Mustafa Erhan Ozer
| Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 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 2025-10-04 12:04 -0400 (Sat, 04 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" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 2143/2341 | 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 12.7.1 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. |
| Package: SVMDO |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.9.0.tar.gz |
| StartedAt: 2025-10-04 04:55:04 -0400 (Sat, 04 Oct 2025) |
| EndedAt: 2025-10-04 05:01:09 -0400 (Sat, 04 Oct 2025) |
| EllapsedTime: 364.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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: 948,2309,1468,6715,54915,3293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,6775,57678,27344,84889,23543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,54806,338328,6403,10243,6183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10195,3159,1812,7355,50506,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10560,471,7381,6932,5255,29881
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55340,4899,10157,445,5191,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5563,129787,2864,161247,153642,1019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5498,55572,3062,5501,3489,590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 632,285,1435,1277,51608,85365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1373,10094,539,5799,9971,353500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200186,2559,445,169026,10,4976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2875,1509,8243,4899,1376,81704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55270,9091,5551,63892,6445,5095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,79068,1329,1889,133396,90480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1583,9021,94235,4159,5350,1717
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6576,336,6789,1806,9868,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51458,55283,1175,11254,5092,1802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5562,582,2689,23417,513,5445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22796,27125,6476,43,56848,3767
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4306,4684,6403,4312,4976,51116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9388,537,4879,2729,85446,54704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3954,2762,5617,9559,1072,7297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3934,83985,51555,10019,7252,10423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1909,1678,55186,133,51181,5306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91869,2243,63931,55858,4683,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,8431,5189,142,479,60386
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84649,8799,407040,5092,2805,6464
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3162,517,55186,1801,83985,9507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5837,10935,7345,462,1393,729230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,3952,718,9451,55065,405
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2695,5192,116085,28951,858,54902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,1270,335,1409,7025,115286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84274,6715,54968,265,26354,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55532,6897,10250,10128,6009,132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,2746,51611,3708,83985,51604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2786,55863,57761,5194,56848,79133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,216,2629,57505,1056,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 706,1890,821,6536,7275,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203859,3952,2908,10466,2034,79776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55670,221458,6648,79053,119559,5551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6901,427,3875,1589,54675,1175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7220,2695,57380,2194,5162,10128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6263,27125,4149,7389,5584,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6514,842,5293,10457,644096,5230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2590,5625,6602,6928,1371,6833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60386,29880,407008,3562,338821,10
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2936,54805,5291,3992,31,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7347,4988,4668,9131,113235,3351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2030,6564,793,51604,6354,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56923,6566,2932,150,84317,132001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,3425,5588,7220,7018,283120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6383,55005,3606,9095,4712,5270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3565,407021,10008,3290,84833,10724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1543,6934,116150,2539,10316,572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6716,3949,3551,7225,3481,348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 196385,644096,1499,2099,6248,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84274,5194,5972,942,9559,4306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1906,54600,11222,411,55630,100506742
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,6897,55937,6514,124454,5184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,389,492,3708,11254,55863
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5826,1737,1493,5654,25821,4144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,79133,54549,5919,107075310,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4012,4143,5445,5728,5406,126328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,3576,170302,116931,28951,5798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,1582,54901,1968,1645,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1149,1401,388962,55331,80207,5250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55863,4704,32,6248,51204,9526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79949,4780,10379,100131801,795,9526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9498,112817,56999,148979,2688,2303
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153642,2949,8945,7019,6236,63892
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57818,3242,4712,81034,10577,4851
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4851,8560,3949,6389,26503,84947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6439,7037,582,177,5409,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 650,7424,2166,54539,6522,3558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84274,8772,29926,152926,2875,212
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1371,10221,2303,1786,158,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79644,574447,150379,3920,51119,593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1232,2639,211,6582,4288,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124976,5162,5972,32,3141,5370
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7287,28976,64432,241,1347,134
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 857,51458,5563,7292,51167,53905
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3240,1910,1584,7319,6602,5467
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1072,51128,1608,793,29881,3636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 265,5250,5369,285,5592,345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10724,10753,846,3558,6602,152926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,84334,6351,1593,2936,665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3710,10724,23062,406991,1019,3708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4688,6774,200186,2847,7040,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 476,90865,7841,8639,6521,5264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4548,9451,8722,5654,79736,1992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7325,4143,3663,4040,123099,84317
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 112817,3565,7345,55937,1607,4282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54968,1956,23236,6891,3692,7840
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79731,5241,6774,407006,3283,585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644096,3569,4878,54675,6888,2334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1678,476,6938,7078,57192,2587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 594,6324,83693,3033,191,8803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27344,116931,3375,2159,10195,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1208,8854,3170,8694,768239,9429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22796,2696,3356,285362,2903,8473
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4285,1277,79053,2790,4684,25828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84572,5465,64805,22797,32,2787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406,8803,2878,5538,7407,1645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4713,5825,5213,2806,23236,80339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6901,11093,51608,56729,1393,7325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2767,5601,5188,5789,1807,64432
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 268,4137,434,10667,50506,212
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5286,2157,10128,10013,6748,1363
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493753,388753,491,54982,1543,5313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 590,3155,2695,26003,821,1734
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338,84062,1491,15,434,10842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,6891,65993,9997,2591,5230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1798,56999,9868,3558,6908,857
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7428,650,5444,539,2903,26503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353500,5601,5257,54806,1769,1802
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
116.014 2.149 118.298
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.729 | 0.059 | 3.840 | |