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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 2119/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SVMDO 1.9.0  (landing page)
Mustafa Erhan Ozer
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/SVMDO
git_branch: devel
git_last_commit: 7851a60
git_last_commit_date: 2025-04-15 13:15:07 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SVMDO on kjohnson3

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.

raw results


Summary

Package: SVMDO
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2025-08-08 21:56:16 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 21:58:10 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 114.5 seconds
RetCode: 0
Status:   OK  
CheckDir: SVMDO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.9.0’
* 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


Installation output

SVMDO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SVMDO’ ...
** this is package ‘SVMDO’ version ‘1.9.0’
** 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)

Tests output

SVMDO.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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: 91574,7248,91869,65985,3284,5702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3708,57818,155,3990,3791,1080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 341,1200,37,4720,434,5230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51085,91574,3708,116931,3113,9076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11222,1992,11093,5824,81689,54549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8560,4126,6476,6401,5971,10269
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1650,57761,3030,3074,9332,5328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,53335,374291,9868,1582,8854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3358,5538,9971,347411,239,6352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1392,387787,411,1586,10874,10094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2937,2572,2053,1394,107075310,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,51601,790,6464,6934,2776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,3240,4915,353500,5306,6338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3251,6821,285848,121268,5191,3557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54205,219,3157,84649,51738,479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1339,3339,10102,3791,10269,50674
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,471,10891,1889,84061,6821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,8202,1175,51611,3418,81034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4232,2919,51099,26003,335,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2806,4656,8841,6934,23417,6462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,56606,1435,4722,3586,4879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9512,1734,6696,3156,91574,4149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406991,10935,1509,50484,3356,10195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,84239,7942,100,7384,7248
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 336,2904,708,79633,391051,9415
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,1678,64432,5617,2693,3813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1371,5192,23417,56052,1584,6342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10008,1435,7287,3062,84649,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,7084,81570,57085,10874,57570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7494,5551,4544,134,558,7018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54539,10383,26003,491,10724,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22796,4015,3945,23369,81033,8473
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55278,10999,348,10599,4285,6906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 581,200186,6492,27329,364,10643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,4846,7056,217,1401,9498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 284958,10382,85446,85476,9180,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 185,51082,847,57620,10667,54806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7320,4153,1182,256471,3054,10891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 959,407021,7528,409,388,10466
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84340,9091,5068,825,2752,35
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80267,7424,5161,6901,27232,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3570,5962,2693,582,3703,2260
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7450,10062,1757,51548,490,6403
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7078,80339,55186,57192,4852,1812
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6492,5184,1650,5580,10911,120227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10102,7054,7048,231,3576,389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148979,8648,7376,3630,1509,50506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79644,3351,5346,3551,3375,1906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,4357,5367,8639,5445,9365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1116,539,92483,4968,593,5625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3033,185,5744,10682,1075,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,2998,10128,2524,51555,51116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2752,2118,5617,211,5250,4851
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8842,3600,9414,118,54968,217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8879,3483,87178,266,5447,1583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,4851,51458,3123,2805,3980
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255738,6354,7248,4982,5562,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4609,162417,1080,55340,1607,6999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8050,6389,10316,490,2235,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5787,80222,57570,6522,9054,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5515,283120,64601,1435,56997,10991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 885,29926,48,3098,1022,7054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10642,7376,2119,2746,6383,283120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3995,2638,7351,4312,93587,2875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7350,51649,55270,2678,1717,4704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285848,51608,2571,56848,57818,55037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3304,406937,51204,54901,3586,5078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,5592,2100,51085,10642,57511
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3565,811,133522,2593,3938,6786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7037,3416,3119,6934,4288,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1232,7498,7388,32,160428,28976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8665,3813,4547,6445,170302,2936
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2788,1514,27429,1869,275,10102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26191,3708,1186,100128525,292,1644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5590,7248,151306,599,6338,169792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,9868,2280,1340,7319,1789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4149,4846,7388,10221,10686,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5625,6339,1558,10,359,51608
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4351,3113,4851,2495,9076,79644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5228,3440,1232,7347,2947,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,84334,4713,1182,26227,284958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 405,948,355,6770,1641,1581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7941,8803,5105,4598,10560,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26175,3875,776,7528,846,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644974,10667,26227,8471,9131,5370
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51167,23530,3251,22978,2147,5313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,3995,6772,85569,5967,6513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3953,1080,28976,79944,1605,5728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 210,6616,3600,4803,6531,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 383,6647,84062,3934,9507,1490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5078,10875,162417,56999,51649,4627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407008,10938,821,2984,2243,4358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,54575,4552,644974,347411,79949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7350,1843,51092,517,26119,3155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,11222,491,5288,7057,10891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3066,3645,23409,4668,3312,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10243,2303,25974,1268,63931,51206
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3507,1019,11231,2110,92609,56923
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6868,5054,3356,25813,5330,348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4854,56919,8567,31,7100,7319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1471,3308,116150,3122,56848,5860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,10616,3606,92667,406937,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4982,3576,4357,664,10874,55163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5096,347,846,5188,5919,51601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,1374,10642,5214,7040,3240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,435,203859,2998,3242,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4338,6492,7466,582,1678,4609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55750,7372,7431,640,154,8802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5580,55340,336,1992,79731,1608
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9927,857,57761,2934,51241,6678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9131,492,10226,407009,9560,29928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,5091,3382,6582,2030,123283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9377,6786,4609,643181,1232,10157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3291,10845,54896,83884,56259,84706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2110,2835,55630,629,10875,1558
--> return NULL...
2025-08-08 21:58:07.445 R[62552:491995364] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 23.525   0.391  24.220 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.2640.0131.565