Mustafa Erhan Ozer
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 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 2025-11-21 11:39 -0500 (Fri, 21 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" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 2133/2327 | 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: 2025-11-21 00:36:14 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 00:44:16 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 482.5 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 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-x86_64/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
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: 1641,80207,2786,201305,1268,51004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3562,1029,11132,7515,55532,57017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1728,2517,1019,4137,2184,26003
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9365,90624,9409,80339,23474,265
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5919,308,590,54148,10682,316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6535,656,5071,5580,114548,5367
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80339,6531,8841,8813,55644,8877
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6834,84317,7284,7019,664,4594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 514,6531,407010,231,2334,6748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,5184,9997,83854,9445,51094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,6786,51206,57048,9575,54549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85476,4887,654,10062,1072,7384
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3586,51300,114814,1645,3991,2152
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6324,7390,706,367,89874,4982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7167,84447,57380,407007,79585,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116519,6462,6716,3791,7388,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 432369,51021,4779,2063,952,1786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5538,11131,87178,9388,2328,5331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1489,5350,2271,5781,51052,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54600,51293,5972,3482,1644,6934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,64689,51204,6402,51300,4715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6341,2948,84705,490,213,255308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,150379,1232,6521,128486,6788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221935,1812,2908,23304,776,8675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57192,100130015,4023,10383,406947,3351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,407011,54675,55753,57128,1075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80339,23175,211,4889,6609,6616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23369,100128525,2746,3416,10580,255231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2166,640,112817,10019,3091,6522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3779,132001,788,5621,31,492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23411,6519,149775,1801,686,1200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8504,5538,374291,4128,6248,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158,7252,4233,211,2762,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54802,1175,5365,3934,2646,2063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3569,3081,56052,29881,2056,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55863,7078,7388,91949,51422,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3783,201595,7225,3113,81704,4015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23369,2147,89874,212,1509,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 476,341,8854,1910,7386,7480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2159,292,79633,6564,92609,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388585,6834,2932,8818,92483,3551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4288,627,5265,3953,1718,6565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406938,29968,162417,3486,3949,4311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54968,189,7057,54809,3569,2793
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51117,477,5191,6009,79796,1950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27141,463,6770,63874,9498,4712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,5660,593,4779,79776,51176
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2944,10537,6521,3586,6389,587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,2641,5629,340024,5293,5346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,3101,116150,84693,8504,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3145,10226,2946,6775,5962,181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1471,54578,4976,3141,5211,27235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5350,84275,7084,5160,768239,55034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10352,52,407006,1444,56606,1859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3570,23462,6536,7292,161247,219
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27089,175,6898,6774,55331,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4716,2303,120227,9630,22845,462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53905,1281,859,6387,2793,216
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8651,4694,11132,3329,593,197
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4128,8431,60,51085,5190,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79796,4319,29968,2055,10269,5321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2109,5538,5243,54675,5562,1353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4232,1588,9021,79087,2115,3938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2034,5126,6821,2334,80339,2645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6696,7384,706,585,23462,79001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1815,6718,8772,6319,101180976,55037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3562,8932,253943,8802,10730,2310
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,7167,2517,6514,55037,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51241,123,819,8600,91574,824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3565,5019,203,11093,5009,3995
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 125170,3460,1672,123,857,640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 284184,1186,23590,80339,4524,92667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10000,9698,3489,7124,3645,5836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26088,55343,6392,7019,388743,4760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285,7386,2099,26521,28957,5167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27344,285362,6716,6897,104909134,81033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65993,6834,5925,51241,2328,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3551,2731,6383,1185,2767,2745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7919,506,463,5406,5373,29960
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9414,51176,239,4153,4288,57380
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,1956,10686,1340,51422,574447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,2745,2948,3710,54982,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5373,18,4684,407006,27141,2055
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2998,6182,9560,4968,7038,8803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6514,55699,4726,8648,1028,231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,796,55343,51441,6582,5009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7919,79783,50507,1717,25828,1355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5257,6774,51604,201595,7098,9056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23163,51117,7412,406937,5211,7035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 355,6324,1071,8803,9451,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123,3710,4552,84274,3643,4853
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,1345,200810,407006,3638,56848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54806,3552,5631,6403,29968,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,5228,5328,54896,54148,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7248,51083,4854,25821,53905,93587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1589,10466,79633,6531,160287,6566
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 128486,4000,6556,1028,5743,801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6324,23389,3074,283459,1672,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 348,7157,80347,10999,3423,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285848,1029,3486,7386,498,5805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2792,570,10316,487,50506,55750
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3643,64131,10379,51085,7412,7325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 316,338,2948,506,477,28951
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,55065,6492,7352,57192,330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8050,7220,7100,407011,7351,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11095,3033,7528,8942,941,4853
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23129,52,54205,3157,145264,104909134
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388585,2348,100,51608,10911,9380
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4126,6248,5580,2693,5787,1890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407008,1369,54210,2056,55486,7528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,7350,7220,94235,253943,471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5345,7019,929,868,9997,2592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23062,6548,6340,2180,6925,284184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,114548,2645,7099,463,549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6439,2303,1497,435,10577,2170
--> return NULL...
2025-11-21 00:44:07.441 R[772:60536398] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
199.862 2.353 203.791
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.901 | 0.045 | 2.219 | |