Mustafa Erhan Ozer
| Snapshot Date: 2025-11-17 13:40 -0500 (Mon, 17 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 2025-11-18 11:40 -0500 (Tue, 18 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" | 4826 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4561 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4562 |
| 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 2131/2325 | 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: 2025-11-17 23:52:11 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 23:54:25 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 133.8 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: 2158,3119,572,100506742,440138,4137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2752,217,6934,5105,407004,7100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,79572,189,406,3309,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23556,4654,3645,79144,83439,5250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5350,4915,4886,3673,4709,353500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5654,79144,91869,5346,7428,1514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23129,7385,85479,57505,11096,345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53335,5789,1641,125170,54106,6445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2820,28957,9663,51119,487,23411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4282,407021,4976,3351,2052,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,266,27232,124976,23395,9971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11222,2629,3358,1230,85446,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,341,3251,1786,1595,221935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 590,63892,6821,283120,8942,353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,4887,22797,427,1355,7287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3489,5515,338,3113,516,2166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5629,6789,796,116228,5369,23304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7030,27010,54578,344905,56938,2888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10642,6391,5789,81034,8665,94235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,407010,6789,1436,1607,283459
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3565,1646,5447,2697,5373,7099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6389,55818,10250,7528,1355,1644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,85569,2260,2695,26191,126328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7376,5019,2592,10999,2516,5345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6198,3813,410,6390,3174,6519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133,2694,5473,353,4012,4358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6340,3684,90480,7048,64601,10
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729230,2203,5580,26521,55486,6565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55788,5126,788,4286,5571,80270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406937,152078,2571,26003,64601,2243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 488,3290,3460,55037,7078,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387787,1268,4128,25915,4311,6389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406982,6772,1956,513,1594,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5972,3596,3034,23474,6898,34
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1644,265,26291,2739,10667,5213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2806,5190,2645,539,706,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5789,92609,149461,23600,51103,7528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6928,5346,406947,1056,6347,389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,4942,1493,7409,353500,844
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1443,427,63931,10577,37,948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3062,5276,2729,644974,80270,2784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3565,5828,5265,7248,6890,3382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7172,10686,3483,55186,54578,54106
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6492,64900,31,11019,5330,5071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149775,3638,3291,844,1594,4860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 142,2559,6647,2787,5621,9560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 32,407007,79001,81704,401,7035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5618,3791,10965,339,3709,92667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9056,388,27125,4704,85569,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3728,1734,2739,54205,23600,4149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,84902,55340,5443,407040,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,2099,51024,6183,255738,1802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 121268,388962,55343,9095,7942,5501
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92609,5241,5745,2099,51181,9095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,4144,79731,8803,708,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,4878,650,51649,15,25915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6514,1514,1508,85569,8504,825
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,1442,6609,203068,10019,599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29078,51204,3773,29926,2693,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5830,2786,2835,79949,5370,3485
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2169,6439,4851,9663,1607,7287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51021,4852,8600,55818,2169,10221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152926,6794,285126,22852,79053,6616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2936,51478,1175,201305,6948,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92483,952,2729,54576,3630,1185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9559,26088,3658,10682,55343,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,1718,4311,5228,3156,10643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,80331,6602,5644,200205,3383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1352,3953,590,1890,54809,27232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5096,201595,3156,8050,11231,22868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64805,7480,84274,6906,3156,9759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1558,4285,123,10019,6356,3606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81689,91942,23462,3596,211,23543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1244,25839,476,492,7388,5126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 161247,10382,2745,18,34,406991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5727,479,79644,10382,347,79087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5328,132,549,9380,3930,120227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,6505,2632,384,10642,5584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2762,10730,407009,84947,175,2524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7048,85569,518,6382,2628,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4712,2115,51241,3283,2694,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124976,64788,116085,6565,5293,1869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,2592,7471,2119,125988,100303755
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2243,6464,3939,462,4722,5313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51316,10911,79731,2593,149461,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,80267,10965,4282,23409,3779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5447,388753,25821,4684,50507,208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 516,8678,2834,498,5830,83884
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,51604,2805,2731,84902,3034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27235,166785,2904,7345,629,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 463,4704,5306,2778,118,846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10965,5805,51458,4247,1559,4299
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353,5193,137682,4729,2890,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79796,54968,84447,10020,130120,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 241,3779,1393,406937,124976,54576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3938,2693,89874,79944,54809,4695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 186,11093,10891,2180,10644,868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,1559,4232,64240,105372280,6439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53905,6901,5293,3119,3339,4160
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51119,3995,265,256471,6649,1392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 384,7494,10135,5728,23654,7052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406934,81689,347,4713,435,3357
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56052,2314,1605,133522,50507,1356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2745,2184,283120,3425,5315,4609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3158,83548,3082,130589,56997,84705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132,491,6678,4313,7048,5162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6198,2328,1812,5126,197131,2693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7100,2280,3558,4760,63899,53335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3557,572,10841,9076,708,389692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3159,284958,6927,3684,2950,3418
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6389,55670,79087,79158,116519,84239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6794,632,3440,5584,9672,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6548,3899,54805,7100,1737,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 825,125988,9388,11095,6554,8743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 842,10094,3934,85446,6564,125170
--> return NULL...
2025-11-17 23:54:20.680 R[11514:66019438] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
26.940 0.434 28.683
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.293 | 0.017 | 0.533 | |