Mustafa Erhan Ozer
| Snapshot Date: 2025-10-30 13:45 -0400 (Thu, 30 Oct 2025) |
| 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 Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-31 12:03 -0400 (Fri, 31 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 | | ||||||||
| 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: 1.10.0 |
| 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: 2025-10-31 04:42:00 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 04:47:57 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 357.4 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 4.5.1 Patched (2025-08-23 r88802)
* 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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: 3990,1558,57570,2731,3795,3953
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4313,8932,1559,9414,3425,2161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10094,26503,9095,811,2762,7019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,51441,2876,50484,104,55526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5621,10135,3480,3624,200810,3934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57817,1557,268,2542,2348,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57215,3081,124454,4502,5288,1071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26191,22901,6522,5499,56729,4879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10991,84987,2063,5787,4547,655
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7431,10644,24147,572,3077,2235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1815,213,6897,2348,3995,7466
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7295,7386,8818,4153,7056,3482
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7919,84239,5193,6182,2806,549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51119,5618,197322,10159,199,4159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,7498,54476,28951,23590,57511
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51094,492,23530,11093,7220,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 284184,15,5167,514,7056,336
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2835,664,819,4716,54539,6505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 181,2792,1786,3685,26235,4719
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3606,6183,3673,1806,2785,253943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51181,1650,1607,5563,6198,590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3482,644096,27235,5506,11222,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 185,239,1769,54802,1636,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,7037,23410,6338,9382,48
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,2328,7040,462,123099,53335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2712,51660,80070,9479,4723,4803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2949,145264,10842,1595,6382,29968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8604,7421,3558,9180,55186,4705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,8600,3373,7376,55065,7098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54809,5629,80207,3117,958,5184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2166,125988,51128,79796,728,3565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9868,1644,2334,121268,8243,516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6199,1757,9479,51422,23409,868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 129787,4942,1392,57817,10008,10221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26227,488,10524,210,80070,824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5313,5601,175,3242,1435,406934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3458,54331,29881,291,10466,3304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203859,1346,32,3145,6770,11231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57001,506,197,1444,3119,2847
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57128,51204,2542,5195,10269,7084
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83693,57511,7919,5184,2487,3990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1352,3596,84062,5190,6391,2516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3783,410,120227,10686,5274,3308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3627,84317,445,4233,285362,10165
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201595,10008,5972,29960,23516,7078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6716,3709,105372280,5369,10352,292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,58528,5702,51021,3759,6462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2118,2632,948,5052,405,8678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2787,4790,54798,3684,51079,3283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10841,26235,4338,795,27089,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4126,5579,79776,3638,811,8854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,255738,2517,2587,133,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 842,1234,137682,5250,5327,5350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5702,406982,463,23129,2697,181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6775,4598,4878,5126,1559,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,2056,10524,5836,79633,7157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4878,60684,790,7409,216,5588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10682,2203,6834,2673,8639,384
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7347,51167,514,6248,6182,6403
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2934,10911,197131,51738,10466,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,4713,79644,2538,2798,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4233,5465,3684,9692,350,3418
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407009,487,4318,8675,3329,56919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3606,3062,8309,389692,2787,4299
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79587,1728,8675,3145,9672,219
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201595,4312,8665,2588,9969,2820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1716,652,477,335,221935,57570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22796,2052,2784,55670,4357,5306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493,477,115286,5515,83985,406982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,9919,4627,387082,10938,79001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23129,6582,200186,488,1369,91949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3638,3482,5473,4728,6554,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6354,79602,4967,3710,5588,2314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6932,376497,23054,1909,200539,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5306,3570,10841,4069,54476,9076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,7076,518,153,203068,56997
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51293,5581,7424,3283,1489,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23395,80270,38,2539,1734,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 445,388753,79731,55750,729230,6236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10383,7274,3054,63899,114548,1757
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,1203,55753,9415,84706,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,7528,6602,1186,5071,3284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,3030,51601,1645,3242,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10382,653,7077,4627,57128,7941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,9377,9429,842,54902,22796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,7498,133396,3081,6513,347411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55902,406938,6536,1798,514,6948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55526,9241,6515,2739,200205,1175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4860,100303755,51478,5192,4285,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6868,2647,201305,3813,6788,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,54567,5261,9759,100,344905
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2155,55967,3670,81034,145264,4089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84274,3489,5327,3636,7220,3295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79068,514,85479,3995,406913,6536
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,51117,6556,24147,847,653509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9560,50484,57570,7385,57128,5161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51458,1353,5192,55503,5743,24147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,132158,129787,4282,55630,57761
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644096,79053,3308,4232,1595,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1645,9104,7471,10166,29078,239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 181,407010,50507,7528,5139,2937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3728,50943,2030,181,7292,4714
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,3995,7840,178,4704,205327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201305,5211,23304,5054,255308,6929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3490,1409,6609,169026,138050,83693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5193,2949,664,3598,79144,4728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84693,2696,4843,3978,1435,2778
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80224,642489,6522,5599,2517,8639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6908,3703,56919,4851,5837,116150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3489,5160,221935,6716,6582,4729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54567,84649,7424,1490,7528,6329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4855,5207,3692,203,1230,3717
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,587,5625,200810,351,11096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6571,293,6262,3559,118,3949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90624,406982,1859,80224,5329,4656
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
116.767 2.977 120.231
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.626 | 0.034 | 3.616 | |