Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-14 11:45 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2139/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SVMDO 1.8.0  (landing page)
Mustafa Erhan Ozer
Snapshot Date: 2025-08-11 13:40 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/SVMDO
git_branch: RELEASE_3_21
git_last_commit: 8259124
git_last_commit_date: 2025-04-15 13:15:07 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SVMDO on merida1

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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2025-08-12 11:37:59 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 11:49:06 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 666.9 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.8.0’
* 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 ‘1.8.0’
** 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 RC (2025-06-05 r88288) -- "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: 5373,84947,2152,10094,6356,1348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,819,85446,79736,5331,5805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9131,10466,7428,7351,7325,23062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 551,2697,111,50943,84300,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1629,8714,582,199,5538,6720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 185,116150,54901,6932,5925,2147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 112817,1812,9104,10466,1641,51144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4915,55503,7381,10383,5631,6262
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8504,952,7421,1401,2328,3091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2581,84693,6569,3992,84239,4669
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,79934,7386,801,3624,5293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55283,9365,7252,3293,55858,64689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1581,5327,2588,3559,5176,7494
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2158,51117,958,407021,51079,4654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4915,56923,6519,857,8604,5723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8799,212,4713,1361,11019,28976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,9672,29926,91574,79053,166785
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,125988,22797,1347,10229,445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790,836,4758,11019,6476,4023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5274,10195,55630,229,9607,1807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200539,84889,54476,6262,3251,64241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 34,2180,84701,50674,2590,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 643181,4668,593,51085,5595,27235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54210,1646,3759,1499,156,5507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55670,5265,249,6531,650,8600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 516,6198,509,8932,28234,643181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,63874,50674,11232,2820,7097
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8651,84274,3700,842,4886,54931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51422,338,175,54567,1607,2990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,3375,5052,2697,6329,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,51094,11131,3157,10102,5372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5501,7840,9968,2677,6550,5465
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6934,2309,5184,729230,10000,79585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 121268,4718,1869,7355,5250,406922
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6696,54344,2950,1443,5331,57505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1621,407006,10616,3440,35,123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,6582,10019,1559,5826,952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23291,942,4337,4697,8659,55630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7350,5837,54809,1371,10991,1889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7124,728294,811,6678,358,50506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,54809,1589,2919,3145,169792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51206,1435,801,5468,1571,1208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 341,1757,1583,1281,5594,2936
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3156,8813,9180,551,353,5329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3479,5727,9370,4688,6794,516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2937,5580,2710,5365,26354,4594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1571,79133,84701,388585,359,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4915,2952,351,100,776,4544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 811,2695,56052,3489,2717,2194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4853,7319,4282,5730,84572,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 52,152078,4015,79587,57085,51660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11213,4887,3308,6387,85479,6579
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 632,9572,2591,149461,2052,5009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4285,6714,6439,2581,79585,9095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1893,2034,2305,3418,51611,1672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2314,5255,5601,3291,6387,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55024,57176,9698,336,253943,9104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,255231,54915,686,1443,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55572,1373,540,3060,125170,2678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 129787,8648,80224,7355,65080,81033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5962,64116,92667,8841,130120,10
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2516,587,1636,563,1910,1524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,1491,1409,6891,51204,23462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9091,779,3157,51316,200205,685
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 32,3113,131669,4719,3375,1351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,2638,5241,2984,4688,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,2760,3920,5743,1909,26517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7040,6517,8802,407045,3934,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5588,3952,509,4137,84987,10059
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,2762,407009,1734,316,3667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,6811,92935,7276,51081,1348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 491,79944,4069,4049,7385,1737
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56606,94235,92935,1890,23389,7019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,388,51116,9365,132,6929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6439,219,131118,153642,18,2581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1443,26354,7132,64116,132,55858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10857,3930,6891,2746,8651,1436
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2805,48,84334,7048,6571,84987
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7284,80267,3507,7030,2247,383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27429,409,130120,340024,6928,64087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2785,64801,84342,132001,2271,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,25839,5901,291,5295,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26003,64801,8841,1401,4000,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2348,407024,4233,6774,255308,151306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26291,2702,6556,3032,7528,6576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,336,6888,2678,5595,7018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6786,3636,1678,25974,4313,9414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729230,3630,9927,2834,11255,6554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,6391,1356,4722,2762,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51293,3158,1234,64801,2266,1650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51204,847,7084,6352,104,477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,8942,6182,6339,55970,5744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80070,5270,3606,9630,4089,5428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84889,8560,1329,1543,105372280,57176
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,338,7287,3351,3425,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 189,221935,2717,5836,90865,30061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1737,54476,81704,1182,208,4968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84902,7225,8473,7276,5728,7025
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,513,285,1813,5321,836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57817,5950,7132,9180,471,1374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,6948,9575,3552,6262,37
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9945,57085,2280,940,549,9559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,100131801,5631,83854,6833,50943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3551,6347,56729,79053,1644,6898
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54902,27344,1345,364,2099,686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8877,5962,3939,160287,22820,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65080,3240,4744,6821,9698,6890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 31,5241,7038,3489,6199,11019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2643,4247,64241,79949,197131,1442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1392,5592,1813,145264,941,1645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,3490,268,124976,490,7841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2647,84340,572,5789,538,54675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,55024,4049,407010,152926,2628
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1589,53345,55699,3596,563,7052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5660,6571,407045,819,64805,686
--> return NULL...
2025-08-12 11:48:52.226 R[71625:314281507] XType: com.apple.fonts is not accessible.
2025-08-12 11:48:52.226 R[71625:314281507] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
176.145   2.347 183.082 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI1.2790.0791.997