Mustafa Erhan Ozer
| Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: RELEASE_3_22 |
| git_last_commit: 86871da |
| git_last_commit_date: 2025-10-29 11:23:08 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-11 12:05 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4670 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4604 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 2163/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.10.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2025-12-09 12:55:50 -0500 (Tue, 09 Dec 2025) |
| EndedAt: 2025-12-09 13:08:20 -0500 (Tue, 09 Dec 2025) |
| EllapsedTime: 749.5 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.10.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runGUI 1.352 0.074 8.393
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.10.0’ ** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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: 498,8802,3034,7054,1356,53346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3667,9698,56922,3308,26191,4700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1734,3627,55902,3684,9091,388753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1585,842,160428,6786,1584,43
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 283120,5327,54982,7276,10642,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123263,160287,941,90480,7350,79731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5330,51024,29960,3557,4968,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,11231,2157,7376,2677,6929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6648,1116,197322,54106,51144,326625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 594,91942,1950,1361,126328,341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4128,4338,858,27429,6342,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 847,5328,5370,249,8648,7388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1738,25839,50943,34,4669,11136
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2896,3172,4089,2064,1200,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1992,345,5270,10383,406982,6352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 549,1185,952,84693,4153,644096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,37,1230,7919,54552,7428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10724,6391,7097,570,1352,1312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5295,57048,85446,54575,4524,10243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5295,5345,100303755,197,844,1369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1717,407040,2200,3077,5250,858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,55937,203859,5009,64087,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6925,56922,10577,4899,9415,3667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,1737,22797,2328,57678,156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53335,6492,79633,6556,83854,54704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3485,8841,11231,116150,5618,6571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3636,10379,5364,4720,387,9868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10102,4319,9414,8471,811,54704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5189,2638,2629,60684,2184,5826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,80207,567,79602,6616,84649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407008,3290,10013,208,5730,10874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,3557,124976,4695,6351,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10352,1497,440503,347,23600,7385
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10874,3054,178,3240,5571,207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,149461,1910,958,29926,3784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5501,3953,7528,6788,6948,1607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2731,133396,6821,2118,3651,3558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2147,6445,4015,5096,350,4299
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 650,1200,5092,3991,23543,2628
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,3651,6890,406906,2152,3483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29960,55937,5730,205327,5256,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5313,5306,2487,6352,1329,391051
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,29843,26503,79633,3158,79572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50506,4306,29960,5191,4232,51117
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 654,4828,9630,57176,23530,24147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2864,22796,5563,10845,1543,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1606,653509,10682,2310,8841,5194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7172,10382,686,2100,3899,5313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 129787,5836,5443,6715,54704,5919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54675,1813,2713,350,6908,6928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10195,81570,9663,6464,10644,1889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27125,644974,91869,56922,5473,54205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2695,51082,5126,54575,5580,1807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203068,2934,846,84833,5176,2695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,2592,3673,479,3791,55863
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64788,27141,1718,4758,54704,216
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 940,3339,292,7076,51293,10019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23753,2689,1149,22868,1442,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6324,3565,5350,6183,4968,79644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2538,6383,105372280,3938,5498,7252
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7295,51103,79934,3145,2990,6261
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6329,26503,23062,1028,779,51660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3638,2100,231,132,7320,291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9560,6515,5236,2584,5230,4726
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,406913,779,11222,5599,3113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,54205,6564,51555,124976,58528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4502,55967,2548,5329,6569,84334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 178,4149,3081,353500,9054,1645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,2792,2690,361,2310,836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9451,10116,111,6906,1859,4015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29929,1582,1803,1889,3304,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6821,3586,387082,7421,3773,1468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,153642,5293,9370,868,406937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5286,3077,2937,3995,92667,5207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27232,2820,100,5228,51293,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5644,121268,84902,57505,6550,3586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,788,364,1182,407024,4704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4023,6788,3627,7384,51555,479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407006,4609,54896,2647,1869,2030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,1268,376497,3291,1376,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51660,27429,56919,9180,1593,5277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80270,406922,1757,10724,22852,5445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 650,2717,8842,1277,3945,3569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,7389,3938,7295,2166,48
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,55902,211,4160,29929,477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,107075310,1807,3373,405,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1348,6925,538,1909,56259,5373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5194,6748,3709,654,79783,25974
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,23163,5161,3600,2152,4125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,5538,1956,1812,5592,335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5161,462,5270,148738,186,189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23038,79087,3576,4854,285362,2643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2305,111,6576,56729,4684,124976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1337,1116,2155,23530,11093,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5321,11131,2990,10667,7037,84342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5241,406947,5967,4915,10250,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5373,2516,156,2101,5071,1992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2806,3357,10667,111,353,8678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7350,2542,4012,8309,285362,9945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123263,2787,1149,819,2170,112817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55270,729238,23175,1353,7347,10229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7030,4713,4049,4654,5744,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7295,53905,23400,2571,130120,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2990,111240474,87178,1559,56652,1346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6556,54576,1312,6550,55753,3992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104909134,201595,3700,10128,27329,5501
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10157,1968,1813,9054,655,23417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,7351,55340,2696,54476,23654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2642,9868,9572,54549,2592,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10269,5176,10842,64131,6351,1234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 655,5236,1956,846,2582,6715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2161,84705,89866,5444,4125,632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407006,2194,5214,7054,5176,6772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54344,2875,5192,5345,84274,5330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8604,7078,169026,123263,2487,7040
--> return NULL...
2025-12-09 13:08:03.629 R[32929:107765279] XType: com.apple.fonts is not accessible.
2025-12-09 13:08:03.632 R[32929:107765279] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
110.188 2.200 135.111
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 1.352 | 0.074 | 8.393 | |