Mustafa Erhan Ozer
| Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:33 -0400 (Sat, 01 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" | 4774 |
| 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 2127/2321 | 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 | | ||||||||
|
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: 2025-11-01 04:09:13 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 04:14:25 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 311.4 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: 567,729230,9409,9180,2629,185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6932,632,8675,4126,5825,6403
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,23410,2115,11035,5188,54896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4846,406934,8803,599,644974,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,2152,10577,3638,7100,84334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,539,2475,55699,203,4864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2099,81704,10157,3141,2314,64087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,5241,11136,90480,8813,2739
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6716,5122,55863,2335,2169,50484
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1559,4288,1606,7528,7038,3931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 207,2752,341,537,2308,4722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6647,27344,4089,25821,51206,4758
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,5091,56729,253943,51422,335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9663,486,80270,57192,23753,7036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 581,405,1509,2847,3995,217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1650,1672,23163,7412,22797,2597
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,1813,388753,2006,842,5828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2348,55065,1436,205327,537,4780
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55788,3490,130120,1401,3663,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23369,92667,9380,8642,2790,57215
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51083,6387,8722,4668,665,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10559,118,338328,26762,9526,445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 516,55937,5160,5971,10195,55863
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1056,471,101180976,81034,10269,10643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64801,2729,178,104,4729,1571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 219,847,54806,137682,3251,54549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5730,5176,64919,201595,3482,6714
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 506,51085,1675,728294,51092,4828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2113,27089,9560,8675,10682,217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9388,138050,10466,4544,51478,5194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1641,2305,7494,147007,2056,253559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6462,30061,60,84693,4311,3483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90480,85446,886,92609,3062,10295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2642,3155,3290,5193,3489,2158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 654,551,54577,3565,197131,1806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5580,5406,79585,8842,2799,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,10013,1629,6906,10116,51441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4887,1374,22868,1376,27249,3658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2934,3032,54575,5971,1312,551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1208,2030,5295,54896,123,6531
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 291,5054,824,5618,5295,152926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 156,1493,1621,8504,54549,4828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6888,10019,57505,387,2729,60528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3309,92609,1443,9332,8517,427
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29926,266,54344,65080,6901,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23543,26003,5660,3283,51293,10999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2146,25828,7026,1802,388962,7054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200186,7054,9415,8854,2108,54704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10019,6439,1436,4337,5654,4311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84340,147007,5192,1514,5825,283120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 93587,5799,9054,6932,4357,8651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 33,558,7919,7407,1175,23129
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,356,795,100,3357,55902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 355,54798,26354,6821,2752,10938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,3123,6248,284184,50507,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8639,197,55863,7284,3482,10874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7386,25828,64689,51649,22820,3155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5971,2646,23530,8660,581,3562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7078,652,2629,1346,84706,627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2524,10382,326625,6402,463,558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8462,5365,1544,3479,440138,55863
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5702,1072,5631,27089,32,406934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55699,23417,384,2280,2053,6329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55278,55526,567,34,796,6445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54567,5139,83884,4306,1589,114814
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4758,3645,1629,6868,729230,55768
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90480,9919,11132,665,434,7076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,6324,253559,5498,1728,2006
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 253559,5255,51083,3779,6341,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,2805,4760,7084,9021,3087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3417,84317,18,2896,210,325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,2992,10644,779,79158,653
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7941,55902,5330,56848,3119,5373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1585,2517,5499,2745,2641,514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79949,644096,5080,2731,2784,655
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113235,4160,5264,79644,4233,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92483,7422,7494,80207,4502,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7320,2147,1558,3418,7388,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1644,4726,493,6948,4594,23590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7915,1373,113235,558,2950,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54476,31,51300,177,7038,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6182,7347,53335,203,3155,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6772,2517,356,2790,587,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79001,2690,790955,6556,2108,56652
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54331,347411,5255,5789,4886,1401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4069,10841,10116,51478,6696,79661
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,3087,1208,9374,4669,665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7431,162417,79158,1022,3685,2762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 178,434,2762,55967,57678,2538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1312,2908,2876,2642,200539,999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 642489,8202,3309,3032,5594,388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3174,6774,2643,239,84693,57761
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,2108,27247,50943,84274,84649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7035,3145,1802,2690,183,5068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6748,6948,4286,7052,7841,517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27235,2767,84889,513,3309,1203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 137994,11096,2118,10221,7289,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,706,653,6891,7252,6770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8560,55788,6339,2524,1201,3486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2030,54600,27329,200205,1717,11222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,796,8722,161247,87178,130120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57761,5315,491,2683,7391,1019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2878,11095,1646,123283,4854,9971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7289,1893,6934,152078,81570,63892
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4702,7840,8462,156,10730,119559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100128525,4299,1629,493,91949,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26762,125170,5255,3638,5175,6354
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5054,1956,4728,341,10316,1803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2934,79068,1802,116085,9997,1571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4023,640,23129,1803,29928,2548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7325,10243,6609,1769,5265,1558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56848,1185,8722,55186,199,3779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11035,55699,169792,2695,1201,593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5830,5971,2767,22978,2944,3440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,2740,10874,8651,6584,1352
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
65.967 1.758 67.852
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.808 | 0.096 | 4.637 | |