Mustafa Erhan Ozer
| Snapshot Date: 2025-12-01 13:40 -0500 (Mon, 01 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 2025-12-02 11:36 -0500 (Tue, 02 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" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 | | ||||||||
| 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: 2025-12-01 23:00:37 -0500 (Mon, 01 Dec 2025) |
| EndedAt: 2025-12-01 23:03:14 -0500 (Mon, 01 Dec 2025) |
| EllapsedTime: 157.1 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) (2025-11-04 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: 51660,388585,5799,655,4968,51601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1801,790,3458,6354,4728,3482
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10020,219,440503,790955,57570,4358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6556,2798,7515,34,1351,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1584,57678,5580,211,3250,4976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 284958,219,55858,3062,80267,100506742
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64689,55858,6789,2169,256471,4695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54344,5256,6351,8660,2581,1282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10000,1201,7056,51167,3978,7841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 498,518,10537,824,5239,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4668,11254,23474,130589,347411,5465
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65080,2593,201305,6715,5277,84889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2303,51085,3700,5740,3645,5467
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54539,124976,5501,339,50484,5321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2629,1906,6319,4889,51604,83884
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55937,3358,999,8675,6565,54675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5428,5442,79783,4126,7275,83548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3899,152078,3934,4864,6236,57380
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1608,2790,9560,3030,10842,80331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79731,55753,9054,463,51024,1345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8567,6901,9420,4864,3952,8665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407011,1468,11254,4828,1175,27141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6678,1363,23474,8517,3159,51660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,1442,79068,407045,3920,596
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,10269,5321,493753,3700,2697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2798,51738,7052,27249,26521,5787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5105,5837,1373,10116,79572,5702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23556,1027,26762,132001,25821,84889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3251,55572,55937,10159,347,846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 411,6492,538,55863,2804,1356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,790955,9131,205327,330,84705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221935,55034,2517,3636,79633,9056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 410,1348,10059,5592,10560,6536
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9365,2158,387,22852,1508,55270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1435,116931,440138,653,7274,4337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5447,338821,137994,2581,6183,5367
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9370,80207,26191,7376,5860,4744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2998,7391,91942,213,201595,6387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23409,4878,2992,84239,8932,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3920,3624,5970,593,326625,4780
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7391,4758,4887,22820,599,51099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29929,105372280,1992,54344,9131,518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3479,4842,434,28976,22978,10128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6571,4973,2760,4854,4306,2593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3417,23304,4694,64689,2155,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 857,3418,3899,2690,9095,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2115,56919,3082,2119,338821,6462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,29960,10000,406938,1230,43
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28976,6536,56606,6476,101180976,203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3692,84239,8879,9388,51478,4713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,1650,406938,121268,105372280,9560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1203,29947,2169,201595,3606,1401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64801,4543,367,2591,6554,3440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10423,374291,1444,5972,5277,351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2949,941,1641,5096,6582,6374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6999,4967,4089,186,1737,79068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 389,84693,57085,2908,518,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,1909,55283,2693,4357,91647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65993,4049,7471,27344,60684,4313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4337,3990,64087,29880,3570,160428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51441,4306,6678,150379,486,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 462,5191,496,325,53905,3980
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8639,3329,617,5078,1281,118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1678,3813,11232,406906,1645,3576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,132,10316,284184,81570,51099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 640,5962,5745,54549,4694,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89874,7252,2791,122961,6531,344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2247,729238,3065,3934,197322,1200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6927,31,6352,2516,5629,107075310
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 665,685,27249,6564,7297,1471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9672,9388,5274,51004,7248,7391
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2587,8722,5009,3565,3667,7345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53632,2170,63931,9180,3115,8862
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2628,23556,2118,1645,407008,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407040,2161,4715,3060,836,7167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5188,9779,1571,64788,594,2063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6576,153642,2878,8431,84693,51004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27232,3553,79934,10580,4548,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 24147,2538,51024,846,3170,7350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65993,255308,6897,55331,1232,7037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4627,2591,56938,4860,79644,285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 140803,57761,4683,3157,54106,409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2108,255231,407004,3813,2539,2243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2776,216,5256,885,23530,718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,4803,3791,10269,1524,81689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22852,2538,3358,5828,506,6535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,2720,6339,844,23462,6392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3627,2169,3978,57215,2587,3156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,409,5476,283459,5184,10195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 867,6340,1443,10019,7498,3931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6536,4973,51555,5925,3119,4716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6908,8772,149461,2647,55788,91949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 440138,114814,3159,5743,1351,5256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 857,4843,5184,116228,1757,8862
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,2683,948,8195,6901,3645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 156,151306,29881,54578,56923,4306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10643,6521,599,51441,57128,5538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83693,488,5346,6389,6927,2584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6536,3954,23409,10316,1859,5328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6356,56259,3624,7386,10166,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2767,10891,84902,4976,217,2876
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2710,4803,100128525,10875,55186,84334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8675,4803,3074,8665,64240,54567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,8462,1645,1644,3440,3119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10094,3032,9180,9692,407010,496
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 664,2760,4311,551,5625,1327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51604,80270,124454,10842,1524,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9927,5068,4942,6556,2591,8504
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1201,79633,776,1893,268,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2835,4035,4049,90624,3115,9575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5306,4286,27249,2642,56848,1812
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5288,3312,57817,25828,4705,1591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,2785,7292,8932,152078,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 87178,6009,5071,3156,57678,116228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1634,5925,6901,91869,6716,1185
--> return NULL...
2025-12-01 23:03:10.984 R[76118:237920862] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
46.722 0.632 49.922
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.314 | 0.018 | 3.429 | |