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This page was generated on 2025-08-09 12:06 -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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.9.0.tar.gz
StartedAt: 2025-08-09 03:21:11 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 03:26:13 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 301.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SVMDO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

SVMDO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-pc-linux-gnu

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: 3157,3934,6834,22868,4654,2683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6535,308,6182,5306,2559,51608
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3663,2690,3489,2542,811,10102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7915,3767,56623,6445,153,7919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3952,5428,3929,229,10875,83548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1559,1186,162417,3992,11254,406922
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,1543,51116,11213,3122,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 463,5406,219,28951,79661,5595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55024,7916,7515,23291,53632,51181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406,229,10935,64919,2516,111240474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255738,8678,5190,6649,2745,7077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4723,2904,116519,51052,64788,487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,29947,4925,3480,1175,2110
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5214,6648,94235,867,249,1444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57817,4256,2200,6890,10841,56999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653509,3507,4282,212,3425,6439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,2835,51738,6579,9388,10226
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7351,587,4758,54577,9919,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9429,4288,4688,644096,25813,1803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5295,1543,9374,644096,100130015,1352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5538,5588,33,653,387787,5257
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 793,2475,5288,3685,2548,859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10157,2628,8743,91942,54704,10560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3312,87178,6401,4159,115286,231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5563,51441,55526,1802,6602,9382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 432369,10013,50674,2495,7915,7431
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3643,29947,1606,1644,5139,2946
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1558,10379,50814,5468,2784,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23409,2629,51092,124454,2745,694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,9388,92935,3141,5239,84334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,5189,63899,51021,476,170302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5588,2590,644096,5507,5740,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5346,3948,51092,2184,7879,5095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57192,3060,3784,9021,7019,84557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7284,4069,5551,84275,51128,9759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 479,5321,26175,137682,8462,5080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,4719,84701,149775,1717,2110
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,627,793,6354,4683,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 570,1672,6521,4853,1345,8818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1813,4854,23395,3158,54106,5092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10250,6898,5588,4668,1435,101180976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3170,3416,3425,1185,367,84649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,8942,10730,1956,3425,84889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 599,4758,83985,79934,5261,1583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 788,5207,2745,51144,1812,3569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6535,65993,2303,6794,2247,6339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6649,4842,2739,4552,2260,156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89866,79001,644096,23462,115286,440503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8648,125988,9388,84701,5743,1890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407007,90865,113235,291,2052,8854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9672,1889,56729,7319,131669,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9868,836,5571,6716,1348,53335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8517,133396,6564,4779,2169,5409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4723,3174,2006,79053,55967,2266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2395,3562,6602,89866,51085,7941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6339,2890,788,166785,57192,4543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,407024,90624,7386,84557,1027
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4306,116931,151306,4843,5792,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 367,7915,3485,6536,10128,23462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1769,4313,22933,629,8879,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 339,112817,60684,4915,8471,4023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7248,5068,56259,133522,7386,5291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,85365,1812,1718,51316,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2056,1346,5728,1116,3479,7035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,1802,2305,50814,2693,3483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25828,2118,4306,2717,1621,4760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10383,664,64900,359,4314,3651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114548,28976,7386,55670,23417,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10383,6565,1056,493,5799,6928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2936,54205,2786,406934,840,728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2745,325,6834,1232,57085,1950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8639,6714,4780,3558,5096,8195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169026,1910,137682,55753,27010,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51052,2786,5798,116519,627,3170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3598,3554,1806,875,9868,4713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56922,4853,54802,3636,5743,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,57570,4256,2119,4049,4982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 340024,133522,4968,8202,2729,4852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54802,5265,5019,9779,6932,10226
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80347,8473,3586,8639,7376,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5207,1444,123263,7084,162417,339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9779,3945,5972,55034,1859,84317
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 491,4256,4704,275,1585,3158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 376497,56606,55753,858,1080,10157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,55630,1769,6834,79068,6569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6339,5654,148738,79633,7386,9663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100128525,2932,25828,79731,4306,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79587,1594,63874,80070,162417,4684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83884,1769,1468,138050,9997,18
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3598,2646,55902,488,353,55034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 999,51206,7919,56302,151,4726
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4313,156,2170,3283,5702,1075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9445,55186,51079,29929,64432,84061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5230,100529063,10159,4712,84340,9241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56302,491,6720,5551,57678,6550
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5901,3606,4012,23175,7412,111240474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160287,54210,57511,1559,24147,3158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 942,6908,11213,255738,4702,5095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84557,574447,79133,7167,2487,8243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84062,2713,1803,55750,9415,9692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4726,54344,7840,2949,585,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7381,4878,5052,779,5621,160428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,4729,2632,23600,656,81704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10102,1645,790955,11131,406947,9429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,26235,55902,3358,26517,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84447,3304,4982,33,10383,147007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,10226,79736,57570,55818,3606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,8050,7287,81704,6324,6786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285362,5799,3113,3283,7056,34
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2055,4878,7030,5551,52,51604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,5730,2847,1471,51206,2936
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4976,1641,50506,5743,27141,4314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407040,2030,107075310,7941,51458,10226
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27089,5009,2689,729238,275,5476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 405,5562,84062,239,4925,513
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 66.822   1.126  68.070 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.6430.0320.811