Mustafa Erhan Ozer
| Snapshot Date: 2025-11-06 13:45 -0500 (Thu, 06 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 2025-11-07 12:00 -0500 (Fri, 07 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: /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: 2025-11-07 04:43:10 -0500 (Fri, 07 Nov 2025) |
| EndedAt: 2025-11-07 04:48:18 -0500 (Fri, 07 Nov 2025) |
| EllapsedTime: 308.4 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 4.5.1 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 ‘1.10.0’
* 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 4.5.1 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: 7352,407045,5243,169792,138050,129787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1589,11131,1769,205327,5601,9104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200186,1585,28958,149775,3945,348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1641,100128525,18,2169,9104,487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5781,56923,1806,406922,8651,51119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,5590,53905,1508,2200,51021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6341,5175,4285,79587,5053,50943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51119,104909134,6714,55024,330,4724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,6356,3145,1027,5162,85476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,84889,7295,51167,1376,22901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8818,9091,2804,2805,3062,325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6340,10250,6513,4351,11213,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200186,23175,156,1203,5592,2643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 147007,6521,51649,9414,7407,221935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,6340,1906,1436,18,5167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5194,3033,2762,5590,389,4744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4988,231,5618,50814,538,1351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6448,4669,22852,116150,5925,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,685,27232,3485,1371,26354
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5805,3700,7099,2712,6566,7287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3155,51441,84275,129787,29078,3954
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5193,7407,6891,4854,6649,1594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6774,84447,89874,8473,8678,63899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,886,2115,549,64801,18
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7412,629,8517,186,10008,7355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7941,6584,9091,5792,79644,57048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4311,6199,361,83693,177,55278
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,10842,8648,2937,7018,1582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,284958,10013,8309,7528,5506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2034,1786,3710,388962,57128,4338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 643181,7915,1116,23395,5052,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3636,3486,875,1392,9572,116228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4760,3948,4311,51144,51604,1786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80267,1373,37,3101,84340,3033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2688,160287,1812,344905,3779,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3157,2702,2984,9969,80331,23291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 129787,3091,3356,3382,1442,3074
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1468,868,1208,2712,5618,55343
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10935,211,383,5370,3033,4988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2647,640,1571,29960,85479,56997
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203068,7040,6789,2314,292,51081
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4967,3458,51660,632,1436,1588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,9095,53905,9945,5291,364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 155,9507,51206,2628,5239,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2776,885,361,50506,1594,4594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 940,10999,875,54896,2487,640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23291,4842,5256,940,55858,3554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53905,9180,55858,213,5644,2642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1234,9429,9672,3357,2729,3087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10019,1757,5054,1607,10128,1718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2099,83439,23474,6522,7030,81033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2152,26235,5321,6647,23590,5295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81570,50814,1080,53335,338,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51458,3759,8942,374291,3931,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9241,91574,1789,9420,10382,125988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5274,406913,388,177,3123,2348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9560,11136,1815,2119,8813,3767
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53335,491,3113,5805,1208,2539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,7172,540,81704,160428,2778
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4299,51103,6649,5621,6811,3667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6319,7407,6521,6648,2952,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2101,84300,53345,5826,79587,7167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6352,3929,199,2119,8639,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3949,2542,6786,477,91949,79587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4853,1812,293,10644,8309,1606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1270,10682,558,11136,162417,3172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23369,64432,6182,6901,3667,8802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29929,51660,64801,1363,825,81689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,1352,347411,3073,2161,5723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3357,55753,3978,7916,5745,3995
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54567,1401,359,150379,111240474,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9414,80070,1208,407024,7036,5468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5781,2597,11095,4851,10020,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3945,54901,405,10269,185,3291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10,51604,4729,2113,92483,959
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5265,1514,57192,1312,51024,7097
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9498,3117,84300,56999,55037,3308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1019,4973,801,3033,51660,10116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1340,406991,8842,875,170302,25839
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,7040,2702,9420,148738,3418
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26235,26762,51660,3423,27089,54982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5277,3351,3684,5660,57761,54806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2919,5188,407045,3600,1889,9380
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7037,54549,5068,338821,1544,6556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5631,10116,181,64801,7274,3082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91647,3990,4247,10221,3145,57107
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57215,84274,85569,6647,1641,2244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4760,10991,2571,655,652,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,6182,6584,2746,868,842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5365,1346,2792,169792,821,10159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2395,51611,26191,9969,2034,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 18,23369,79661,2280,4543,4843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2064,6550,5194,118,5515,6748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1869,5288,6647,7422,405,53345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91949,64116,51555,161247,3073,1149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26235,85365,776,149775,56606,54476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6897,253943,4247,1345,2155,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 348,706,54982,51052,10,6535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,56052,5091,6492,200205,5654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,11254,1591,132158,2992,79087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 199,8802,4669,516,50943,2820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6236,84833,4125,134,7018,6999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83884,10295,5799,4723,50506,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 435,5080,5367,388372,3155,93587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2948,7421,1182,6492,200810,34
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2395,147007,166785,1718,9630,2571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3162,339,1634,6513,1282,1409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130120,1728,4035,11132,6356,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64241,558,3630,7919,1559,5277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1371,2946,7352,2702,2690,6718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5584,374291,3081,1594,4942,85479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,4128,1595,8743,57511,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10157,1234,6248,376497,55163,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54106,4716,51021,3663,3795,6929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1524,1339,2762,5126,7275,5207
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
65.579 1.749 67.462
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.701 | 0.024 | 0.879 | |