7381,123283,64919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5286,2332,2776,3630,152078,316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4842,79633,22901,5792,5329,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5243,1282,10644,5743,10316,7471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80224,4887,593,2950,9498,83693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,409,2688,4547,55037,3692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10229,8772,3458,11035,241,54809
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4035,111,5372,23163,33,3651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79783,1769,48,79133,2052,2147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5327,6696,10379,7424,6472,3293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,5053,23417,563,4351,6948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56945,1601,4760,6341,5834,2745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,5239,9513,57511,5228,1992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6901,23389,4128,8642,27235,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9559,5971,1355,7942,388743,1607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 52,125170,6515,4828,8813,325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2203,79585,5091,8802,54106,3284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3562,9927,186,4552,1029,1374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,6521,407011,10269,3030,5825
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56259,4609,6999,6794,407010,57192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5291,5329,4539,10965,2184,26060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1605,5618,51079,1373,2745,29926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 389,3308,4694,9091,3569,10577
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4886,51241,2395,3795,51079,4967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,347411,652,89874,6261,5618
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4744,3074,27235,4853,5781,1374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1909,10165,2495,1497,133396,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6788,8942,5580,2539,10730,3087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1116,5465,11254,293,89874,5268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22933,6788,5295,2628,181,84239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133396,109,9382,6908,1268,124626
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5501,3627,336,4976,4718,208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5194,868,55699,23411,5789,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56652,4541,3416,2305,6517,51555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5214,1606,15,255231,4760,642489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7384,2937,9374,5409,2642,55268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55967,2161,4842,2878,351,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5192,2157,3358,266,9474,79934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132,886,2152,255308,2731,1019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2180,3033,2729,5860,284958,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2247,54476,389692,1675,6519,112817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,859,6514,886,151306,5162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27010,50943,10295,9971,5563,2643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57215,6583,211,55024,91574,860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3791,2641,6833,1499,6342,4056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,1369,81570,1356,7036,91647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2115,6248,7879,496,842,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,9388,29958,665,10013,166785
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23389,4842,9180,4828,87178,583
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
62.260 1.221 63.621
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.698 | 0.048 | 0.906 | |