Mustafa Erhan Ozer
| Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: 7851a60 |
| git_last_commit_date: 2025-04-15 13:15:07 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-04 12:06 -0400 (Thu, 04 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4617 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4564 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 2123/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.9.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-09-04 00:14:16 -0400 (Thu, 04 Sep 2025) |
| EndedAt: 2025-09-04 00:19:41 -0400 (Thu, 04 Sep 2025) |
| EllapsedTime: 325.0 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.9.0’
* 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/4.5-x86_64/Resources/library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.9.0’ ** 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 version 4.5.1 (2025-06-13) -- "Great Square Root"
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: 84947,355,1801,518,4319,5580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,4306,801,51144,1672,1646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1558,3060,4973,7431,6183,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,11136,53346,3490,4656,54205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1544,9241,100506742,1270,6517,2793
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6932,842,8743,2876,256471,9021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,55283,796,119559,355,5501
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2632,1582,350,54704,3995,6566
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729238,8743,4729,28976,824,1277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 339,5346,788,694,2348,51079
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1591,316,57192,10753,5409,5255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2348,5095,205327,407006,1208,9692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,293,2678,5465,4312,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,9365,2395,407011,7275,6548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2713,348,6009,4709,162417,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4846,4976,6392,2524,23291,4697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23038,4232,268,4722,8462,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7054,1589,4125,7124,27249,55630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28951,118,79944,64689,3553,5295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64240,729238,29968,8604,94235,1586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2159,54552,6772,22845,203068,10643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 516,241,60386,2584,4779,1798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,8879,5702,26235,56302,64900
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7292,1728,64805,51422,1644,221935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,55902,8567,1585,3958,8665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26291,5188,1435,53346,1312,358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3357,1348,5499,348,3240,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80201,2516,6602,359,55278,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5962,7381,7386,9526,1909,2767
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5364,2158,55644,551,4878,200539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9698,9919,7284,339,175,55818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10667,6338,249,9095,2030,57128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1071,2118,4311,335,2678,253943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 351,51300,29926,1558,7385,1356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6897,5444,2694,10195,64601,10642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 212,5476,3953,644096,54805,84447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6261,27429,3552,2582,728,3703
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4887,124454,2793,8504,356,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 138050,29929,407010,79731,999,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,26088,64601,4988,1815,4758
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,2695,9180,52,6834,940
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2247,26227,5629,4256,6183,6775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133,6584,867,177,3557,1910
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131669,1186,1468,54344,1968,197131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8945,51601,285362,84061,4790,6647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8722,477,10316,776,54982,160287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2200,2647,1203,79661,1409,6584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,665,7879,1435,5562,3673
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,23753,4695,56938,8942,999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8604,9560,2588,2948,9927,5499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5291,640,7098,158,3460,3939
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,6536,51079,7172,2243,3458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3383,6720,8665,80070,11213,3091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344905,9095,80347,10891,5563,3685
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2878,4256,5501,51316,189,5713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55278,1345,64601,6401,407024,361
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2944,29947,5331,1182,2932,4319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8600,6720,5660,3596,25828,2538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 643181,10059,6391,54344,4925,5499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,23474,80224,1499,5095,1649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1471,55753,4089,178,2888,2690
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8462,5092,25813,5781,10165,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10580,91647,7077,5350,57107,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5644,55340,2157,83693,1444,2948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 111,130120,54802,55037,111240474,161247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,9388,10352,27329,125988,9759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23291,2334,3250,325,55034,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 694,4976,6579,10423,4852,1649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5193,6811,5176,644974,84340,5096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81033,5105,8651,79736,1029,4153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,5447,5625,3172,10857,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5445,2235,3242,3559,479,5781
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25915,5501,51649,5971,4724,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1601,126328,1392,51649,587,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 183,1582,5563,148979,3486,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 583,2034,407040,121268,5498,10383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,2639,91942,6401,203,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8195,1589,26235,650,6584,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2791,27141,8722,51119,90865,26175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2835,7494,11232,5745,55278,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6890,56999,9409,875,28958,7450
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406934,4702,9414,27089,6324,55902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11096,488,2984,5091,655,11132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80347,1843,9420,7100,1906,6536
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10724,4358,406922,1802,85446,54205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2717,4973,6569,203,5571,664
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 567,133,55034,8932,4779,2720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5465,2792,6770,3767,3295,5175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,5468,1608,5160,6571,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10965,1738,28957,23054,5270,55163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3995,4015,85446,7320,3351,4697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6352,2034,477,253943,875,79796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64087,847,55670,55788,842,3240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7284,840,93587,2932,3159,4860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90480,22797,84706,55902,8659,4728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4285,83854,2235,84889,2517,391051
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8504,55818,64788,8462,3481,80222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 479,3423,7172,8600,57511,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1557,4899,191,7528,5770,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9512,401,6339,6718,221935,4684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5787,4524,5563,6616,3122,940
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 411,2786,10102,89866,94235,3339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9382,5743,5346,34,23556,3551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2904,1489,4855,3709,54106,55283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3953,9919,2932,3553,388743,640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55037,2309,1629,351,3295,9698
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3482,551,728294,2936,107075310,3507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5428,84693,2310,4780,9512,1588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3077,10644,9968,3700,22796,10062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,1594,79783,7078,6522,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 506,3490,6678,154,3032,2731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51738,129787,2064,3304,54658,7388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80222,3358,2678,124976,29881,2947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51555,9630,4311,2952,2158,1175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,92609,2936,2395,2170,2056
--> return NULL...
2025-09-04 00:19:32.285 R[71603:197933288] XType: com.apple.fonts is not accessible.
2025-09-04 00:19:32.287 R[71603:197933288] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
64.454 1.316 66.344
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.750 | 0.040 | 1.075 | |