Mustafa Erhan Ozer
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 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 2025-11-21 11:40 -0500 (Fri, 21 Nov 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" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 2133/2327 | 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 | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | 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: 2025-11-20 22:52:19 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 22:54:52 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 153.1 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: 81689,2647,6554,6579,1583,10059
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6609,11035,200539,161247,488,583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2348,2475,7388,358,7220,583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26762,84987,462,5617,5331,846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2348,84340,3684,3077,6556,4543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6602,6890,8945,1718,100130015,3954
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2729,51082,249,2099,779,51099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3791,197,23411,728294,1028,2309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92609,55526,5315,427,617,2697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,54576,3242,3551,92667,406991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 364,33,1672,6938,2805,6748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3155,3949,118,5288,10000,1340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54798,1605,10616,1537,23417,3425
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5571,1346,57215,51441,6356,7084
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1869,6609,7040,3939,2159,652
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10560,9968,7376,132158,2729,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 355,2641,55486,4314,5830,4722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5265,126328,1363,2587,9365,4286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6888,60,8642,653,92609,1594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10128,25974,6382,490,2784,2984
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4543,3554,2673,8660,3033,406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2932,1675,5139,4594,1270,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11231,1329,10159,2752,27235,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11232,5447,2309,2646,2952,7345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55186,7038,8945,1644,134,2247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5971,406937,2170,8560,4118,91574
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,50506,55270,9945,54106,2677
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8879,35,10128,11255,91452,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2904,2280,1595,656,5799,654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1815,7100,1201,125170,5654,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51092,8714,406,391051,1605,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 292,57620,8854,2055,5078,54106
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3440,11019,83985,54675,5167,3929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,26060,6774,23543,6906,132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56938,2876,6566,5499,2475,114814
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1716,113235,79587,434,1583,4879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5507,4337,4842,7319,51094,123263
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50507,3490,572,819,55065,587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6770,51024,3952,842,6339,4968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 942,9560,2328,64919,8854,10020
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85365,5328,4669,5092,7879,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2334,216,1737,7035,23516,116085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493753,116228,4502,3030,6833,3357
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4069,9560,7879,6319,3795,8743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1401,8665,2157,5660,2030,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2110,3939,3033,9919,293,6678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5295,3759,3174,3988,6261,5315
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10000,122961,5306,24147,55034,2820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2710,3624,1444,160428,4720,148979
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6833,2516,6576,54578,55163,355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7295,1738,353,1803,1509,54476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,84342,5191,389692,6716,8877
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1555,55902,4853,10020,5321,10842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 249,54915,2113,821,2166,5580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 585,2571,435,1019,3685,5213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493753,1544,3351,435,316,2334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3558,10857,3485,23543,5255,654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,84572,51024,84062,3938,5476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,9091,1968,1585,6514,54968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3417,857,65985,1346,3309,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84902,4968,2629,2247,51099,4779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5781,2119,4000,563,2752,341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54576,6198,7355,6517,1584,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5139,55278,149461,4319,84342,10965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26088,54552,9091,3375,23062,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3931,55005,81689,627,2538,54576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80267,3773,54915,3645,10682,4337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10560,1435,56997,6906,4803,4669
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2739,5288,4925,2517,55630,7057
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353,23556,178,43,5091,4887
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7098,151306,57818,91574,6505,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 593,131669,1028,64919,4915,5901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 999,3554,1514,25821,406,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133,2303,364,540,2161,3939
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387787,4988,2683,100303755,5824,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5967,158,5799,53632,3939,5184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2793,105372280,5654,410,55863,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80070,9971,790,2348,3351,2784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6811,5213,122961,7412,3156,51316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1646,5580,51204,4285,2876,779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,10243,7919,133,4137,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,387,2180,694,6329,93587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,8877,7157,50814,643181,6720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4879,1072,2944,477,43,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7048,4338,152078,1376,51119,186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65993,5919,2937,161247,23369,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57215,9512,493753,2673,5467,3795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5367,64241,265,9414,79068,51
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3117,2806,1601,2678,55863,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3383,4842,4654,7480,10059,5789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3791,56606,3558,79133,8504,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,650,788,123263,9451,100128525
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3358,490,9968,10686,4149,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4728,7124,1281,3373,1801,55753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5590,652,2678,2767,85479,6789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,2260,4125,563,6515,26003
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116150,6351,4988,844,686,585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10159,37,4524,6354,4718,2587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2147,3931,55750,29929,540,55526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6548,154,54578,405,4313,3308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 253943,54802,111,348,585,5465
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7385,5019,6535,5444,5369,11096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653509,6720,11095,7421,1537,51181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2946,3667,2310,3091,5370,55005
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2243,406947,114814,4126,570,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,6476,55902,55340,8799,3558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4988,4035,5595,132001,3958,80270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53345,4973,7421,2952,2888,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51167,409,7915,1649,2516,3077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3586,111240474,54344,5506,1175,6649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3482,3141,4942,488,84706,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55753,8743,6351,178,253559,3293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 58528,55644,6602,1339,4594,150379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,160287,57570,3081,1352,120227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 958,2155,629,7919,3425,4319
--> return NULL...
2025-11-20 22:54:48.641 R[90197:108675512] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
46.953 0.490 48.936
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.304 | 0.016 | 0.496 | |