Mustafa Erhan Ozer
| Snapshot Date: 2025-11-10 13:45 -0500 (Mon, 10 Nov 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-11 12:03 -0500 (Tue, 11 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" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 | | ||||||||
| 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: 2025-11-10 22:42:36 -0500 (Mon, 10 Nov 2025) |
| EndedAt: 2025-11-10 22:44:34 -0500 (Mon, 10 Nov 2025) |
| EllapsedTime: 117.5 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: 54567,9559,2539,80070,2847,2673
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57017,121268,8665,23400,2805,51094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2559,8050,7274,6199,2778,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10128,284958,51611,56848,26235,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5306,581,54809,283120,1019,51441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,125170,92667,27247,463,211
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3098,3685,1497,8659,3638,2487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56259,8942,3576,8642,55967,51085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,6927,23530,60684,84062,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7409,221935,134,56302,491,5781
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169792,567,2947,4247,23163,1806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,3710,2119,6999,6571,10616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2310,5329,255738,131118,1346,112817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2984,4976,4744,5515,54567,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,6890,26003,37,6536,84649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3032,147007,79087,7038,3077,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1345,1175,170302,2949,1277,4855
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9414,2952,5730,847,5162,3251
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3708,4654,2063,4700,1027,27125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79585,405,22820,4357,3082,1116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 656,653509,10642,1968,207,2194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,2587,55858,150,3117,1182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3098,249,29928,150379,8722,410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84342,22845,2591,2888,166785,105372280
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10537,24147,513,79133,3958,1889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79633,1956,9759,3948,23556,350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 208,9420,6009,84334,23163,5080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 706,2266,7099,2788,5052,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1371,284958,3562,7528,51181,2334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84572,8714,3351,57505,4915,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83548,2475,498,54539,5925,80224
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 138050,23038,148979,5592,63899,9445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200810,4318,10316,2785,6556,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51601,130120,1678,200539,7942,51119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2184,942,308,54931,10062,1571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,2653,3066,7515,6584,2683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2308,57817,5787,5473,5621,29929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25821,1581,7172,249,79783,10560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8600,81689,518,63931,2243,10062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4684,8604,3293,4700,79001,93587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7084,5162,8842,2157,2952,1734
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1149,84342,123099,10580,2984,23530
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,1675,8651,1281,952,56259
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60528,1468,275,6901,3598,6647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 340024,11222,2992,6009,10165,2683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10423,8642,5625,4233,4973,7480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,84447,1555,7098,9759,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221935,793,6833,6356,7084,5499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64087,1607,130120,29078,55863,859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,2542,1601,64601,191,558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 216,55024,57048,64788,9429,83548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10135,1589,121268,3728,387082,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4654,60386,5291,4299,2309,8879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728,84947,1201,488,111,23417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 859,64240,348,23462,2799,29928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7412,3930,200186,51478,55486,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7841,6929,493753,7388,2328,1558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22933,376497,28976,2184,5444,8879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,477,4716,2908,2146,4925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57678,10730,5092,10874,79001,6390
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,7422,1650,2847,2395,2776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84705,1234,440138,191,435,55768
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53335,253559,3033,51024,7297,5592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10135,3767,11035,107075310,1649,1203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2113,55644,26291,100131801,410,1906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1329,2778,7040,1182,57761,1340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56652,6329,55037,2903,57215,6582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1490,388372,10382,55526,1401,23062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,8932,7494,1444,83548,91949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9409,7097,2582,51094,5618,55037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,90624,291,6182,1490,411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83693,1401,3309,840,10316,1356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3945,1346,10580,3423,51103,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65985,540,3141,847,7220,491
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,131669,644096,3480,3293,53632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2785,1353,7350,4313,1208,283120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729238,5799,10221,6531,3066,64116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,54331,9056,91647,487,84274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5214,27125,6868,119559,8722,1203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90624,79736,200810,3122,3073,27010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10559,7048,6319,1581,2184,3980
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,3091,7389,8309,79572,208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169792,3115,54575,4915,23411,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2717,4049,55630,55902,435,54798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132,558,5621,1027,51004,10559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3375,27329,6182,4982,125170,5551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9607,11254,1149,4702,6932,5584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2203,6718,54982,434,594,2597
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,51052,8877,1436,51204,1591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 801,57192,2109,8567,2932,374291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3060,4709,1186,9526,9607,10062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7422,2243,170302,2896,57104,84947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84275,2572,5243,8243,8202,4855
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5950,2243,4790,2582,2936,116150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22820,5741,8665,2169,11096,2932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2108,2702,10102,4803,1890,1075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,7030,92667,5621,84706,151306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5214,152078,55037,84239,126328,1409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3663,116931,91949,2934,1186,942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5499,3570,160287,2597,2542,2786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3929,29926,6476,80270,7038,2793
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3460,5728,4338,471,405,10537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9409,5792,3980,8665,10686,29078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57192,2864,1244,347,6261,5250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56302,2247,48,18,7841,137994
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,11222,5538,27247,1608,51660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2646,7038,1893,1075,81034,330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,406982,358,3759,64689,22868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 581,6439,3954,10524,4683,64240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54577,7941,1442,8879,3284,1595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 105372280,241,2194,836,9382,24147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51608,388585,3073,8945,4288,3784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3030,3570,2303,4089,134,5713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3082,201595,5321,253943,9779,64919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64131,339,37,5052,8604,11232
--> return NULL...
2025-11-10 22:44:30.905 R[78460:682517700] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
23.925 0.374 24.762
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.301 | 0.015 | 3.372 | |