Mustafa Erhan Ozer
| Snapshot Date: 2025-12-11 13:40 -0500 (Thu, 11 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: 2bc7e27 |
| git_last_commit_date: 2025-10-29 11:23:08 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-12 11:35 -0500 (Fri, 12 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4874 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4582 |
| 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 2138/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.11.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2025-12-11 22:54:12 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 22:57:03 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 170.4 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.11.0’
* 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/4.6-arm64/Resources/library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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: 6530,54575,1361,2334,80222,5428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2118,124454,3141,43,9095,5594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84769,55750,1493,10533,6374,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65080,11019,2524,3953,51052,4126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5192,2203,131669,5925,84300,84342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1351,31,846,462,6948,2559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4842,6934,5239,4722,2113,842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,2998,3636,7275,517,15
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1019,5824,11131,200539,4719,688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2305,1376,79796,1806,157848,5468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22978,3606,10135,19,1401,126328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4968,9056,388962,5551,26521,64805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2542,81034,8884,23590,3490,3087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,92935,63892,10667,6492,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4313,10019,6721,367,11213,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6390,3060,3586,7076,4855,4702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7018,4968,79602,55863,1071,10841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3670,2944,166785,410,150379,116085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 506,64432,11254,5837,6198,5950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5629,253559,23236,54205,60684,5594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2937,2582,7915,1468,57085,241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92609,80224,6906,5078,80222,4688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 574447,1906,1393,10841,57107,5329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 162417,1807,2653,4123,6576,92483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,2729,9382,821,653,3952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10644,1555,29880,9692,79661,26762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57620,3081,1281,685,5286,84557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,53345,1581,1717,115286,2109
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54968,10,406913,5192,4760,6714
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 570,653509,819,197322,10891,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152926,6901,7916,2645,5787,3980
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55034,2348,10195,3553,3122,4233
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406982,56729,376497,84334,8841,1716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,3899,23556,1443,6009,6523
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 31,9131,344,729238,3329,4878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 330,8639,83854,4702,54331,1586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7352,2791,10008,4864,92667,6439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79949,2937,81027,4015,6714,3156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2581,8651,83884,11232,23274,10457
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5723,9409,338821,5962,55005,8675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 796,406934,5447,7351,1337,84557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6382,55268,54511,275,54205,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7841,3658,4825,8202,1606,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1394,79633,3558,54675,7292,34
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3988,89778,2200,941,27232,55486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80270,3954,57107,2590,2638,6833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,10599,5105,26517,285126,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1737,491,3073,801,55863,142
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5176,5268,7372,1728,708,6261
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3490,9927,6718,83548,4852,7319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8471,6382,338328,6374,4143,3791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7428,2790,7916,3351,490,1468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 213,10938,367,1281,4714,2646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4247,3552,3651,26521,1019,7078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 87178,4779,3356,6387,4232,6318
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 463,3351,84902,51604,124454,51052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4723,599,5444,201595,155,9507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81034,4716,3980,4539,6811,5580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53905,3692,3930,3638,2271,4719
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407006,23054,9498,6341,3995,27249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5372,2588,5052,3290,493753,4758
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5972,23038,3554,4915,9429,5498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9479,339,4318,5265,54704,23400
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 952,131669,7389,6389,29947,411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407045,3460,476,5369,7428,5288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,84504,25813,664,567,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5498,3074,3576,2516,100506742,4982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2798,4247,5167,8560,688,7916
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5228,3552,10644,54901,51079,506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3703,150,55572,23400,2582,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197322,581,64241,9056,3062,65993
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 137994,344,130589,2690,347687,51176
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2745,5538,2572,33,285,3065
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,34,9560,8879,9507,80331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2581,7384,79796,1468,51024,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,84239,9095,6531,23395,6770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84274,79133,1843,5068,8862,5860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6324,5499,120227,3643,2332,5629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790,1806,339,80222,9945,2762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1514,388962,23129,2113,538,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5442,5506,5825,201305,4722,4118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 213,2739,4758,55486,2495,84061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,91949,2158,5126,389692,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10560,4915,5584,3554,351,7471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79572,2653,79133,56999,3954,4256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4925,10019,3304,5476,7351,407009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64432,496,1769,7025,6403,2052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1675,788,4729,8842,5096,229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50507,1906,3145,4803,2936,10159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5473,5346,7355,7124,6324,10875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54148,3485,2940,4887,54205,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7347,22868,6470,3667,6445,2235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51116,51204,3416,4684,2064,100303755
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406982,5792,549,1807,189,5192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6530,65018,166785,5499,5702,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26227,1373,5191,84947,4760,151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57176,3091,1201,23417,4683,56919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7030,3425,5501,138050,89778,64087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27429,1843,53345,3062,9759,54552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57001,4089,7384,6582,8642,7841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8772,1200,26227,50943,3562,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2992,23129,9968,5194,4539,706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7082,10059,5078,9104,4232,2864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,29880,10295,1646,1557,308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10221,79633,387787,7252,3158,5256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55572,3304,64432,55818,6678,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7172,776,7941,6579,10243,11095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3791,79731,6523,3990,5972,3779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 409,5195,388585,4233,51004,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3119,6514,241,5346,125170,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344905,203,79133,28951,6390,2180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 409,3673,2289,10352,1956,5744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5563,656,54577,2762,5473,84701
--> return NULL...
2025-12-11 22:56:58.367 R[89788:372267833] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
58.140 0.679 61.071
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.338 | 0.020 | 3.294 | |