Mustafa Erhan Ozer
| Snapshot Date: 2025-12-14 13:40 -0500 (Sun, 14 Dec 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 2025-12-15 11:35 -0500 (Mon, 15 Dec 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" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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 2138/2332 | 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 | | ||||||||
| 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: 2025-12-14 22:48:07 -0500 (Sun, 14 Dec 2025) |
| EndedAt: 2025-12-14 22:50:21 -0500 (Sun, 14 Dec 2025) |
| EllapsedTime: 133.8 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: 80070,9507,54901,4286,219,23054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2646,4247,1650,3242,3030,8202
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4851,6236,157848,406906,9607,5826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6786,4035,7376,821,2752,5228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 570,6383,6347,3576,1890,185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6938,5373,118,6720,25813,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6897,84447,148979,5551,2834,55065
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124976,150,6890,5919,8877,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6550,6898,8743,53905,57570,79133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1537,25974,5654,3630,5255,6714
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 249,9672,4000,83884,9630,1646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57511,51167,26762,84769,7528,1312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5740,7528,5230,57001,635,5551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3490,387,201595,1589,3552,57818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3115,83985,1230,2936,23038,7054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 858,490,2593,53345,64919,89777
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1514,5230,1601,3712,5515,3759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79934,5551,1595,2984,3624,4728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23516,2203,6616,6569,5184,51167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57817,4118,2587,51555,5792,10999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2280,355,57380,89866,1591,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4780,2475,3065,84447,51167,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 94235,1606,53905,3242,27429,821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 35,2194,50507,776,51,3081
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7157,51116,1537,8714,2475,2646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 642489,811,2395,1586,3145,10269
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1807,5745,4852,2746,583,4790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9672,53632,56848,10616,154,4779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3417,6464,2538,3938,4594,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5730,796,4720,958,132001,9663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5595,344,54576,285126,3945,7424
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51116,83548,23600,347,27247,338821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57001,23543,5972,64689,56729,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 186,2110,123688,582,1893,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92667,5789,2308,3992,3954,5228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,100303755,2119,406934,1893,760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4627,2590,51204,81793,1347,8879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10157,344905,23291,3638,5009,55268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5723,2166,4256,10891,4609,1585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6536,4695,10559,32,5078,3685
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1443,590,5291,1268,3032,8564
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7841,3170,1021,7099,5195,63892
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7132,7052,5515,8408,2332,55005
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6536,1728,1859,56652,549,253559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3596,4855,137994,6566,114548,4547
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10020,79133,1650,5646,4695,81027
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7347,128486,100,1497,6929,80070
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 166785,1606,3062,241,89778,336
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1489,4988,3030,2896,347687,9526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,191,6357,10533,353,56999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54931,3304,5579,9374,51660,6868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92935,131118,197322,3598,2559,2888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4285,340024,761,116519,875,4035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55670,2984,9919,3576,6517,2152
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4719,10128,9560,54931,1906,3250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1717,6821,50943,599,83693,1606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5053,4654,9663,2146,212,55340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 345,92483,3357,1606,440503,54901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 479,64900,5836,11254,175,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 471,840,10667,3565,7941,4988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200539,18,9420,653509,2878,387082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 239,1716,3570,477,64240,6462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,29926,3813,116228,84334,119559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4149,55526,51601,54576,2876,133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3479,29881,4704,5798,51204,1072
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,79934,92667,6888,3565,2588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25813,6492,51738,3091,2740,85365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8660,6318,1508,54552,2335,968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2888,33,4915,2632,824,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55902,4000,201595,1815,345,11035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5723,4704,4705,383,94235,10094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4118,6387,4286,28976,1508,10857
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10938,4535,7428,255738,1728,6554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2834,160428,85479,407024,1392,9377
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,5162,83548,1230,7385,64689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10333,6906,326625,9498,2332,1347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23409,6387,5365,540,1348,406934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 183,653509,3081,3440,4299,9104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5837,91647,2888,4879,26521,6470
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2395,4318,60,57085,4049,4118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4879,5826,3145,26762,10753,7345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6772,6391,55270,7026,3284,2194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,100506658,64131,2052,2157,2332
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10857,1717,87178,10102,80267,1497
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407045,84833,3416,23400,1734,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27232,2890,3991,388585,84447,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,5584,3663,134,55186,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5207,4803,56923,6515,23291,10842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,217,3636,8714,1621,407010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 411,7347,5193,2056,3065,1591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22901,1514,5741,63931,1734,54575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,858,8087,51052,1346,10965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4712,344905,4864,54539,5836,407024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2280,84504,51204,407040,1182,100506742
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2034,4709,496,7082,5629,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1244,177,3417,54915,1672,2119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26227,7381,364,55970,5740,9420
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,2113,4779,823,58528,5277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,3240,29108,5828,6571,5646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2247,2159,1906,2184,5741,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6318,10642,65080,1909,4976,23543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,821,3489,6714,23062,2642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10616,4973,5255,216,158,5571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6357,9559,5798,81570,197322,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4713,348,10226,27344,4318,3712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2169,3119,57176,6535,84649,132001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1728,84706,51082,100128525,5239,5188
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27429,208,100506658,1815,6317,166785
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,6183,57215,284654,506,5162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26762,387082,10533,3423,5194,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10423,2308,6897,4337,7407,656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 586,196385,5654,5728,8202,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,114814,10423,2690,540,479
--> return NULL...
2025-12-14 22:50:16.647 R[96702:400538370] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
24.896 0.433 26.251
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.324 | 0.014 | 3.320 | |