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This page was generated on 2025-08-12 12:10 -0400 (Tue, 12 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
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-11 13:45 -0400 (Mon, 11 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SVMDO on lconway

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: 2025-08-12 00:37:43 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 00:43:16 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 333.3 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 (2025-06-13)
* 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 Monterey 12.7.6
* 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-x86_64/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 (2025-06-13) -- "Great Square Root"
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: 55753,285,23590,4286,729238,51081
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3948,56999,22933,7879,8665,2731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51176,2713,788,26762,2729,3156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,7412,5618,4704,181,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11254,406,122961,2693,2888,6403
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406991,2720,1803,2328,7350,23400
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,6576,1589,948,959,2539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407021,203859,63874,3482,166785,217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 514,7372,8799,367,60,7276
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2516,5176,596,4915,3875,5265
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1028,29928,952,10157,643181,63892
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4976,2760,1584,2632,5264,685
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5270,2992,6833,2334,5571,3899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3673,116228,1757,56999,6868,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1355,6476,3122,5313,316,65985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7157,4128,2695,2194,5193,56652
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5830,10165,91942,10524,23274,6898
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5660,10753,4688,11232,10466,6934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1801,3703,5595,4842,65985,4023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 125170,7036,1672,10891,210,54576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,1629,101180976,23417,4843,26003
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,2203,6571,6938,140803,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5365,338,4719,477,1641,3081
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,4544,8504,4153,5256,29947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9759,2572,6445,4319,6834,517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8854,87178,2110,388753,53346,4286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55630,11132,1361,2683,63892,664
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5189,54982,2108,9451,347411,10013
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7325,1786,10559,409,1585,364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5078,796,858,54658,593,6888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5781,4684,5071,189,6531,4144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22901,4286,2109,79587,2677,7297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 685,221935,6566,5444,6774,1859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 948,6715,1544,5126,5837,5091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1601,518,2641,2056,54968,3990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3141,7097,1071,79731,107075310,2949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 122961,407040,84274,231,1909,58528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4982,2688,1312,387787,885,23054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,2542,63931,4357,51082,3382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2752,6932,8799,189,5331,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,6198,3606,1282,3123,26003
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4233,5331,51293,90865,284184,5828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9945,201305,6906,1728,858,23411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6696,2690,9630,3899,407011,10229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,4695,2244,55788,1182,5588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6576,54968,686,84889,5584,5139
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2243,2992,3988,7320,91869,4879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 488,3284,941,2632,2495,175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1591,7292,116228,26235,125170,3077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 427,344,665,1537,493,51458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4233,1675,1585,6354,5364,10524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2146,10965,8560,407011,79053,64131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 664,3309,6821,80222,10159,7916
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27010,55902,790955,10466,23389,1022
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1149,10642,6897,1786,7289,6616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1813,60684,6716,221935,2548,255308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63931,958,940,694,54931,27141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5054,2395,3033,183,389,79796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 345,51548,26235,5595,2303,3562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,181,488,2582,56729,79133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64432,84649,51116,1798,728294,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3875,340024,4855,125988,729238,941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5592,4247,5792,84833,8722,2888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9095,64900,5329,81704,5211,3157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55572,2161,3489,1028,79736,2642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169026,4137,4627,9056,50674,517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7347,8504,3284,3358,411,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,207,627,5250,6929,3651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5621,10577,2646,3489,3569,6565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80347,1737,64801,22978,57176,1646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5243,5370,132,1175,8567,3483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,93587,56945,410,1072,79585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4724,7407,231,6786,6720,51052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,407040,492,80347,1393,181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1583,3356,9429,84275,1471,9382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388962,51181,79585,776,326625,8243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65985,6609,4688,1807,358,5161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1910,5228,8660,2052,6374,3155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,6382,137994,5972,1028,6554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9429,6521,52,8694,325,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 629,79944,5255,29947,10667,2778
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6389,1801,5445,116519,1339,867
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388962,130589,5654,4311,4854,2729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 410,94235,3159,652,51649,54549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2804,6340,4288,5590,1595,1634
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 15,513,132158,84889,23038,9021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2034,1443,3507,5126,10559,5228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5241,1893,170302,80201,5618,84902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1075,3358,22845,57128,158,3062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54205,1393,84705,2184,2947,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5276,7372,9076,81704,9559,81570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55034,3712,7167,4988,3953,256471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,5805,3684,10724,4299,79602
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2834,3703,7466,27232,26521,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51604,5617,2147,6715,2695,1645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2395,2006,38,4311,9415,2118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 795,6401,27344,3945,4852,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 34,2731,514,4702,90624,51024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,26227,1813,124976,2834,3073
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,551,5236,23474,51081,2271
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2990,3728,790955,7879,4654,10250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1812,104,1116,23274,1586,51608
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23654,509,285848,1621,3293,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,51085,7276,81704,644096,55532
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84342,549,643181,10379,5373,18
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,91452,10094,7916,2944,23516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27429,3479,50507,1889,2937,6584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2717,5428,28976,4855,3440,389692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,79661,5350,2805,1352,212
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 486,80201,9663,728,10845,27329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 940,55670,2030,4718,538,875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5825,84701,54552,5925,137682,3170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7275,5306,5901,5798,1409,55283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3483,3375,221935,2643,2328,9559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 867,9927,694,153642,858,114548
--> return NULL...
2025-08-12 00:43:07.641 R[36324:439894213] XType: com.apple.fonts is not accessible.
2025-08-12 00:43:07.641 R[36324:439894213] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 65.244   1.496  67.464 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.7580.0501.392