Mustafa Erhan Ozer
| Snapshot Date: 2025-11-26 13:40 -0500 (Wed, 26 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 2025-11-27 11:39 -0500 (Thu, 27 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" | 4865 |
| 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 00:35:41 -0500 (Thu, 27 Nov 2025) |
| EndedAt: 2025-11-27 00:41:23 -0500 (Thu, 27 Nov 2025) |
| EllapsedTime: 342.1 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) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
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-x86_64/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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: 2147,10295,549,285848,79633,490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3553,340024,5053,9382,4609,275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1802,9630,1363,56848,200186,6748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 166785,2572,7498,558,1490,64801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27010,3773,81689,55902,4705,23062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4319,2875,8945,9572,7466,169792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84902,57192,4125,3145,6908,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55278,8862,3481,8639,8722,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,6948,10094,10020,7056,3099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5967,1581,7841,929,4552,2645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3312,116228,9945,22901,27344,9241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56052,2194,7295,8202,9663,57017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5805,1634,79602,1950,5406,2559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 537,79796,2271,1244,643181,5595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6354,2690,124976,4889,2952,3479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 567,6403,6890,104909134,5618,1443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1583,54704,23462,6522,51611,6770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7355,2063,51611,5828,462,29926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,2947,116228,23129,51081,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4716,5176,4143,2581,9076,65985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7124,1581,1537,10644,8462,5105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10295,1582,91949,5660,4049,207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56922,388753,6897,2720,7450,29880
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4719,5825,3670,6236,35,51181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22868,55331,9759,2280,5214,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 409,54675,25974,7407,183,4286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84701,5189,1646,5409,5644,3242
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,100128525,9451,55331,3383,4000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5313,7025,596,115286,23291,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,388743,9607,64689,5091,3250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6356,2260,2888,5445,6721,5787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7494,2944,8471,2056,867,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2647,1022,3486,55186,8050,1950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6648,406906,5328,7132,200810,54205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7372,10537,1345,3779,87178,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3054,101180976,55034,54576,291,6775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,1909,129787,3295,51167,1186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 175,1906,6183,2903,6891,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6356,84239,2793,3091,2169,92609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 24147,7124,6354,197,4524,768239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4598,3899,2588,513,4704,35
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5728,6448,35,63892,7919,10682
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7076,51176,5789,8842,57085,4319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,1497,517,199,10965,5590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 178,5702,4311,84833,79158,1890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1514,2166,1186,1801,83548,2548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 642489,122961,4338,27141,55526,51649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,929,4049,387,22796,10730
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10616,3813,56938,55486,5257,1369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5295,57001,617,3728,2593,4544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,952,5428,9630,2919,3156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1606,255308,2702,5126,3308,7352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79133,125988,142,410,2876,56848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9945,4311,1072,1595,1812,50943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,4598,801,846,7292,27429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406991,57380,29078,60,5068,5498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,169792,406947,7515,389,268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6535,5741,3779,5009,1401,7319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5370,493,7054,1641,1027,4306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,2244,64131,118,3551,4887
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338328,56259,3934,64900,653509,9429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 959,51167,166785,50484,2793,1056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,388753,1634,25974,7372,200810
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54205,9409,1373,7319,8694,1843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,6929,4846,284958,9104,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7030,2588,1716,51608,116150,7388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6519,2632,790,8841,5345,55768
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1650,5261,9365,55037,210,11222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 191,79133,199,9512,5919,5625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,55526,632,384,491,6748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148979,1200,6492,2152,1728,5660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6772,10229,3339,7026,83693,60
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 718,3087,107075310,8799,492,11132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84274,6261,10295,388585,2717,2101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4357,10062,57192,57761,5328,2689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 253943,7480,57048,5730,6439,9526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27249,65993,5291,6319,123,2119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203068,156,644096,2806,26191,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5207,391051,407045,3636,55753,1909
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 268,57001,11254,5445,10195,100303755
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 341,6868,1812,210,51660,1582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83548,162417,191,27232,196385,64432
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51241,6347,1514,5798,54210,57818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3598,56623,51083,130589,406982,410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10059,6439,5277,406922,514,6906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406982,2052,5741,10875,640,1585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79731,5189,7381,29960,2693,2683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3383,340024,5373,4654,8202,200186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4864,1489,6566,291,5824,6789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8050,64116,57128,253559,3250,19
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2587,694,7389,4779,10221,10128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7355,10019,84947,285362,29843,23474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5805,537,2303,2495,336,4976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2688,6571,133,401,27329,3312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1601,23395,10643,5584,10229,24147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6898,5860,6464,2309,111240474,3251
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 316,3636,116931,3759,2834,6906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7450,6566,2688,26235,2745,3309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5837,570,83985,427,1345,9868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,1859,130589,8678,348,2244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 326625,1075,7840,3813,51176,653
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 340024,4548,1644,54148,1508,2639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10644,5365,3638,3423,3673,2791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 58528,56922,10102,116931,2109,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79001,54576,2063,3685,2099,2314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23411,2335,1803,3627,3558,518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2335,10599,1734,326625,5781,7037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,7941,2950,149775,948,84902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10159,4846,191,5631,125170,7424
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 868,6535,8803,5175,4548,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5507,2740,7252,53632,256471,3813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 38,1950,3250,350,60528,10382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10195,4851,1361,435,1906,1337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131118,64087,1329,3813,5744,5195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,2876,51021,84902,10580,5730
--> return NULL...
2025-11-27 00:41:14.063 R[22685:23280896] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
63.800 1.489 66.301
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.760 | 0.044 | 4.008 | |