Mustafa Erhan Ozer
| Snapshot Date: 2025-11-03 13:45 -0500 (Mon, 03 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: RELEASE_3_22 |
| git_last_commit: 86871da |
| git_last_commit_date: 2025-10-29 11:23:08 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-04 12:04 -0500 (Tue, 04 Nov 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" | 4902 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 2163/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.10.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | 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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2025-11-04 00:43:02 -0500 (Tue, 04 Nov 2025) |
| EndedAt: 2025-11-04 00:49:20 -0500 (Tue, 04 Nov 2025) |
| EllapsedTime: 377.5 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_1.10.0.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 ‘1.10.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runGUI 0.779 0.038 5.007
* 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 ‘1.10.0’ ** 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: 56848,7325,1621,9559,347411,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8243,112817,5713,3373,104909134,5770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,3931,2539,2303,100303755,3624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7325,2878,2793,1394,55572,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2303,55186,100131801,55526,340024,29960
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51081,189,7391,7879,5919,64116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169792,25813,54896,3170,406,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2203,325,65985,4000,23236,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6576,1348,6535,7347,1230,1558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1607,5330,10102,686,7352,6932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3645,2159,5781,9607,1581,940
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3570,10730,57048,5241,3636,3663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,9945,64919,5330,6715,55037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,57048,338,5740,10991,9445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53632,1812,5860,3667,6897,2937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84062,640,27089,2653,652,124454
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152926,4702,6522,3032,10102,406913
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5372,2804,6772,1281,2155,123283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 107075310,2113,28951,150,185,4967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 351,406906,4854,7025,1593,1889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,55186,388743,7167,27247,875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,26235,2108,338,5595,22797
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,2689,857,1442,540,10616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6649,9180,5213,2697,25839,5740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9663,729238,506,9630,5346,64601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3557,4683,2731,3480,6772,10382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5468,3375,344,5798,4159,593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55343,11132,203859,1337,23417,779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5188,28976,7422,4700,2949,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10166,4256,6721,2740,308,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5972,55532,1537,9241,10008,2260
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55024,10008,2798,11131,7248,100128525
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4709,4713,26088,3162,407008,338328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26227,3988,5644,2948,5373,10537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,92935,2720,308,1584,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6929,2034,1557,10165,3939,79661
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2904,477,795,9526,84557,3251
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5406,79572,10250,38,32,249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 150,4548,9131,1591,5581,2992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56606,5236,2678,5506,2280,55283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23753,51548,2628,26517,56848,1869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 150379,7030,56652,50814,25839,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 486,23600,266,3562,4915,7295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387082,152926,1636,1468,407004,6821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10195,3992,4311,7471,1374,6492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,3586,8642,8714,6748,85479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,79736,842,9415,10128,178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1489,5631,212,4843,28234,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,55065,326625,229,2820,3759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4853,19,2055,2934,2113,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 642489,2638,54576,7025,5860,411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,253559,7276,4338,3934,5228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7407,685,3710,80331,285126,205327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6925,54806,1544,5176,79661,3813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 253943,1634,5498,1607,8243,1028
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2308,5713,1645,405,407011,1347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2271,1281,229,53632,1374,55788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10221,3304,1843,5443,169026,51611
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9429,3358,6678,55750,4159,7172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 364,6901,4915,10013,7515,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,2170,55503,940,384,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1757,4319,84275,4688,4598,6928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2642,7347,10616,1807,10891,5595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1340,26503,3101,284958,5315,3627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 170302,6569,9759,1956,7077,123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79934,151,6387,84649,5476,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,656,4040,23516,551,10379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4313,4669,7372,1497,10845,1728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8243,55818,116228,8694,3113,6476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57001,26003,54331,27249,253943,1352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,4853,6788,91942,5442,801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6339,3479,4854,6868,6476,2314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64432,2308,11254,3291,427,217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,54205,5590,9560,3988,2948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1906,9056,2834,63892,477,23474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,10020,3552,64240,1559,4684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149775,1594,9414,1497,10020,115286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2592,9672,3291,9559,3684,4684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3240,57511,2713,2101,1843,50506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5277,387787,3458,1606,64087,7076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5660,1950,2597,5261,6383,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,10062,1906,1728,57570,471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64900,9415,7941,8473,5274,1910
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2804,8648,27010,353,1489,5728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2678,4035,7942,55644,6515,10999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114548,492,6925,2890,203068,3645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23304,644096,64900,3284,4842,796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5621,11254,3081,7384,56999,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5207,405,84572,54344,91574,6351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,1950,2876,3899,7036,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1493,92935,359,3600,5551,3638
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,941,7389,7030,175,131118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1869,51176,4716,1027,7077,4548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2328,55503,3423,79944,4925,1369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1493,886,2584,100303755,5295,7355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,169026,81704,5799,23236,4899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51117,26291,2875,55065,5595,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3670,4780,5617,2798,2896,2055
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 359,55503,593,3708,6716,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4357,7078,81570,93587,131669,2590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,201595,1893,6566,3784,308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6342,7421,55532,6391,6564,2593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,5369,7466,4312,2678,1116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 551,1629,29881,91949,9559,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79949,26227,411,10250,5328,132001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 284184,10383,4968,6715,3284,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2934,729230,53632,153642,3308,6898
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1583,112817,2688,7942,4015,6774
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,54802,6616,462,2063,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 239,4925,3284,5971,493,2998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25915,4668,2628,9968,8862,83884
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 191,6564,1806,91869,4299,5092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2159,5563,4886,85476,55699,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7220,54931,407045,217,54806,4000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2063,2647,1376,10379,6374,406906
--> return NULL...
2025-11-04 00:49:10.995 R[48482:726808563] XType: com.apple.fonts is not accessible.
2025-11-04 00:49:10.995 R[48482:726808563] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
107.285 1.634 109.858
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.779 | 0.038 | 5.007 | |