Mustafa Erhan Ozer
| Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 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 2025-09-27 12:05 -0400 (Sat, 27 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 2136/2334 | 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: 2025-09-27 00:38:33 -0400 (Sat, 27 Sep 2025) |
| EndedAt: 2025-09-27 00:44:08 -0400 (Sat, 27 Sep 2025) |
| EllapsedTime: 335.6 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 Patched (2025-09-10 r88807)
* 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 Patched (2025-09-10 r88807) -- "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: 2896,5328,7351,2588,2804,6579
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 111,1789,728,4855,4118,1244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2835,1571,84342,596,4023,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2990,265,255231,84300,293,4358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3576,406937,6609,2683,5571,1027
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 941,133,2280,367,79068,4351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5950,2793,6448,29947,3875,570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1345,9498,55937,6403,4502,133522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5053,81033,5364,959,3159,2690
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4968,2100,2152,5161,55858,151306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2597,407006,793,1401,2328,63874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4358,479,1203,213,1072,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7025,80331,5781,5256,2793,388962
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 581,5367,2695,1581,2864,476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57620,2592,2064,367,406938,292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3033,3417,5468,84340,347411,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3060,493753,60,487,114814,3645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3920,51085,5139,316,4854,268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2788,2694,5728,8473,2944,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 177,29968,2653,338821,9969,87178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2592,7841,6890,7248,7424,7026
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,4715,3624,7409,3988,11093
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,3066,6439,6536,6403,23062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10599,6789,642489,570,23516,6890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3712,1203,1348,90480,6696,6928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,5579,25974,2695,211,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,7347,5826,186,5971,6347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,1968,2806,7421,367,79068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5631,952,32,7498,51167,7036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6519,5826,51128,948,330,5601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7038,5193,91949,4668,5579,5962
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9663,9445,3930,411,929,80070
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3938,10999,9560,2052,53335,26088
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9759,476,3559,55163,6888,84342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6448,6649,130120,570,5189,119559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,5054,2990,10938,4000,5507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26175,6833,123,56052,1351,5468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55503,4669,3065,1443,7494,7424
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,3670,5538,6925,5188,8813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27089,7018,2806,7076,55532,5836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8471,1175,4256,197,5207,2064
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11255,3329,7172,10116,189,9692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116228,1371,5562,517,2642,2629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 686,85479,325,2063,9374,9414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7431,231,2593,364,7345,6182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4842,79633,551,5288,7284,3708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4694,2582,26227,479,6897,123263
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7372,405,7515,100506742,952,790955
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1889,2475,153642,100506742,1234,5053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8879,4700,6891,5228,10842,253943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3123,84275,8877,79068,3559,3383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1789,3990,55970,2720,26119,3673
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54896,7025,5730,4851,140803,5069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6906,7350,55005,84557,9692,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3624,51094,253559,9971,7319,3643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11019,55186,388,4286,2790,3485
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2244,197131,56652,7466,8854,55937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51119,5781,3122,6505,4299,10250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,3098,10135,1029,3645,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54575,57104,9056,3670,316,5313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3651,57215,2524,23556,644974,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4694,3658,11254,29926,2305,4049
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,664,4502,706,5069,28234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729238,9526,3586,84239,2677,7056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 351,490,111,80207,1583,7035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56052,2516,293,6901,514,4688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3483,10020,2835,793,7941,3759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,92935,10524,55034,5506,2847
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,64240,3483,10935,51024,2710
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,116228,2308,376497,51094,137682
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7274,5919,5331,4684,268,1200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79731,6401,11019,10841,1672,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3551,138050,51649,2244,3600,6649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406913,26088,2647,5191,2203,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,84902,80201,5257,55526,694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2641,256471,54205,5286,2243,57620
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221458,25828,2740,200205,51441,29926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 175,572,5631,3074,2952,54567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 537,2475,10020,5009,43,4299
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22820,5743,2184,11095,4069,7450
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,2948,55270,7915,9692,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7385,10116,4726,4694,338328,4338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3062,4524,407007,6351,9332,4318
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56259,2582,84317,10128,1595,51601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5270,1337,842,27235,3489,7466
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388743,79776,2944,6788,1277,29968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8854,10269,706,51316,5265,84693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6647,51204,5787,1339,4968,401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54576,5617,3291,3117,3990,79796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54106,5295,5364,11213,33,203068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79633,1559,6564,5189,5787,10379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1889,1281,6584,6786,112817,2571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,10295,4976,6391,3489,4779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57817,1376,406906,9945,54675,374291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 627,2113,6948,10938,1629,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1356,148738,239,54577,1353,9969
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6401,5364,64805,6788,55486,2524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 599,1601,5265,2542,29928,196385
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56919,7391,8600,28951,9380,3562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6609,5315,4790,10537,2113,51181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56606,55065,708,407010,1789,7099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 819,8567,644096,3978,440138,1595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,7036,23654,29947,387787,999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8567,5789,3709,3991,3375,84334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6898,330,6718,5617,84557,338821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 118,8651,3600,5194,8659,25813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158,5617,54798,26354,10059,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79133,4247,9507,199,5189,5744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3569,493,1346,5563,3123,10599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56945,1650,558,3416,5256,10166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1890,2908,10874,3423,4543,9919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7384,655,4722,3728,406934,5590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55340,4712,1116,5473,9409,768239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,8862,2280,445,3479,7040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 137682,3658,3250,50506,3172,6720
--> return NULL...
2025-09-27 00:43:59.418 R[22753:395185007] XType: com.apple.fonts is not accessible.
2025-09-27 00:43:59.418 R[22753:395185007] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
64.026 1.435 66.394
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.824 | 0.050 | 1.427 | |