Mustafa Erhan Ozer
| Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: 7851a60 |
| git_last_commit_date: 2025-04-15 13:15:07 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:08 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 2155/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.9.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SVMDO |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SVMDO_1.9.0.tar.gz |
| StartedAt: 2025-10-17 14:18:00 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 14:25:53 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 472.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SVMDO_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.9.0’
* 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 loading without being on the library search path ... 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.9.0’ ** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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: 3569,1361,6929,55343,5830,2784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 440503,4714,152926,498,23038,6569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3312,6382,56052,1497,387082,10221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3417,4543,10269,57192,3551,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5291,407021,5161,2559,9927,1352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57085,43,26521,293,27141,7841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 942,3767,1468,570,8462,4697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4627,6340,5713,3054,23163,51458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1950,51021,79949,795,4318,7274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79585,22820,55937,1394,654,5571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64131,26235,79087,6403,4311,3358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84061,23543,2166,6834,201305,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5191,79158,6183,293,105372280,4700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10102,105372280,7018,56259,4712,6999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 178,55858,51004,2890,6901,51116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406906,11222,6522,84340,7385,51099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9451,2944,51128,151,3990,23411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6901,1645,664,537,3309,7030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6536,708,91452,3382,125170,7035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5313,132001,2805,3240,7351,5826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5255,2739,54931,6198,54806,8743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3938,3373,6199,5228,51555,53335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27125,5770,3988,152926,4035,1353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8431,150,857,1812,2677,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 537,9180,64805,7040,2697,7052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 492,6515,51128,9241,25974,6492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5409,4864,825,4547,5971,5291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1769,1489,476,208,80339,55278
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 111240474,2170,6183,3791,462,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10000,65985,10383,51103,388585,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11136,1543,84649,104909134,2584,51079
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 488,6261,84947,3710,255308,4285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,5239,22901,1497,8050,858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132158,9945,142,6514,6519,6932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133,2683,114814,2157,2806,122961
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11254,1345,3158,2166,4758,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57511,94235,655,55486,8639,5836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,142,4697,3606,7528,23054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 350,4695,9365,56652,5476,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2303,4968,2539,5328,10008,4714
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 549,7275,5191,5836,8802,29960
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2731,10128,26003,3767,1716,640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 859,4760,2542,7841,6521,8803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3356,3952,2791,3875,514,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6263,642489,10991,3945,643181,407024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2632,79087,6340,118,57817,24147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148738,121268,60528,5189,186,4889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57818,2673,51004,1644,2878,23236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8799,1807,2348,23400,54931,38
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,3934,3295,5599,5257,5971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,7424,55005,6554,121268,54809
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 256471,116228,22868,116519,2158,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25828,5592,339,64801,411,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729238,84649,11136,3073,5581,10269
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6182,5625,51,64432,2180,6566
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1559,8862,1812,779,539,6901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8473,4144,6569,4843,155,1555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23600,10857,7498,255738,9131,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10243,488,151306,5805,29078,56922
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,3559,6811,1584,2936,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5409,120227,79934,664,221935,201595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1442,2693,3553,30061,51099,85446
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203859,22901,6891,5741,6342,3157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493,3559,219,5837,6584,6009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,2055,5515,11132,7355,5162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4357,3293,56623,3060,28958,4855
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64116,779,5188,2152,91574,1444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51082,929,3417,632,7381,54982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1029,285362,10295,51079,23411,60528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6579,57017,5836,11095,7345,25915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64788,9479,4319,54805,5331,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3123,1489,3174,8659,8309,1807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50507,1859,51604,100130015,5406,9526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 491,10580,821,9445,2055,84061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,655,7100,846,4700,23291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4594,22852,388962,5306,5740,5584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,5860,189,4137,406937,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3586,80339,5538,56652,31,1950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3708,3507,7289,4282,27125,29960
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56259,2524,4886,137994,7132,4314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123263,3155,51604,9575,2235,11232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64241,90865,2152,653,7528,471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6519,1436,221458,5091,25813,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26227,2180,1537,4758,3507,8202
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10159,1889,9056,63931,6929,338821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653,57128,5798,1230,6649,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,10000,53345,4683,6890,231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,29078,29880,22901,9451,51116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80270,885,10841,6616,4143,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,2847,7057,1584,266,509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,4728,5826,4299,2689,5346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 868,9374,5270,53632,84342,4828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,3172,10599,4702,3980,1544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5515,31,4720,642489,3382,54567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 119559,11254,8818,1956,2588,284184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2932,10891,7421,5350,51649,3485
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2592,9969,55526,3645,18,50814
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5409,2806,8431,90624,886,6505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54802,79587,51099,27235,2495,3988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2799,3710,6383,24147,407011,9698
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92935,1329,490,5744,79144,3507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4713,55630,2760,1593,29960,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55340,5825,2745,596,56922,1992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,1557,339,5331,2804,6356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3939,131669,5009,1203,401,6584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2739,5467,116085,486,1491,358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,6616,6342,2030,2788,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 181,3958,6531,8309,7919,3949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29881,2395,91949,9241,2695,23417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3667,5621,1393,840,6898,3651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,1789,5919,3087,30061,153642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63899,3099,3990,55572,9382,9526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,4720,6948,5321,6821,7385
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10000,1363,54802,2760,51116,54901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2690,6811,796,948,389692,178
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
135.818 1.458 150.027
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.760 | 0.019 | 1.758 | |