Mustafa Erhan Ozer
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 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 2025-11-19 10:15 -0500 (Wed, 19 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" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| 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
| 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: 2025-11-18 23:00:01 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 23:02:14 -0500 (Tue, 18 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: 351,355,10457,162417,8722,6564
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 929,10616,100131801,91869,79068,55186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4728,5095,3791,79661,1889,3440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1348,4968,1080,10643,2052,56052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,169026,406991,55858,3158,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1728,4160,3673,5571,57570,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8802,100303755,718,26227,2592,3700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 824,8841,50507,5184,57511,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55283,26291,5781,2876,285126,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56052,6464,55818,175,389,1203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,3712,5256,407007,6236,7292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10008,2688,7030,1471,846,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3065,123283,6584,6774,4627,10157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644096,1234,2584,825,2784,3172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255231,7252,57215,940,6794,9971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7035,2147,123263,10875,6906,819
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8842,2793,498,5465,10094,57620
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1489,51085,406991,653,942,2548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1678,4722,8678,25813,1813,7390
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203859,599,3351,84274,594,3663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1636,948,686,1890,5443,3117
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10842,3673,22796,178,10537,5054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 540,80347,2712,53905,4299,3624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57570,27429,7325,3624,10128,5972
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2677,5192,388,5167,221935,55863
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,2762,5350,1769,27235,2590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9779,57818,3638,27141,283120,4720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7084,5584,401,6390,6009,2170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2847,53905,3060,9409,2548,6925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1605,126328,6548,4012,8517,9076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 265,2778,27247,27141,811,5373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7167,1232,824,3709,3954,239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4716,8932,4712,183,2335,1606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2152,4552,1641,5327,56999,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2632,6932,388962,3570,2689,23411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1116,2643,3489,1557,9927,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5428,23304,3486,1641,1968,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55034,3569,2053,3651,93587,1595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23054,3115,10013,149775,7287,6602
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2155,1757,55818,8504,5506,54802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1571,3425,55343,4125,7388,5192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4842,537,1906,3030,155,293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,6261,10135,4656,5346,407010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5184,11254,54798,9560,6550,1490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9692,7841,26235,4125,6770,8567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10062,5190,56997,27141,63892,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4256,1716,5105,25915,5331,1491
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5228,846,3357,2639,1312,25821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64087,122961,1361,1581,80224,54148
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2806,3627,5052,25839,3157,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1200,155,10643,1468,3123,55283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,3795,100506742,2516,2949,8639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3783,405,1716,3082,2053,2597
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6338,1409,2646,1803,391051,10226
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7409,2099,587,56052,1717,6565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2203,26060,391051,55970,22797,284184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388743,427,160428,3988,26191,8600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,84889,3791,7040,51204,142
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84889,51241,2571,5126,7390,85365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 479,9091,4695,5465,644974,790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2641,3423,3627,5498,79944,7025
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 122961,56848,8722,793,1490,3553
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6999,650,653,80222,10019,79776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406982,3122,593,3373,23600,496
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55163,253559,2629,79585,4548,123263
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6890,4728,2628,3709,9572,7038
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,200810,493,3113,5592,9180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8651,7422,6338,6718,462,64116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2776,149775,7916,10383,8431,3938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84705,79001,347411,4318,387,54675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2793,5069,4012,1621,123263,5367
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7320,338,54549,656,90480,4715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2786,5009,51422,54567,31,10991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 107075310,7498,10599,2584,7471,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114548,5261,3485,57620,574447,5214
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5787,728,9672,10250,1281,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3952,5095,796,291,2194,2539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10841,79949,7019,9971,5770,7428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 941,7351,4233,23417,4846,26060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1392,4543,2524,10682,56997,308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,79158,5126,2395,347411,119559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2864,2739,857,1185,55065,27235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5799,3938,55163,7035,4744,5563
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4846,3312,11254,1489,2952,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7052,10008,7424,197131,2334,6576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1337,197,3483,84706,5328,10991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 19,486,9572,8567,406982,5730
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54931,5798,6564,2184,169792,7412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50506,6770,4669,958,1493,200186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64241,1798,131669,3767,6888,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1444,540,2348,120227,4976,147007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8665,1027,148979,6338,493,6262
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11019,65993,2559,3929,5967,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,406,3425,51548,445,107075310
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6579,407007,4828,51422,3240,664
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6389,1072,8818,51316,6888,4524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 107075310,51441,84340,5092,51548,3480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26227,51316,101180976,2524,6319,9779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28958,6928,401,3242,1585,92609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,779,1815,6576,7471,3339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1348,1678,6811,10874,5499,53335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,23543,5781,54896,6248,4023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,5068,1621,2834,10243,5256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27429,2760,5447,54552,1803,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,56938,4337,23389,83693,10269
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79053,57017,8802,51458,7319,23062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55858,1022,7385,5373,8799,51478
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2641,2184,5594,1786,3948,3122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,885,9630,2949,54575,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9370,162417,6383,1340,387082,23516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2647,104,55037,27232,3351,3065
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4694,2235,10991,11231,1337,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 581,558,3074,29960,3356,498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9382,84317,407040,5702,253943,23411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,1591,1595,5255,1737,1675
--> return NULL...
2025-11-18 23:02:10.039 R[21190:80170103] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
26.579 0.427 28.244
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.311 | 0.018 | 0.505 | |