Mustafa Erhan Ozer
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 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 2025-11-27 12:02 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | NA | |||||||||
| 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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2025-11-26 05:10:42 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 05:15:48 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 305.4 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.10.0’
* 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 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 ‘1.10.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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: 6891,6263,25821,4669,2696,10059
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5255,388,123283,406947,2184,1352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3562,2308,477,3663,4314,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1471,2159,51,79796,6833,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57818,2055,868,5175,60528,2539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7076,6522,43,440138,18,1232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5160,56623,55343,137994,63899,9575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9779,124976,5498,4000,9672,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,1376,23654,1270,10423,842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2170,54806,55186,2266,2590,5644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4925,9572,2495,1906,2639,6522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5468,7078,7384,4915,3351,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,4688,2110,5288,79001,4502
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1509,197322,2158,2055,51458,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4126,3283,3773,105372280,9076,5241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,391051,150379,6492,6439,1629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10157,3482,6794,9241,5195,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5068,2673,23304,2645,23163,6517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10269,4159,85365,28234,29926,493
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100303755,51079,54575,7376,1080,4705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,7077,64087,160287,3490,84705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7407,1490,57817,241,60528,84902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,100130015,1345,5745,3159,8942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1361,942,64805,4306,3709,5660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7056,2948,4976,790955,1769,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80331,463,10999,2115,2588,10383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3636,51167,2804,7319,3791,3728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10845,11132,2949,2524,22852,6198
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,10,1582,5189,3242,51555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,6774,23543,285126,65985,6522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7450,292,6392,81034,3709,825
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,90480,7026,840,594,6772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6464,7019,55902,3383,5744,151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4069,4716,7172,563,10295,387787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203,3172,2200,29968,9380,11231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6319,156,3576,2582,7098,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2169,5068,10524,285848,387082,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55750,3717,29926,145264,11035,407007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55788,23409,6445,210,9572,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,91869,401,6402,255738,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2475,9927,91647,471,6716,6821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3507,8600,2752,7466,26291,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 355,4313,3172,1537,3156,2638
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57511,3684,55005,1268,2678,4035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1589,126328,51082,51176,22845,3077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,3708,5515,4925,292,9779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54802,388962,3703,643181,55065,55343
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 599,3638,2539,3113,539,572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,26175,2890,57511,7274,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,5167,1815,5744,84987,142
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3992,665,376497,6999,8879,7275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90865,6390,10059,2713,5789,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 463,4069,1593,54549,2694,55902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91452,2952,6564,60528,3091,54576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3990,407004,2713,10008,54210,6556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6556,1346,23389,175,26088,7421
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 875,29926,7287,445,80201,4351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3290,959,4724,22901,5191,3170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5826,6901,60,10062,5702,7494
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5447,7412,1200,28976,6648,284184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4338,1843,4247,3949,1789,7320
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,57511,10062,23530,596,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9672,9945,7422,27247,1956,1056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 488,3351,5581,2677,5288,1185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,23274,5243,5562,142,4760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55037,8642,5792,2678,64601,9414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100303755,51241,6648,56923,7132,653
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29960,811,10094,7879,514,160287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9512,9692,3717,406906,1200,51083
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2538,123263,1843,8862,7018,132158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6513,3978,4688,55163,8473,2683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10226,4973,3295,4143,4153,1555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2984,407008,8431,79144,2752,846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1356,185,9131,407024,219,81034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10382,2746,6402,9498,191,3991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255231,3598,137994,2588,22845,4760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6718,213,26227,131118,338821,7048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,10559,203859,212,5621,10382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2904,8841,361,6548,793,200810
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51422,4889,4728,5660,518,23654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,2166,1786,116931,6519,7274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83854,7078,54552,57107,10730,5625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,3710,5409,6199,3795,7036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,7381,23411,63874,9692,3440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3480,55788,3423,133522,1813,7386
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1337,3565,476,5188,9512,183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5447,7409,9420,2587,3157,391051
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53632,2581,50484,7054,1327,3156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53346,11232,361,570,6929,54575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132158,183,9076,10911,2740,6566
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,1028,9332,1185,4697,3082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2713,7391,593,2695,1769,6550
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22845,4552,4718,617,255738,10013
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3293,2517,8431,9971,26175,55503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23590,32,54915,387082,5621,3339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2908,1468,1605,2166,107075310,406937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347411,4069,57192,2696,54915,6389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3351,147007,5592,43,6576,487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,2180,2793,5167,253943,7388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 788,1588,1490,345,2334,55644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65993,55967,1672,2517,3123,5629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1509,7320,5563,7407,1339,291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5276,1588,5126,2243,6517,10295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83854,9365,7019,55937,3627,122961
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 31,821,1514,221935,22933,57017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91942,4854,9572,6999,5176,5787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84693,2888,7347,5293,285848,123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100128525,90480,3034,1582,1798,1893
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28976,51119,2820,3658,6347,1056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2099,3156,10911,51181,56938,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8879,5230,2305,3033,84274,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 570,2638,142,2395,6938,3304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347,3486,4299,3159,406,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6929,347,537,152078,2990,27344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9630,4700,8722,27125,6678,255738
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
65.255 1.080 66.468
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.688 | 0.027 | 1.997 | |