Mustafa Erhan Ozer
| Snapshot Date: 2025-12-14 13:40 -0500 (Sun, 14 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 2025-12-15 11:35 -0500 (Mon, 15 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" | 4875 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4583 |
| 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SVMDO_1.11.0.tar.gz |
| StartedAt: 2025-12-15 05:02:42 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 05:07:43 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 301.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SVMDO_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.11.0’
* 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 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-3.23-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-10-20 r88955) -- "Unsuffered Consequences"
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: 6928,55670,3033,29958,2720,836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3795,7097,29947,22852,4144,1244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5837,2348,7376,5824,91949,123263
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5286,1318,6464,6774,4886,7026
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4351,80222,6338,3759,26521,123283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4700,9365,1356,2113,4627,54704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2266,2752,84274,5467,3383,5191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2695,5230,7386,133396,9969,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10533,406906,2778,1606,4128,5828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7412,8942,4688,2820,147968,11093
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,336,3357,5588,33,63931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,8504,549,2864,55526,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90624,84239,1493,3600,55526,1116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,6354,5313,23409,2639,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54331,199,55858,652,1345,148738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51094,90624,1859,7289,1232,582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2571,55283,8659,5467,1586,186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3948,4337,3356,9054,50943,3304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5447,255308,7347,952,11255,284184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 821,5442,1555,5175,2799,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,5787,355,52,1203,4012
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5321,6774,10842,54511,356,133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 539,2788,4729,4543,4540,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,5071,2155,549,2786,2629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5346,7076,2146,56652,570,9104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,4968,51079,3304,652,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54798,952,50814,6775,5507,432369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1185,5257,7498,166785,2572,50484
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5580,558,9180,3670,23654,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5291,10577,840,186,2266,27329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26235,5834,10724,53346,120227,29078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,8517,10965,54805,3312,3992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3060,1028,1649,55644,51052,23038
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407021,80267,6531,203859,7412,2147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1149,10991,33,51119,6341,32
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5243,2524,4779,29929,2247,266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3081,84987,266,4669,65985,4524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3119,84300,239,5826,644096,2729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29968,4878,2697,221458,6834,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3952,655,84557,10020,1906,2639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6445,5506,406906,5595,10400,10935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2890,1807,3115,407021,1646,10195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6319,80331,5571,405,632,7494
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,2243,79934,10616,2697,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,131669,6531,283120,858,55902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10062,2542,406934,4548,80222,3991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729238,3784,79736,9507,25839,8877
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,3081,6583,5230,5594,84902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10560,10891,1363,1021,407009,3034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2645,189,26191,5236,341,2760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5078,4311,1471,10999,57511,4723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4688,5798,3099,84701,57128,6329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116150,4544,87178,10159,5071,491
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25839,5080,6888,256471,23600,186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 266,3600,6519,51611,9445,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6908,8604,376497,33,123688,7431
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200539,7350,186,56302,7157,8243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,84649,27247,2787,55788,30061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60,205327,275,2628,4842,4337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3945,8854,5184,6262,3284,6531
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7422,10524,1373,5428,55037,6571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,4843,3569,4702,1244,4879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6548,5364,177,3673,1351,100506658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5295,4125,91942,2109,10642,85569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4023,79602,348,6356,857,92483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6352,54539,617,56922,23236,8202
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2645,50484,3586,685,79001,1355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,821,3673,5805,434,3290
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1409,1649,84902,796,84342,7026
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,100303755,8675,60,959,3978
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1558,197322,4306,5631,132001,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60528,2628,3358,4598,128486,2303
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 376497,8517,55024,847,2673,169792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,91942,26521,1646,54896,479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,4319,85569,26354,169026,4695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3638,79736,2166,8087,2694,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1312,1890,1645,10644,406,8799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6352,84061,9997,491,1351,54567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9429,6888,3934,2590,181,23236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7248,84504,3482,6932,26517,79068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728,4313,1601,4851,11112,4842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29960,3627,152926,6531,4982,477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,790955,6183,5654,4704,55750
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6772,3032,6566,51024,7287,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4513,6383,200186,5444,4508,35
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2334,5618,434,51477,10935,27249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,101180976,5211,3482,2147,9560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 793,6198,51458,5644,2638,4539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5139,4704,10537,3929,7325,9451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56923,8202,65985,54549,51548,116085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5265,84342,10229,2668,1893,516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 177,56922,84769,2063,6535,25839
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 570,7132,635,3030,79133,283120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5702,2834,8854,999,51206,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 367,4049,2950,79144,51144,2947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 498,586,1815,9104,2805,2571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2641,5601,55343,824,2713,3113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 118,50484,4123,64131,53632,3066
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1557,3156,57017,389,84902,6492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55967,23410,572,284654,7274,4942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7077,216,498,1543,9513,5306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3990,5654,3692,498,2305,221458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388372,54476,84705,487,796,55788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5160,3931,65018,7077,6934,57678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,84275,570,60386,4713,22820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56259,6714,9382,5255,23054,5506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8517,2992,1672,58528,5161,1718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221935,5069,10019,7388,54205,6531
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55268,5228,2328,3931,2668,353500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653,3357,7276,4040,1340,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6263,846,351,9968,3899,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26235,2548,948,137994,10020,9180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,7096,10643,112817,4889,9332
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
61.318 1.802 63.333
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.769 | 0.085 | 4.600 | |