Mustafa Erhan Ozer
| Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 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 2025-11-28 11:40 -0500 (Fri, 28 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" | 4866 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| 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 2134/2328 | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.11.0.tar.gz |
| StartedAt: 2025-11-27 23:03:29 -0500 (Thu, 27 Nov 2025) |
| EndedAt: 2025-11-27 23:05:45 -0500 (Thu, 27 Nov 2025) |
| EllapsedTime: 136.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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: 55343,435,221935,54982,9560,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3382,2587,574447,1497,6445,5139
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29929,200186,8722,3375,537,60684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55699,4049,406,9414,1869,2834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,54809,9692,665,1022,1234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,51441,6789,7035,183,10730
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3158,166785,132,790955,4846,5195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55699,205327,3559,27089,5770,8567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131118,2642,51441,249,124976,3643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29960,56945,857,1644,3117,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8471,166785,2538,4878,3077,55858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3673,22901,3486,9388,3440,388743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4035,3155,79633,10911,1329,285362
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,85476,10875,153,57761,23395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,3356,2876,4089,3586,356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4878,8050,2180,3156,10135,6341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5270,5162,84833,51119,3953,56923
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 656,26291,147007,26003,57818,55503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6448,3703,3795,6439,5277,821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22797,4899,51555,27344,5465,10857
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1605,8195,3066,57818,10269,11231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8195,4704,285,2110,284958,6649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7274,1353,1607,4760,26291,253943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3638,3643,3066,6821,51738,1859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 471,9091,5306,2653,23369,5579
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,156,389,1859,5444,2947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5563,55644,10730,10686,361,11095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81034,1608,51079,2064,3995,9076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2203,5306,50506,2639,284958,5962
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2590,2946,3329,125988,5713,170302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10559,120227,132001,2745,3920,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8659,37,5207,8803,231,388753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6392,1353,491,632,79068,3658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 122961,1409,2683,5468,63931,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 253559,3242,7498,7038,83693,1175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2835,4843,1718,50506,5243,5306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23462,8651,3728,10724,57048,2694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6720,718,4715,79644,177,1803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10059,23395,1890,1027,3309,10841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81033,3416,57620,5373,824,23062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,388743,2542,1244,9054,114814
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7347,64116,3458,4286,4149,51094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,120227,181,119559,63874,1347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4760,79585,55340,5364,6382,5409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9091,213,9076,34,886,811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7391,4311,1717,582,3329,1327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,1312,8471,6439,1582,266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1443,10466,463,104909134,23417,6550
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7054,6402,1992,53345,23590,1393
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,9968,2992,825,54600,51144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5507,1645,1201,1815,10911,57001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26235,3643,476,5184,1678,6476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5092,4982,4968,3284,1499,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,3606,6403,9672,1890,514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285126,407040,4023,1442,11035,8517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6647,85479,5091,2678,9512,81689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80207,5175,51458,3087,10938,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 166785,821,840,857,56623,79133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54552,4758,10128,593,8604,54982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27329,581,7498,2110,55750,3295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11254,344905,178,6833,3624,3283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10423,23654,509,3486,5330,10874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1409,170302,132001,160428,114814,488
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10559,4023,5193,811,7480,79776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104909134,51082,5228,10135,203859,1586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100303755,4311,5019,7274,2947,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23175,153,1889,1201,10559,3251
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,859,79934,51441,54931,29078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 112817,2309,29843,2161,84572,574447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4720,7528,487,27125,4722,3304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3952,768239,2572,4669,407045,1230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1374,5256,8600,84947,6199,1734
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 958,6517,3791,432369,2628,493
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 435,1056,7220,1555,25974,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2314,407009,4744,1080,79001,55283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729230,55863,23417,4973,10379,3712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7879,6897,2235,1629,29968,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338,89866,5409,79796,2266,64788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2495,8694,84902,7515,8675,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54675,5236,1244,5581,2673,694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7480,5631,2155,3418,7350,1588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79602,100303755,5551,5967,821,64241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6938,407024,6391,5781,401,1277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3329,57107,29929,56652,3077,6351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10226,26291,3627,7077,7515,2581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2587,5730,1806,5080,80222,29078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56052,958,80201,6609,55670,2157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,3416,22820,1910,4144,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1028,406906,57001,79776,844,3576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2310,2169,8818,5228,1027,1786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2693,5184,57215,5175,3122,255231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1200,1356,5442,51167,22901,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 115286,5467,64601,685,776,3357
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54476,2108,2798,2834,6714,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7295,644974,60,4718,4973,496
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6382,1374,5465,23417,25821,84693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3309,54798,5188,1071,1889,25828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,79934,54968,1558,2875,8818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4694,1373,84342,1968,189,549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131669,5330,3081,9919,3990,3351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4143,1203,3159,10682,131669,3077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,284184,50484,3145,148979,5194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26521,8471,942,5730,6351,3949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10352,4712,54809,3291,653,488
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51181,10857,8639,183,145264,23462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,55331,9607,84693,10,84572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3101,5713,51458,330,7297,84342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,121268,120227,2746,54549,1116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27344,5740,1345,51116,7841,54982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79053,126328,23236,15,1234,83439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,3417,3767,34,6535,100303755
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,2690,407009,7276,7030,10
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9692,2762,84705,6517,79633,5241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1490,7372,708,4694,51204,3783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1589,2642,1348,5329,60684,9377
--> return NULL...
2025-11-27 23:05:41.250 R[7829:194649236] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
26.274 0.422 28.181
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.284 | 0.015 | 3.371 | |