Mustafa Erhan Ozer
| Snapshot Date: 2025-11-23 13:40 -0500 (Sun, 23 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: 2bc7e27 |
| git_last_commit_date: 2025-10-29 11:23:08 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-24 11:40 -0500 (Mon, 24 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4605 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4568 |
| 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 2133/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.11.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | 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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2025-11-23 22:54:46 -0500 (Sun, 23 Nov 2025) |
| EndedAt: 2025-11-23 22:56:57 -0500 (Sun, 23 Nov 2025) |
| EllapsedTime: 131.8 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.11.0’
* 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/4.6-arm64/Resources/library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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: 4705,6382,694,5370,2118,199
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,55967,3418,7038,51176,15
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5499,57085,54576,9414,7124,7471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3416,5071,4233,1175,5053,1268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79731,5211,8942,2696,653509,2524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3158,2587,857,3813,50674,6339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79053,1268,149461,10874,29947,3159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6897,4547,8462,217,10524,5584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2710,256471,3709,56919,27010,959
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63931,212,2717,2119,5188,26235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4889,4282,6788,4855,9445,6505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22933,8600,948,2053,5713,7351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2932,10250,92609,166785,79602,10842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 345,4854,3250,4552,407010,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26227,5962,52,3115,5499,2110
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,2593,6775,51478,3934,374291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4023,359,4232,4684,3122,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,10730,6794,51441,840,9512
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23417,6925,51555,27141,5184,10423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4988,6888,1029,7292,11254,8243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4654,54575,54931,231,57511,5498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 539,51128,3099,2184,32,1644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 409,3358,85569,498,4159,2335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5579,201305,84275,64919,2693,1080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3479,22796,1186,5330,10195,9054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8932,64116,401,540,7320,824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 118,1345,8604,3066,6888,999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 959,7879,308,4286,43,79776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64241,189,5770,6609,2052,10686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,131669,10221,10874,25813,22933
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 768239,7035,1339,1583,1234,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26291,7347,34,5971,6770,388372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2166,7035,4718,487,7037,4282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1374,1056,51024,3091,23530,6392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124976,537,6834,3157,84701,2762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5230,4627,1582,6616,558,1738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9409,10020,3559,653,4886,64432
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 52,54968,9698,51604,2034,518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10019,5255,64601,5571,6579,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2310,4729,9420,8471,153642,51094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,7355,3119,875,51083,2180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23369,57761,2952,1890,388962,6934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 150379,2110,10195,55005,1373,10352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,2100,325,9056,7351,338328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1675,5584,2101,84061,5255,6888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2303,4247,1373,1906,5919,2203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2791,56922,2109,383,51079,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2688,7018,5644,5499,22933,2064
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5328,63931,3073,3162,2063,64601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51021,5588,2158,9388,116085,7124
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51611,347411,5467,23753,4828,5824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,5345,6464,847,6374,54704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57511,53632,10643,104,1348,7018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84300,7372,6716,51604,4852,6897
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,51458,779,5091,4790,5207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4543,4697,3930,5727,8243,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7351,7355,3651,84061,26762,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5122,51,5190,57678,486,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8714,406934,842,2805,91574,186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6263,4712,27344,1621,5498,345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23654,1339,27429,11035,26235,6339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2639,405,3119,6888,686,627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3304,356,5291,6647,1201,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7422,1019,6999,54552,3929,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84987,23389,5365,2305,7376,1738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,1345,347411,57678,6341,91574
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51204,7376,1718,186,24147,2731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5192,65993,84300,729230,84889,5105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 842,55486,23530,3172,55753,100128525
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 432369,4049,4299,55024,2998,338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8195,26119,6582,1369,406922,847
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3034,5805,10000,4925,1394,574447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53345,407010,283120,57511,9409,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 183,51548,1392,359,2820,5331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3663,3087,7019,8714,6716,6183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30061,26003,126328,847,2052,4318
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 867,55343,4337,51004,2875,156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6356,7347,4288,2641,2739,6647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55163,6550,929,60684,3709,9451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 593,80331,9507,6934,2572,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3485,3670,284958,54577,22820,6517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5919,3091,6925,7431,7100,1369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8659,7098,940,391051,25828,265
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6392,1208,3645,284958,5346,729238
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,2588,358,54658,2903,137994
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6890,2266,5243,2243,1346,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6263,5617,203,87178,84334,116228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100529063,2517,4669,779,824,5161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4627,406937,6890,9698,2717,5265
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23462,53346,122961,53632,10352,2161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2908,353500,5972,56302,3351,26762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51649,1789,5214,23304,6342,407011
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,5162,161247,348,435,563
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2099,3339,56052,656,353,9630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 140803,26191,5291,4846,3875,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5236,229,867,5826,27010,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6696,283120,137994,55005,1028,844
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5193,2180,91949,718,6774,55858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6927,56302,27235,25839,593,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2592,10577,2919,4502,1801,9021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,11222,5468,4160,1444,339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,111,1649,361,3795,338821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23753,7292,3159,629,1608,10379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5972,55967,84902,162417,1080,7352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3251,1329,3899,9054,91647,203859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8945,2646,9388,10243,4705,2990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,537,84833,51293,7466,38
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54931,2517,3552,2200,4988,27429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1646,3081,55340,130120,3945,599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1585,63874,5211,10159,112817,2155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7390,941,54344,886,6515,10269
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5291,23753,6678,1200,57192,9414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2786,6770,64432,440503,1621,2310
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8722,9572,5551,558,2645,22797
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,149775,6565,6439,1812,1444
--> return NULL...
2025-11-23 22:56:53.259 R[72248:137620512] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
25.904 0.411 27.836
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.281 | 0.014 | 0.494 | |