Mustafa Erhan Ozer
| Snapshot Date: 2025-11-19 13:40 -0500 (Wed, 19 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 2025-11-20 11:38 -0500 (Thu, 20 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" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | 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: 2025-11-20 04:40:10 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 04:45:13 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 303.4 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: 90480,64788,60684,55186,5327,356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10857,84902,4089,5091,2152,28976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9131,1769,5230,941,84557,5069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6821,1803,3284,1347,10383,60528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4358,6888,1606,1621,123283,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9663,5631,3938,1757,2693,10560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4722,7320,55005,1363,844,53345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3295,4312,3062,100506742,3291,3958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55818,114814,9380,81033,2876,3251
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3054,54658,4524,26191,80207,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2896,22868,2890,2155,1593,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54205,84334,316,2647,9451,54809
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,477,8945,25828,51548,2099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1232,2792,2158,3703,5313,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1056,8803,84317,629,6382,11093
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1208,2720,1270,116150,1234,51458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7390,83439,32,5792,23600,7057
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729230,6387,219,57192,79158,123283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5243,1950,10128,57505,54658,80270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,5621,154,7157,57128,2110
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7019,23369,191,435,3066,105372280
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54809,496,406934,293,8567,55186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114548,1621,80267,221458,54210,3717
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54896,491,1340,5792,389,116085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3759,2694,32,54476,51660,2903
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169792,1606,25839,55532,5330,10166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2328,1200,3784,1277,9630,63931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,54802,9076,9526,8841,9945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,6548,4982,4842,7035,4722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790955,55750,1409,4000,650,4744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27344,29947,2260,538,3172,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84572,56848,6464,6324,54331,5373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3791,2166,90480,6517,79087,2247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,201305,55270,4128,3930,5792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 341,5211,384,5313,846,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,56302,5584,256471,80224,1393
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5194,2767,9971,361,5962,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,6387,4828,5507,491,2590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89866,574447,3240,54931,842,125988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10352,6340,91452,5476,55818,5250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4899,51021,2110,5476,5345,9919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2632,4358,27249,846,55670,80201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285126,79087,6868,56923,6329,2542
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2646,5644,54148,1499,79783,513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4889,2584,57620,1717,3767,959
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1738,1435,2740,53346,10116,170302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6566,3554,84239,406,85569,2792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2487,3418,9054,84342,5270,656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2944,84062,8202,6584,477,9241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6236,1182,2949,351,5277,9507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2798,216,6356,3692,5139,4726
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 31,80070,5728,149461,3559,640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8932,10642,55644,9698,1491,4137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4723,6932,1815,55902,55331,4780
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,27125,387787,6338,6715,56923
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,8818,26762,5162,2888,51604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5345,64805,9377,7289,284958,79731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29929,3356,706,54552,10269,64788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6906,197322,83884,2034,5428,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54577,2937,3558,10379,1802,1435
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4886,4744,197322,5126,121268,51021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5824,5372,26119,3978,1584,8942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89866,8567,5241,3685,51052,57176
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,7099,57620,6786,471,221935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2064,8243,7035,56052,514,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160428,959,6721,409,2702,1340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7391,3931,4143,5498,11222,79731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4780,10537,5214,4758,4878,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,3684,11213,65993,4973,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2875,56938,2864,8813,10128,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2166,9969,3145,3479,2729,22820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6183,150379,9969,1582,9054,9507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64689,10999,3375,54902,9445,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 389,1558,6678,137682,9779,3240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,5601,23409,3481,6374,5365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6183,51099,2919,6932,23556,7030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6351,3485,26762,9698,3481,57104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2804,1583,999,4318,55750,5447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,4887,186,1435,3382,7098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149775,55037,55005,4720,4524,120227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 199,2693,91574,4149,7319,10642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1813,3627,842,64241,1738,7352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57104,1843,824,5213,51660,8803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,7076,585,718,4544,10221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4709,3995,5727,9451,54205,55967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,5192,9076,4915,406922,6536
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6821,92483,7347,54802,4744,57505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,2702,345,3082,84701,2161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5370,54476,3251,57678,84557,9451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5830,84987,4313,5230,5789,824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 142,1355,4049,1029,197131,216
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 776,8517,3119,79633,1337,130120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55644,1717,8772,5590,11136,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4722,6925,407007,6505,51206,3779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7167,8600,10875,130589,85446,10383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3643,210,142,5406,23304,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 348,1801,587,819,10423,1769
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 161247,221458,776,4879,125170,55532
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,2305,5370,2690,3953,942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3082,10295,3598,1443,5228,4705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3077,6833,2006,10,3773,3416
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1909,6602,5563,640,10457,3795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158,5256,824,1641,51,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8799,7386,4524,821,5799,2590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2762,7407,4543,9969,8678,5581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3708,1277,7132,116228,1346,5562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2308,3485,51478,5465,166785,79731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,8243,27089,4286,130589,200186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84947,63931,338,23274,642489,3779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3673,3638,686,51094,347411,29881
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3779,2593,1374,51092,6522,5167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26762,5741,94235,5328,1734,2119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2693,1649,4552,2152,7320,10165
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4285,55863,51079,2152,10560,10599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5068,1589,9575,1675,3598,5745
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
64.973 1.127 66.217
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.769 | 0.113 | 3.915 | |