Mustafa Erhan Ozer
| Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 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 2025-11-28 11:39 -0500 (Fri, 28 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" | 4866 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| 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 2134/2328 | 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: 2025-11-28 05:09:52 -0500 (Fri, 28 Nov 2025) |
| EndedAt: 2025-11-28 05:16:25 -0500 (Fri, 28 Nov 2025) |
| EllapsedTime: 393.0 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) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
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-x86_64/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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: 4015,54539,6383,51206,11232,30061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,54968,376497,120227,686,6390
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 35,5162,2673,4594,123263,199
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160287,1738,3684,123,2119,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3425,2271,28957,593,344905,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9607,29929,5370,63892,8309,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3934,285362,388585,410,2157,10686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26521,490,4915,999,3290,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8879,29928,284958,3460,83693,940
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 126328,4012,55788,3995,4544,57818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 821,643181,570,4803,3931,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353500,344,356,85446,1312,23600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54902,11232,3992,7372,9927,2581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1543,10352,64240,4716,3062,4233
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22868,2804,51052,9498,6868,5184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,5264,5551,2524,3586,5571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100,55699,2646,2731,388753,3930
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,1376,952,7052,54658,518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,2108,5092,84889,358,84334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149461,92667,6319,9507,4982,5551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26235,1499,7098,22978,151,26517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5970,4683,5792,54331,132,19
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56606,23530,9630,3930,5971,197322
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3920,3600,6354,64131,1555,5331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,351,8600,5122,3945,574447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11132,1028,80339,353,132158,2946
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55526,5601,80201,7450,137994,5256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 427,100529063,51204,5713,2791,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55902,844,80347,4035,1675,84705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,4855,5195,617,4668,25839
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3670,130120,341,6789,10643,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1374,55024,6556,51081,178,212
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26119,462,9095,7372,80222,6891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4864,23129,3703,2628,51119,801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,91869,1802,292,3934,6716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10195,4118,2487,5515,8722,79053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9095,4854,2798,3490,4828,462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30061,26003,56945,8462,83985,55163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9451,5369,2180,104909134,790,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,3480,43,23274,80201,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151306,1019,2542,6387,54577,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1312,7528,2785,9698,1621,401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50943,124976,54567,2642,2587,940
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3339,29928,6906,1348,57511,4358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11255,5293,5967,79949,293,5962
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5194,344905,4314,5581,10013,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169792,2804,857,120227,9332,55818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,1843,627,582,3651,10599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7391,119559,1543,3759,7350,10559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51241,642489,3170,53905,427,7431
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7048,101180976,952,91869,51300,1514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,6340,28957,3565,56923,4942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90624,5069,9969,1718,7252,5167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5590,4012,3242,5631,25813,79731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9868,3667,7056,91942,3358,37
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,64131,6579,3295,8854,51119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,26235,929,50814,79133,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8842,3606,445,111240474,90865,407024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,153,3358,517,5331,24147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 125988,3813,1373,89866,1717,5506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4035,3416,406991,5078,384,51422
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8678,2642,10457,5327,8877,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5787,958,2864,4137,85476,84340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2632,5189,8050,7384,1369,154
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1798,28234,5184,5590,2804,3557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81689,6522,3929,10991,5506,353500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79949,100,3174,563,79087,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6263,123,574447,5723,22845,1270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,2030,293,25828,10020,83693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26521,2932,4852,32,409,3159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11254,7037,1537,2778,5321,8678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2244,22797,6897,79133,9095,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151,1270,55278,58528,10020,5499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4968,2695,2581,253559,3174,1672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6898,10644,1909,629,9180,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4256,4889,4780,7355,9415,2804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2118,5447,2395,94235,1607,2146
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1071,11019,1489,5054,54539,3155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8772,51085,3480,476,85476,79736
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84342,3795,116519,844,1644,2244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1346,2395,26762,7879,2998,53632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84275,6678,2639,1909,54148,819
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,4973,56999,540,7275,51004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1499,387,64900,5501,886,57215
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5789,1558,2641,4899,6774,81704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,6389,3117,85446,6928,57017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,100303755,643181,35,486,407045
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255738,348,4609,126328,2582,3667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50674,5789,5660,5195,83439,5295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3939,4925,665,1585,55278,60
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9180,28958,5365,2152,10730,23054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5428,3980,1234,1950,51206,4852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10250,5830,56997,3795,5501,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6906,3624,10295,6347,51021,5330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123,406906,3479,5476,2052,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,3990,11232,4790,64689,4159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,5370,5264,3712,345,56938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5562,7386,51441,8243,801,1232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5257,142,5213,10686,2244,9927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10221,487,867,2695,3990,5551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79602,1080,2584,293,7879,54968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27089,5925,10730,1889,10135,4314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2243,1591,7048,347,790,7428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151,7172,1807,3081,3980,29928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5588,8639,54675,5176,6531,9698
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4760,3553,572,8854,81034,79644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 376497,5925,1071,55788,4669,9507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10250,492,84833,2063,338328,7098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 948,22845,643181,9868,123283,27125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4942,3554,4697,1813,51021,22797
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,118,26175,3099,241,4899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84889,2592,6649,116931,142,255738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25821,2006,91869,4552,2100,27089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27232,3717,942,3423,4049,55572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,7320,4015,729230,26762,432369
--> return NULL...
2025-11-28 05:16:15.646 R[48817:34183834] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
109.675 1.727 112.591
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.691 | 0.035 | 0.894 | |