Mustafa Erhan Ozer
| Snapshot Date: 2025-11-12 13:40 -0500 (Wed, 12 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 2131/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.11.0 (landing page) Mustafa Erhan Ozer
| 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: 2025-11-12 20:33:10 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 20:35:23 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 132.8 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: 10724,51,844,9607,7528,3643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 38,8818,54809,94235,52,208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56945,5467,4878,3596,2475,189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53905,11096,56999,9095,217,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6774,6554,2314,100131801,3073,5364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81034,498,5501,2161,5730,5213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,940,28958,3293,5950,4669
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4695,80224,85365,9575,9180,80270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1789,8694,2673,3291,1672,3077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3708,517,54968,255738,161247,1185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3953,11035,7351,587,57048,4973
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131669,6715,5617,3645,51293,132158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2109,383,55768,201595,4851,2677
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7350,5970,9945,3309,123099,5346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57380,84902,26762,154,54915,3250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9969,8803,4654,6565,3425,23556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8665,6898,948,200205,7320,55270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64689,3155,4709,5723,1583,29929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 842,2673,79087,57017,406991,166785
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 518,23417,2109,7157,6579,2115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 643181,7098,1471,1634,50943,221458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53346,5799,3099,5584,407004,790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,1268,28234,6579,5080,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2310,4299,9779,29078,5274,514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 111240474,2591,5207,3312,23516,189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29947,9445,56302,7276,345,3242
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,23054,2034,2793,10599,27329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5837,4040,795,5255,2118,1646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,351,8560,84239,7386,6515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,5315,9692,160287,4851,28958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84987,5826,55005,285848,79949,57620
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3938,406913,3032,6584,3382,10062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,158,1281,1601,29843,2746
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1607,3081,5971,6464,388962,351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,79783,2571,1175,3251,29881
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51117,51099,4852,5538,2647,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5579,10382,3074,79144,685,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8504,5009,6391,6999,4852,7320
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10000,2932,3562,5321,55670,6811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6248,3087,55503,5213,1608,5191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,3643,5054,6897,11131,8678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3645,1244,2695,125170,150379,886
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5860,407011,316,4942,388,387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10316,51079,6531,1815,308,5211
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4695,3875,1717,79087,8945,6522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2524,492,5167,5631,54901,231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 410,2308,3658,7157,8818,5770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7019,6772,7412,50507,197322,4886
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7351,10842,29926,10682,56997,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79572,7048,10379,151306,7841,4153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55750,54539,6794,3712,10102,10166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,6834,1675,3115,1232,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6183,340024,3155,22852,364,5409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124454,383,154,10195,2949,5184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7319,38,149461,5213,2542,5364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5950,5373,284958,52,9451,3065
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7428,8813,3099,2984,81570,23543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5364,4544,3565,23369,1508,3948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,9607,5798,35,6354,2052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56997,57380,4319,5444,79001,23409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 292,599,4705,8660,10682,2542
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100,2115,3569,1373,2820,5592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,5631,491,3062,364,5962
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,200186,3030,5631,8309,2643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407011,4143,790955,6821,84701,2776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,81033,10730,3899,1327,2593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 582,7099,1843,9382,2864,10842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,7409,35,1356,5445,6548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,2785,10165,9479,116228,2487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132001,253559,6199,3066,2305,6535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132001,54549,406922,11096,4744,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3062,130120,6505,26175,25915,5601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8659,1621,55788,203068,79585,26227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,6236,3304,5160,6464,694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56922,9104,200186,5743,104,51649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 551,5444,123263,83548,26235,10062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 585,55270,406934,5364,2169,2904
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10857,4502,2119,1471,2034,7421
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 185,52,7428,8678,5372,284184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10062,79133,1329,55278,84334,2308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1608,5584,330,7038,2896,581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84447,3351,7248,2643,6929,6571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84274,6392,56652,116931,63899,79776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5364,4684,201305,154,6948,10643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2936,51601,1544,5329,10195,7292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2591,4879,7421,2632,55670,291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6448,4702,1584,55340,285848,338821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1075,653,9945,115286,256471,790955
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23409,491,665,79087,8879,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8050,3251,55967,28951,440503,6356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5139,4728,344,285,5291,5562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728294,84693,137994,85569,160428,2903
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2108,4232,5798,367,56052,90480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7289,2113,3481,7916,26354,795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,359,3992,8648,54549,706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55340,9388,388743,407006,9779,1200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2896,2784,1555,5365,572,5250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,2584,249,1786,356,5139
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2099,5515,241,10019,5122,8854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5053,91869,5644,4982,5105,2303
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51119,10724,8639,23516,51316,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11231,486,4125,10352,9380,1869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25821,1277,2159,26227,9332,125170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9370,9380,54901,2805,6248,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4803,9759,8517,129787,53905,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,84239,56922,2055,6602,81689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8942,53632,1537,25974,3709,91949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 958,63931,6342,55750,10560,203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4889,81689,7167,10559,1444,1786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,5588,1585,5184,1072,3557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7100,4790,3309,7351,3308,81570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132001,5836,1806,6383,8639,5078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2847,3170,2784,1493,9575,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 952,64432,3638,2799,51649,1672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 391051,38,9479,3098,5192,1208
--> return NULL...
2025-11-12 20:35:18.886 R[46172:8919301] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
26.221 0.406 27.387
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.298 | 0.014 | 2.132 | |