Mustafa Erhan Ozer
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: RELEASE_3_22 |
| git_last_commit: 86871da |
| git_last_commit_date: 2025-10-29 11:23:08 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-01 12:05 -0400 (Sat, 01 Nov 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" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 2163/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.10.0 (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 | | ||||||||
|
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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2025-10-31 22:28:34 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 22:31:25 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 171.1 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.10.0’
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.10.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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: 2934,8659,9380,26235,6476,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,104909134,2200,405,6789,11254
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 708,27235,2517,79572,55970,948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9672,2266,7352,26119,118,407011
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6339,5618,5825,10616,4899,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91942,10730,10226,26521,6714,57818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1514,2944,5230,4716,23291,407010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3490,574447,55670,5551,207,7284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,5293,779,54805,406947,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5468,857,344905,8842,411,55186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,10938,4694,1581,4012,2947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255231,5798,56997,2903,8560,4744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1950,55572,10466,79644,83884,4722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 539,1738,1636,1806,3645,3569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388753,488,406982,10524,6261,137994
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5367,538,6788,115286,1200,255308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1329,6999,3291,6522,54902,79731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,2805,9445,10580,1203,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1116,1029,10019,3558,9420,563
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3958,347,100130015,6890,2590,6342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,29928,3978,23530,84557,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10724,6576,10423,4306,558,1588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7019,1588,7099,54806,6714,3122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5563,4594,3795,1022,1649,54806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133396,92609,6464,10599,55670,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,387,7248,5293,1571,5288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5580,2260,407045,2271,2335,2200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,6387,7167,55863,652,4988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8714,5506,27429,5621,1312,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,5728,1621,6925,3284,3483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5274,10379,1312,6566,2950,4153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3624,5660,655,632,90624,4547
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388585,3552,5727,91949,4288,255738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7078,7407,23236,867,1363,463
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790,116085,1557,1558,5184,2587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 549,6678,2752,4942,6721,1514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,2788,25821,7412,4126,54931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2266,57678,3490,60386,471,7471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 551,10094,64116,2720,5274,79158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9374,28958,1909,11095,10352,5728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1232,285848,5617,3440,6515,91942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53346,5919,10,364,10062,57192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,1329,55065,31,5370,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5901,4313,795,7450,29078,3712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5590,4149,656,2548,6678,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6908,5277,3155,694,4502,79144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2712,10165,2052,55186,6198,5798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 265,9968,9370,5019,376497,5442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3293,1186,5588,63892,5321,7297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,1717,2778,1802,1282,54805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1230,51611,2052,6786,4889,56997
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,63874,2056,2683,7381,4313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2653,2235,265,201305,2952,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,1859,5727,54806,11093,1593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 825,178,2937,1071,80207,617
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 351,844,2786,92667,2990,5327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6609,640,53632,6772,9526,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1893,8243,107075310,10295,7025,5499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,5328,6548,51119,10250,7350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2235,10020,6521,5617,479,6565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29078,491,64240,8642,3490,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4846,5080,5744,10008,7100,9575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1769,84947,5950,26521,51099,9382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 166785,10243,10457,3440,5592,5594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60386,8431,55937,6319,3242,170302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3304,3481,2639,407004,9572,8639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7352,3875,53905,3576,6387,8471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51441,4153,81704,85569,10135,3958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130120,7422,6248,55065,4843,25839
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9968,3486,1071,391051,4247,540
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 359,6439,6354,84701,3638,9382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3929,1593,207,3988,7345,2792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6261,5372,5442,57192,22933,8659
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 549,9779,2695,5837,140803,5551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80270,64087,9091,54805,3030,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91452,123,407008,5313,1373,4232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116150,3953,3791,3684,795,10295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4609,1182,6811,8660,84572,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2055,115286,160287,92667,4915,492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4860,5445,2590,1277,10577,1524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,7076,1558,197,1497,256471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7295,1815,8772,200810,83439,10845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3158,4319,6403,790955,6929,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5327,655,1813,23400,359,2548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 640,2876,7841,3417,2170,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2056,1028,2784,387787,650,1843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 427,5327,5264,6888,2678,2030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4256,1798,11131,5190,406991,2099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 208,1649,407009,6514,4688,2247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5122,11254,149461,5373,4137,7036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3952,7056,189,5473,28951,3759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6505,57761,7515,84447,2475,3170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,3087,19,2592,2936,4023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4089,5162,491,8678,64689,1650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3141,26521,3490,539,3030,55486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2710,2571,4233,1401,886,506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,847,796,7078,4982,471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10221,51083,3170,9512,6531,811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51094,5743,3728,3174,6927,79087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4069,2166,4758,477,116931,79776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3329,11232,656,3162,5213,2006
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29968,22797,3995,4709,63899,2158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149461,3250,4282,175,133,7100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2713,6198,1401,3115,6445,3351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,1490,2793,518,1537,38
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,1149,5744,1798,407010,51206
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9180,5727,5122,207,2944,2200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4851,9630,7319,2950,4853,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1769,3638,5594,1348,463,1361
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3779,55970,26521,1621,6338,410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6329,406934,462,5625,2919,283459
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,5925,54896,2689,5770,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55037,3240,5257,3117,120227,729230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56052,10560,7026,25813,2280,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406947,54575,3480,2791,3482,643181
--> return NULL...
2025-10-31 22:31:21.475 R[4340:603174392] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
59.140 0.773 60.651
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.309 | 0.029 | 3.324 | |