Mustafa Erhan Ozer
| Snapshot Date: 2025-12-12 13:40 -0500 (Fri, 12 Dec 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 2025-12-13 11:47 -0500 (Sat, 13 Dec 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" | 4874 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4582 |
| 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 2138/2332 | 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 | | ||||||||
| 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: 2025-12-12 23:03:27 -0500 (Fri, 12 Dec 2025) |
| EndedAt: 2025-12-12 23:06:02 -0500 (Fri, 12 Dec 2025) |
| EllapsedTime: 155.1 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: 4683,2538,26191,5654,3291,27235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 229,2820,2934,8813,81689,6523
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,1591,148738,353,5053,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5595,64241,83439,5476,2896,5346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,1392,1327,1281,5498,9104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2760,2739,256394,105372280,5265,3490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22901,8862,1786,6748,22868,152078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54806,5592,115286,3485,1356,2332
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407009,1409,1471,5078,6928,2328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55278,2203,3565,493753,54578,2335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8408,11093,123263,2878,1355,5167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 376497,5476,8772,293,79602,4886
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 43,255738,2878,57176,3172,10135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,6934,338821,325,2778,5789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5727,2940,4540,1718,1950,2645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3101,116519,7498,19,148979,5972
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83548,1490,2110,6716,79133,1557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3158,6351,51300,10229,54552,58528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2934,55503,435,57085,221935,2998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11222,5350,387082,5194,384,8202
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28951,2834,5328,4852,5631,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,60,7099,80207,27125,5053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3638,9365,23410,51316,4886,5836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6678,7248,5211,22868,54802,2571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 488,4779,1537,155,5162,6387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,132,3606,10682,6476,64240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3117,2597,6934,4149,10753,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6356,116519,3565,50674,156,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,3667,123263,22978,123099,5580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5834,1489,84447,84987,154,10195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 445,2992,115286,1586,6715,1234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113235,4864,801,55340,11213,7076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7248,255027,8675,4512,5828,7096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2063,1581,60,10537,177,2108
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,1355,212,3082,2645,84447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2998,2109,445,653509,5563,4543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,3141,10857,10094,25974,2639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,477,10533,23516,10269,10423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2643,388,2146,23753,4889,1493
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3174,132001,2053,1803,5288,57570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,84340,407010,91949,5213,57192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5654,2271,100128525,197131,7840,5268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 718,10644,4922,208,708,1022
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29928,10135,1950,9575,55768,347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 367,2289,1583,125988,3358,572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8932,5139,275,325,2835,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7292,30061,6354,8813,3458,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,761,10524,1594,256394,6352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51660,54805,875,1559,9365,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,1555,79602,2052,7082,4149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91452,3309,291,10379,11213,768239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27089,138050,5580,11136,6329,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197131,3295,1353,26088,63899,2108
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2100,2791,23600,5207,65993,6934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54802,7421,197,55970,335,3062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,517,1268,3813,22933,90624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3339,664,5830,81034,7407,7297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5345,1363,3082,63892,11019,3115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 492,5364,5250,183,197,7172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5331,65993,6576,1203,114548,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9365,53346,367,7431,7040,5071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1072,760,959,432369,656,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 563,4688,1557,7124,10938,11035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124976,80222,81793,5275,64805,10333
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2332,2690,563,56923,4089,1734
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57761,3553,1588,83447,3552,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81704,376497,1514,1586,1559,3383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22797,157848,51458,6554,7038,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 948,100131801,64131,407008,6678,6584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3791,5162,440503,50507,348,4508
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83548,5330,7019,7025,116931,3073
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5805,5745,51092,2948,6492,8802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 795,27344,3930,411,4286,6576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653509,5228,4598,1203,6775,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9971,84300,3728,23236,1244,2055
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10102,8648,84705,3074,5919,4656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3658,586,5329,56919,6715,112817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,5315,23543,10644,1728,5054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27010,3082,2729,265,83733,1558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30061,407024,9498,6579,291,1801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3667,84061,1586,2702,3558,9779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9560,239,2063,1356,572,10857
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 823,10577,55644,25915,4715,100506658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,7942,2950,7376,9167,1514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5331,7424,644096,1340,51144,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54344,388743,81034,3709,55967,2629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10874,5328,5176,1606,51092,2888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51458,60386,627,6319,241,7054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7515,83985,1859,2647,11019,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4695,486,57001,54106,867,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7528,51021,57380,10724,55270,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 440138,132,2305,3098,2693,50674
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 788,694,79796,23304,2653,1738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6531,8202,574447,5288,7350,572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,2052,63931,7347,5442,5498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,2119,3759,115286,355,1728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,471,5745,5080,4656,51144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51083,1559,169792,1586,6999,27249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6445,585,10116,316,9513,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63931,7225,7295,4337,9759,8473
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5901,54576,6616,706,2683,11131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5264,10159,1340,22868,3141,4232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7252,6821,5442,54344,2694,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4519,2903,728294,1340,1636,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,6906,407011,51206,200205,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81034,9997,2762,1028,100128525,5428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2778,56259,1080,4508,1581,3899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7084,7391,2309,706,5770,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,3565,4015,5195,7319,376497
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4724,54210,6352,8877,53335,4780
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5595,285362,6492,4825,5256,514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63892,1634,3953,51300,627,5239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,10157,1075,11131,51555,4728
--> return NULL...
2025-12-12 23:05:58.105 R[49880:386353944] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
41.228 0.513 43.263
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.351 | 0.014 | 3.360 | |