Mustafa Erhan Ozer
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 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 2025-11-20 12:05 -0500 (Thu, 20 Nov 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" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | OK | ||||||||||
|
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: 2025-11-18 15:40:20 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 15:51:56 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 696.2 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 Patched (2025-11-05 r88990)
* 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
* 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 Patched (2025-11-05 r88990) -- "[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: 5428,7471,463,57192,2785,51738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54567,10013,4125,2194,3062,79661
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63931,1361,30061,2169,5194,166785
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7916,5644,5580,9507,4089,5091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1282,6928,54931,27249,2110,100128525
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2762,7350,7274,56302,3480,5789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,84701,1468,6609,7388,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,4879,2776,5498,5095,27247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1621,4724,1351,10857,122961,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50484,7320,199,409,100506742,685
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84902,2310,57017,2628,7040,2180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3576,10667,1019,9919,8504,2804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57176,1581,6374,4598,1675,9575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 664,948,1497,57128,10577,5625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9559,55526,6770,4337,79736,5367
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203859,685,5744,55503,410,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3159,3283,55278,268,10891,406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9868,9445,11136,1629,3990,84275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6821,51116,64241,3357,387787,6647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406947,51099,2309,3304,2115,10537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,2788,51555,801,177,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8842,406938,10020,509,6932,1327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285,81570,2798,3670,80339,5629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65993,1186,7391,26088,3717,2559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6564,54901,7036,104,91942,3554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347411,1185,7026,3717,8841,344905
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2180,152926,7078,5192,3953,4683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10874,1559,283120,5792,51167,7054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,3667,409,84062,2100,23556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6263,22796,23753,48,776,64240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2516,496,3339,361,56922,8639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2731,10062,9759,1203,5498,124976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8942,7407,4828,3479,64240,6821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 629,5122,291,4126,5925,3995
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1027,5126,6927,811,440503,5315
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9663,18,3293,6934,6890,4654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54809,57817,1356,4656,9076,7284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50674,6833,8714,126328,3375,4790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64801,2308,10379,4828,5230,3145
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64241,2053,353,22820,4915,7942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6505,23369,4159,5277,126328,4846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2194,3712,57505,2099,4726,5193
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,2710,3712,160428,5091,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23411,27247,55750,10686,388585,23462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5370,3558,57104,3784,1585,10243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,3783,6339,4358,4714,54901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2034,2785,3351,84317,5364,50943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1175,1497,1029,7389,23409,57761
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10857,221935,51117,367,8202,84889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406947,169026,26088,496,51555,27141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6999,26354,5370,64601,4023,10560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,200186,25821,10166,1571,5096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3440,3156,54331,2548,3784,54549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1435,80201,7466,7019,7076,6748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2752,1401,476,2713,1537,124454
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2908,3034,1893,27249,4723,50674
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55863,5588,3767,643181,5713,65080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,4118,4704,93587,3779,1401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51241,6770,2731,388962,5789,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 650,4968,539,8818,11213,1718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27344,3992,6929,217,5175,6182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1361,2936,2157,2731,48,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 768239,3990,29078,477,7225,5277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26003,406,6714,3082,6888,486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,22820,84693,5270,583,3586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5631,847,1798,4049,5563,9971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1232,51167,1589,796,65080,255308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22796,111240474,2152,706,114814,2695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 58528,4149,22868,627,788,1028
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1812,2710,23462,3991,23389,7040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8604,6564,4878,81570,1906,56729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10842,6554,2998,10128,10643,4803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1029,7345,8932,3931,7372,1186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,56848,7225,5193,325,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2115,80222,2778,80207,4760,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9131,10116,538,152926,51608,7428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 796,3569,4552,1585,90624,35
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407045,6462,1373,6514,197322,3117
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,4724,4780,5595,7157,4973
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,50943,538,2641,51119,3479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56945,84274,5054,2147,1493,5901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6401,6263,359,7172,10938,5189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51117,53346,7345,3060,5447,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,7048,3565,100506742,2303,9420
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8743,387,51119,1312,26291,6531
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5507,2200,3663,3115,148738,51092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79585,2053,51422,7036,79731,3934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2864,3065,84947,23163,5599,2260
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3073,6522,3284,7295,942,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9415,6925,8879,11231,6938,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 476,4126,200186,4502,325,2588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4973,356,2109,152926,6566,3339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,50814,1634,844,1524,1629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84447,51167,1606,79001,79796,3569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2052,51092,3945,3709,5369,359
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 664,56652,387082,2643,2875,3119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,217,100128525,3308,11096,599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 111,50484,10559,2697,51555,5972
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55526,4803,7385,54344,91647,8471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2100,4338,3034,2056,5594,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1371,170302,51117,4712,440503,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10157,11222,8818,57017,51083,821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5702,3920,4846,5563,8802,476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10352,5078,2184,55858,6505,5295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4524,1524,3113,2746,859,7390
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23417,5257,53335,10724,7376,100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5828,268,253943,51099,3685,463
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 567,1812,29078,2152,3779,2936
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51116,29078,2799,80347,48,80222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90624,2310,9692,51548,1557,6531
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,63899,6564,942,8675,345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9445,10891,6647,3382,137682,347411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80070,7407,83884,5126,7078,27010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7037,4760,388585,432369,4967,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6556,3077,29843,3098,1339,3570
--> return NULL...
2025-11-18 15:51:44.000 R[52351:29322668] XType: com.apple.fonts is not accessible.
2025-11-18 15:51:44.002 R[52351:29322668] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
181.964 2.354 189.587
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 1.325 | 0.062 | 1.859 | |