Mustafa Erhan Ozer
| Snapshot Date: 2025-12-02 13:40 -0500 (Tue, 02 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 2025-12-03 11:35 -0500 (Wed, 03 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" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4575 |
| 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 2137/2331 | 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: 2025-12-02 22:57:30 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 22:59:47 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 136.9 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: 2335,4543,391051,152078,1186,3073
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8660,9451,6263,5092,80270,6718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2903,9332,8799,2184,8195,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729238,572,64241,23129,3122,407040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,389,8471,55858,79736,2949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9560,132158,8309,161247,1471,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6834,50506,4351,407007,7054,137994
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,885,2696,567,3636,10221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5579,1583,3813,1329,54658,10524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2203,7167,4524,116150,3958,29926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148979,56606,6389,10,55278,1890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285126,1636,3117,7919,5770,133522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,2936,3576,292,3709,5476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4860,9104,64919,4853,6352,4012
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,1581,9380,1910,4744,10524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,84317,1373,7052,4286,590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 128486,1557,537,2064,7099,1490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1232,4337,6505,5274,51167,51052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1327,81033,11222,3356,11019,6720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255738,3948,4288,364,10135,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54902,9056,201595,642489,8841,55526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55283,199,9377,2944,55788,1636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 435,10891,57128,9180,643181,1442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11255,4886,26003,4000,6448,1586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5069,7389,11213,2308,7030,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3554,23411,3373,3934,388743,1027
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54476,4704,9095,1737,3033,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1027,54210,3670,941,55503,1394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407010,3684,9919,2638,1607,1244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,92609,339,3565,9759,27141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3290,9076,9997,4040,593,6387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4889,100,1769,2952,23530,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23054,7078,3728,219,2739,330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4899,8772,123263,3054,7076,1363
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6721,130120,1075,56729,406906,60684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2788,4758,10020,27089,490,8567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6948,4967,34,26291,517,2266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5621,7019,115286,57001,2876,253559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22901,4548,2243,100529063,9526,3624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 929,4790,10724,9380,5327,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84706,84902,56606,3065,54902,2984
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3759,8050,6938,471,6535,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8195,199,6748,718,2055,729230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10874,3416,3920,1629,29947,5350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3383,1277,2875,8660,345,5444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6602,629,54809,6789,5562,1203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2799,6261,7919,9698,151306,3087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,8802,407011,6464,51128,407021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,3875,4015,1589,54931,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4854,5194,356,3170,100130015,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27429,4282,345,189,4040,859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6834,3250,23410,5631,5315,9630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 207,407004,55340,4702,4864,3416
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,5631,149461,11222,84705,239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5214,4035,253943,5184,3598,1594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2052,3980,6678,10911,8722,1353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5306,54658,2335,8471,57678,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55858,3638,79572,79776,999,3992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 585,80222,6774,23400,8879,5618
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 340024,5078,4889,406947,23516,8942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2878,3157,4035,5190,6462,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2792,7391,6928,9672,2170,6476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56997,57128,1028,6351,2628,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28951,79776,2582,221935,407004,6569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 140803,54567,51081,5723,55024,51441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64689,4143,9560,54931,120227,23054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1022,2539,10559,4137,6383,60528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,3565,5836,5207,3875,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55278,203068,169792,517,10166,7942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 952,5406,54675,6391,3240,847
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27235,3159,10,6571,183,5740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3119,2310,55163,53905,5406,3576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2115,79661,1471,4035,5962,3141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29947,55034,5139,706,26191,790955
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,28951,5372,811,3074,197
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 35,7422,5295,8050,10842,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81570,79644,6536,2152,57678,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 345,7409,5122,7919,63899,27429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26517,83439,3123,54805,132,208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7879,60684,6339,5473,2785,2653
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,53346,4160,54576,2108,8802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6531,5214,2064,407007,5723,80331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 147007,7052,284184,51081,55270,5274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7077,7019,5265,5207,80224,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3627,549,1493,5621,2592,27247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,51204,5052,5214,4159,493
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56652,7376,10845,7385,130120,6338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,4358,6696,10965,200186,3645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5743,2180,4925,9420,407008,347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4915,948,1244,3990,23654,8504
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344905,27247,55572,10841,493753,5515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 383,29881,2908,653,56302,10560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1806,5167,5744,5599,5095,56052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22901,1801,2593,51081,5740,3938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2559,4524,590,3157,26060,4942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2729,8600,200810,498,84572,6927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79068,30061,153642,5468,9365,60684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1329,11254,790955,1906,729230,2878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4728,7100,4688,6522,355,56938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3988,6999,5588,5241,5228,868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57176,462,79796,79133,407040,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6929,4694,347411,3172,462,3645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197,2632,5799,4126,2591,130589
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6678,64087,406906,471,54658,6934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6492,540,6579,5239,5306,93587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 885,790,2243,132,25813,1649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3712,3710,5837,6392,3382,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7035,7424,6390,2155,2495,23516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2720,7942,9056,406922,5122,7252
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55034,10159,1022,7172,54675,4760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 189,2310,2752,1071,1348,7480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6389,7025,3717,6678,347411,28957
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51116,7056,285,201595,551,28958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56302,1201,5629,2805,201305,10991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,3295,3490,8879,875,51082
--> return NULL...
2025-12-02 22:59:42.788 R[22147:251950436] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
26.472 0.407 28.057
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.303 | 0.016 | 3.401 | |