Mustafa Erhan Ozer
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: 2bc7e27 |
| git_last_commit_date: 2025-10-29 11:23:08 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:36 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 2131/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.11.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.11.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SVMDO_1.11.0.tar.gz |
| StartedAt: 2025-11-14 04:36:31 -0500 (Fri, 14 Nov 2025) |
| EndedAt: 2025-11-14 04:44:09 -0500 (Fri, 14 Nov 2025) |
| EllapsedTime: 458.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SVMDO_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.11.0’
* 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-3.23-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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: 492,590,3242,7098,10159,4543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26291,26175,1644,1678,8862,9512
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4864,148979,340024,7376,26521,10295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2056,2677,23369,249,79796,796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91647,64241,115286,26291,3931,4716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 498,2908,3122,3558,5476,1493
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4982,4780,2591,22868,185,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8877,91574,2260,57017,54809,2266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2688,177,6517,5213,8639,2180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,5241,5562,2673,2109,6897
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2590,23543,5184,51085,656,5571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,5515,5579,5745,2713,64805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3155,4803,56052,942,5213,4846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6390,6582,6565,338328,11232,55937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1356,51206,4702,3460,23291,2152
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64240,5346,3598,1636,2696,1956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,3703,5789,200205,2590,5071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6566,2690,4337,8642,134,1075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,9512,3553,80270,2990,2876
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 383,54567,1605,1650,91869,120227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6932,6548,284958,268,51422,85365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1815,84705,3030,23062,353,6934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2147,7372,3383,2516,79602,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63892,55572,2792,4126,3988,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84902,6718,2792,1175,83854,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6948,5468,952,2673,2303,122961
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 147007,3663,4544,51660,6341,9429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 842,8431,3032,85569,3596,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83693,51081,6505,3309,54896,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8659,51081,4524,5590,7035,9868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3357,63899,5264,7471,9104,2629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3551,7431,4137,3295,1444,2888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22868,6696,6536,3356,23410,1337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4351,1509,116931,3172,5825,5594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8567,283459,2638,3552,2788,150379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 19,1812,29929,11232,3600,1347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353,57048,361,169792,93587,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,2628,729230,2643,291,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 885,788,57570,2875,6715,63899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,1019,33,5331,55937,3638
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2947,150379,8600,100130015,124976,5901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26191,708,999,9374,51316,3101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85476,55065,54567,26291,1734,406913
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,4015,5925,3295,7498,5091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80267,7048,2641,7297,265,26175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,1543,4299,718,1203,7345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 87178,26521,3283,4878,56922,1589
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729230,85365,537,4318,2118,2247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3309,1584,153642,538,8309,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2952,2653,57761,427,32,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2158,5465,120227,6582,3670,2146
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2746,409,844,84334,4089,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,7225,3174,629,8504,729230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79633,5571,2642,121268,10730,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,407021,79944,10730,1910,64240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11213,2984,55024,79736,5162,5139
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7494,5295,1208,4502,119559,708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2984,1409,57818,1369,9332,3480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,8678,124976,5501,9377,189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4760,376497,1558,10008,5406,9091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1571,1361,840,3356,56997,5824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5428,5594,5261,266,6566,10938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2108,231,4744,1268,57107,3934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5161,2314,91647,22868,7057,5970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 140803,85365,2944,4502,7275,65080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,5241,54578,9021,1544,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6347,22797,407009,8803,4313,125170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5250,5592,7450,2308,3115,152926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3416,5239,821,10537,54539,60
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25813,5228,7345,2834,2517,55343
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,2647,350,1606,6720,7391
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4285,54577,293,5207,11254,7494
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8665,2166,84300,3077,57192,7030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2760,3783,4126,4314,959,1019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6569,54901,3643,958,2475,330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,54344,8813,7424,5105,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,10874,9919,8803,9479,3113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2524,64689,51052,3034,51611,81034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1589,9370,3945,55331,8659,3700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54344,3156,27141,2099,5723,175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11254,551,84987,2677,10537,1355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55818,7372,81034,5473,10059,6927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2875,7919,3375,9415,9370,55340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200186,2790,4714,686,2119,6772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160287,348,3290,2875,85365,9374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 389,265,54902,105372280,4853,4337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10102,1641,405,115286,6515,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2641,3630,94235,63874,8714,3145
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 345,54968,5091,11231,6906,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10537,1392,51144,211,1270,325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,3954,51316,795,2056,4853
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 627,4318,2642,6775,27010,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 706,4552,388962,5538,644974,11213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90865,2310,9445,1363,4728,85446
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2146,23175,22868,120227,1329,407004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1356,1645,189,10842,387082,10165
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3624,10166,7494,2099,2064,64919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3992,51604,2864,4879,231,4299
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5053,476,166785,54805,53905,593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5406,406906,3992,6901,5826,4125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4718,4843,8659,154,85446,8932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407007,9559,51206,55005,5091,2328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 490,4144,1282,9365,6999,2804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57380,8694,207,5618,133,1186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11231,203068,2348,123283,6649,2695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7916,3606,7252,81570,3113,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5970,5367,859,3992,54476,6182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,87178,653509,79602,1584,2119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8660,253559,6382,4040,488,479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1737,407004,2908,6341,80347,3606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7276,7391,285362,5515,57085,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54931,1200,3586,9572,53335,5625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4313,105372280,4712,3685,9021,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406906,8842,3290,940,10159,4988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3356,3240,4000,7409,706,29947
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
217.917 2.017 220.532
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.818 | 0.085 | 3.821 | |