Mustafa Erhan Ozer
| Snapshot Date: 2026-03-10 13:45 -0400 (Tue, 10 Mar 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 2026-03-11 11:58 -0400 (Wed, 11 Mar 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" | 4892 |
| 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: 2026-03-11 04:32:51 -0400 (Wed, 11 Mar 2026) |
| EndedAt: 2026-03-11 04:37:57 -0400 (Wed, 11 Mar 2026) |
| EllapsedTime: 306.4 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: 111,91949,9945,2713,1029,3291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1435,5579,8408,407007,91574,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 346171,43,4312,1548,1813,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27089,4879,5194,4719,5161,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,1175,3308,5967,8714,6513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1605,23462,5571,268,3123,111
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1608,55970,6775,3060,25813,5571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,405,629,347,2668,27125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5468,5428,1027,406982,2678,54552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79633,83447,84987,6342,54511,795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2628,1471,7157,3062,84869,1027
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7048,55670,5321,7381,275,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3480,54148,38,1348,133,3073
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,2632,85479,3383,11019,2936
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1028,54600,55503,92609,84062,407021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 291,5306,81793,627,3030,54809
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51181,4286,2702,1594,2890,54809
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5970,113220,4780,1390,6517,2169
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57176,9572,2787,7386,596,2169
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7376,6772,2745,54106,91647,407045
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89874,6868,5211,3290,152926,6582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22852,7494,6182,7422,10753,407010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8818,4537,5824,113220,4709,29108
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3576,92483,4878,91869,5625,3339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79087,586,551,2992,56729,4609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 283120,968,33,6329,7098,84701
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55486,27239,788,6515,462,10559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7019,407011,122961,1548,5445,2639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51477,160428,54331,599,1802,6772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2159,5080,51611,3920,4654,2949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388753,6439,2932,7077,55186,3425
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92935,7376,3645,7276,1489,407021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4722,64788,3308,2539,6576,581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 847,463,211,11136,4137,4159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5122,25974,4683,9512,3101,3082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6948,84705,823,2101,563,157848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3759,79087,2487,351,284958,3250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26088,941,140803,8651,6392,3980
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,2591,688,9630,387082,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5563,2006,84649,9445,100506742,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,6678,23274,10059,79944,7056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,1401,6576,6888,2731,1019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55065,2587,1593,8408,9066,84317
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2335,5194,150,23543,56923,79572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29078,7284,51081,479,326625,4878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10642,197,293,51206,8932,3155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9051,6357,401,583,56938,1200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1281,113235,6392,266,435,2646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6261,55278,51094,2113,4502,54968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79587,10560,4627,23590,3598,2542
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23400,583,8564,1621,4137,1646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6718,56606,401,54210,6448,91942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3658,113235,5009,5372,4722,2936
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55186,121268,389,760,316,5501
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83733,4313,2053,383,2559,6999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5781,5824,5646,6906,1859,29880
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4846,11132,948,406906,4842,8050
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406937,84649,847,56922,819,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1436,6347,3958,7498,4851,4709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2888,5236,4153,5009,3339,644974
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,89866,1489,7098,4726,10195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8743,5473,8803,2904,54809,8600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3081,151,26275,25915,387787,11213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55065,1393,793,1444,391051,1329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2934,4887,8504,5443,492,23753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 708,81033,5445,3309,7916,54511
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,2113,2805,1589,3670,635
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1543,1489,2109,137994,5256,9559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1806,50507,170302,2146,84769,3949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9429,6770,6716,55858,2538,5277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7466,26088,256394,1608,5176,518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51085,1337,10423,285848,821,6445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 968,5562,27010,186,6602,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26521,4669,7919,9374,6898,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3174,6927,1909,5211,3930,6354
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8564,255738,11096,3066,9927,3073
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9420,8942,54205,409,9131,65985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5789,5644,1678,7167,5588,57085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,477,54675,51604,3417,4160
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,51241,3709,6389,11136,1393
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3242,1812,65993,10730,10379,5824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8710,89874,3309,201595,5581,129787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,1869,1906,3948,1075,3712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160428,11112,6925,2936,8694,53345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5330,3351,229,844,3099,10686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9388,1909,133,5327,7097,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3638,9559,6521,51608,5192,9526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 109,5257,11131,57586,6403,940
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4714,842,29108,572,1345,5367
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65018,3293,1352,779,25839,1593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3953,627,5213,23543,100128525,160287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4144,801,3123,160428,376497,1514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,27344,9474,4851,6448,6908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,3483,84317,29108,5236,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6462,2947,11222,63874,4627,1514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81689,5190,22901,51300,7096,83854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2280,3562,6389,9759,23274,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60386,8932,166785,120227,6576,90865
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285848,6715,3570,4118,5122,9167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8564,253559,213,7030,640,10599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 685,2690,57215,27429,51738,85569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1559,137682,4712,1337,205327,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1277,5834,1807,6356,5830,3074
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6389,84649,7099,6788,5327,51206
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,1544,10524,23054,7345,3099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55572,341,56729,8408,26291,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83854,8678,3586,92667,6515,51
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2055,28234,2109,5230,91452,25974
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2113,1394,1910,7295,8600,2170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 599,1859,6402,5228,80331,33
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3558,123,2495,2638,1646,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80267,2987,9526,23654,23543,344
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
62.721 1.253 64.122
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.633 | 0.033 | 0.825 | |