Mustafa Erhan Ozer
| Snapshot Date: 2025-11-30 13:40 -0500 (Sun, 30 Nov 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 2025-12-01 11:36 -0500 (Mon, 01 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" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 2134/2328 | 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: 2025-11-30 22:57:09 -0500 (Sun, 30 Nov 2025) |
| EndedAt: 2025-11-30 22:59:44 -0500 (Sun, 30 Nov 2025) |
| EllapsedTime: 155.1 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: 3980,6354,599,2034,5506,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,7100,6448,27089,708,124454
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54205,51092,6898,1992,4015,3759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,1234,22978,6548,65993,5192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407011,3717,51608,55937,387082,8932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22933,2184,7351,4149,79644,10020
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57001,133396,4547,389,23062,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 161247,7345,590,6554,2101,836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1281,3309,2303,27232,7097,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 137994,5207,111,345,27010,4842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1356,3293,84902,5740,51608,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3728,5091,3034,8842,1346,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,3552,685,23291,2335,1801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7036,1270,54600,5329,5723,1509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7132,640,5315,2847,3357,2516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,6774,100529063,1717,1813,5444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7220,9054,4627,148979,496,9698
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5828,6356,5824,3920,383,3074
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406,2717,2147,411,5445,57085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4040,8504,3606,29929,3773,3569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,10938,3115,10642,2696,4683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79796,3122,7026,9374,2804,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4312,8854,11255,367,6514,1185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,940,3490,8473,3054,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 284184,7879,4842,496,121268,4899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5972,387787,5723,4715,142,160428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1356,5243,6891,1329,292,3784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4153,3552,6339,3479,181,2683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3954,539,6556,79944,410,1327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10599,5919,795,54802,1392,2538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84889,7030,10891,6794,2688,57620
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4976,4720,201305,2584,6794,486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 384,596,9054,23556,249,2063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55037,4973,405,5727,3485,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 488,253559,23389,51092,5019,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10250,4779,10874,104,5321,1392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4089,8660,7157,200810,440503,132158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 867,336,84987,479,5428,1080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5350,859,336,1435,867,197131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51092,4089,1555,718,6811,4724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55970,6929,6811,5321,55340,819
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,189,6906,9572,3312,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406982,80224,1394,4547,153642,22978
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6647,55572,48,8560,2786,160428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4723,1022,4744,6354,3638,4713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2108,10423,4879,6929,3291,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9445,952,2280,56623,5476,6678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 929,2590,4715,640,3709,7052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 627,133396,1232,56259,347411,65985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5239,4232,1588,8803,56052,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2524,387,3091,2303,29881,23400
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 177,54902,6932,145264,5230,8659
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1329,7471,5702,9374,65985,80222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,493,406922,359,9380,629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1200,5105,2752,10008,4547,56848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54809,4709,8462,2194,2786,3813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8722,51117,57128,1369,51094,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653509,51601,1345,6678,4232,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8722,84275,64432,2110,407021,3123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,5277,1956,54968,9630,2597
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,186,2314,8195,54982,1116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7035,9021,1956,8648,114548,6351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5122,51024,5288,6401,790,387082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4878,8517,51181,4627,5194,51024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5161,3087,8431,284958,10102,353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3113,4988,2760,8648,55340,6678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65080,6403,55526,1968,3458,3795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3759,1537,3458,401,790955,51478
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81570,6934,491,1080,3813,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2804,213,3783,249,118,58528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9414,145264,56606,7351,57505,6535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 686,51478,54931,5286,7275,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6571,3507,4878,10580,5702,9945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 205327,57128,161247,1806,147007,212
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353,83548,2314,4726,405,51021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5594,10577,6492,64087,56923,55532
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65993,8431,3486,355,26119,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2266,2108,116085,2548,2119,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6519,50674,32,51738,6338,56652
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4715,4700,2643,567,6548,6678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 335,2170,3357,8802,51548,153642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10226,208,9241,6788,4594,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2593,51649,2745,2946,7421,1312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1443,5625,9971,64801,4842,1581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6550,9698,2804,2064,3099,3507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1509,1524,728294,5195,7048,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 857,10524,1543,2646,359,56052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200539,5214,5052,4502,56302,3099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54106,2591,1489,3357,5192,4842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3358,8942,3978,3373,56606,10643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9945,407006,2876,406991,25828,1909
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23474,5276,4860,22978,151,6888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3145,4722,3155,3630,239,7030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7274,3073,142,5499,54148,3728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 594,1555,51660,10116,5443,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,229,6579,3329,3293,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84833,9672,5551,5160,406906,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 358,8942,3479,9479,64801,6602
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5243,7389,6402,2683,10559,4723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,1080,119559,7515,8471,118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57380,79158,6716,4726,11231,3759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1644,3978,9382,130120,9414,587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54344,2998,1584,5644,6569,210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 231,3551,3066,10157,6319,51604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5445,790,4720,8802,407011,2689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 617,205327,5409,2731,5828,8694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,145264,4000,7942,79736,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6445,90865,3954,718,3158,293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8567,6199,53346,6794,1345,54802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11213,4715,3382,123283,6715,26235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,26191,203068,1363,338328,4779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,25839,87178,405,952,9370
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2787,2653,6517,203068,4729,1798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8678,3357,6891,160287,8854,406982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,2203,3417,3627,5595,5476
--> return NULL...
2025-11-30 22:59:40.417 R[43139:223597052] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
46.127 0.495 48.294
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.296 | 0.016 | 2.340 | |