Mustafa Erhan Ozer
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-01 12:03 -0400 (Sat, 01 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" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.10.0.tar.gz |
| StartedAt: 2025-11-01 04:52:11 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 04:57:17 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 306.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SVMDO_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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: 4049,7345,4723,9365,6548,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,2592,5713,48,130120,7915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2475,6775,7252,3479,30061,2791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81570,1605,4023,5261,4712,3141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7295,5836,652,2161,383,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7409,153,793,1435,405,958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6009,1950,10891,538,79087,6338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100,1312,51167,51555,149461,10667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,23516,6505,728,7372,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3952,1583,5367,6888,4864,5467
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133396,203859,2314,2571,4855,23129
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 170302,55486,55283,26503,5191,130120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3606,2948,846,84447,132,384
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2395,694,9945,1558,3240,434
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6715,5313,241,5370,80331,2334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60528,256471,35,1200,219,3482
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9076,583,292,6536,5373,1080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6934,410,84889,3949,5473,2767
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3329,3875,9420,93587,10383,26503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,57176,51241,824,4338,80207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1471,83854,435,942,3673,5443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2115,23410,57176,5019,2647,549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9374,7471,1968,4286,6714,389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,181,7528,341,643181,43
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5345,5580,388962,355,55630,104909134
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5274,518,221935,2948,5228,1444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5499,9692,3174,4855,55644,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5193,8309,7376,55753,6383,2516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2639,4723,3708,10157,409,10383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8854,50674,29078,84274,3710,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1208,3670,26354,51441,6649,5579
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133,5288,5702,10730,2170,1468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,79644,5713,253943,7841,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7248,6564,3250,56922,8462,207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8560,8195,6891,3490,353500,2785
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2587,158,79776,5770,51601,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51116,1186,3795,22796,253559,4729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4125,3099,1757,26235,90865,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80270,5702,5601,84317,3099,596
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1352,51649,5162,6721,3673,2159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,3162,496,824,5713,5781
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407006,26060,1646,2806,4925,29929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57192,779,1586,125170,160287,3170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6718,3293,57505,6649,64241,5330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7494,4842,1956,116931,6521,8675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1029,3304,779,2946,255738,51144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1392,5373,3624,2587,779,407007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57176,100131801,54931,266,51099,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3065,650,9927,8722,9607,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4351,128486,1869,1182,84833,100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123,10724,2593,57570,1149,27232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1910,1869,27329,4125,5860,1621
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5787,55034,8772,7248,10730,5442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1056,84889,22933,1027,3418,2720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 655,627,4889,537,7275,4299
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54106,79158,5071,10229,3309,2584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8600,7275,376497,11255,5274,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,3418,2247,151,1393,2792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3418,4715,6938,2539,4854,6788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55331,51103,5476,2876,1392,4314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7076,847,5365,5723,2792,4879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54539,5122,2798,952,407008,2309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,5599,407040,5468,83884,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5193,3992,54658,84705,123283,9095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,2746,2805,55858,55343,132158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388753,1230,2166,2746,55753,169026
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3565,5828,5261,27089,406922,4256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 361,1594,7384,4705,11222,6718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2280,5288,5071,54915,10457,7019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 825,516,3356,5191,7372,2247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6390,1890,5329,2538,1277,509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,4973,6517,7018,5139,33
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28951,241,1950,52,53345,10667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,6721,3123,152078,231,57570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7274,5313,55818,4125,2203,80347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83548,2200,2632,6340,3627,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1629,23395,9054,2588,3032,5498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6531,23400,10891,654,5538,9420
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,2308,25821,28957,4338,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 122961,3636,6374,1493,5515,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3565,48,5860,9607,9374,5071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54600,7099,92935,5507,6263,6616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6678,3489,50506,26235,2266,27249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5256,3295,5836,3122,4723,4889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4312,28957,7466,175,27232,160287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,4705,5498,1636,3077,94235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,5551,3293,9415,3329,5740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7431,6198,6340,4803,185,64241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5595,5274,2904,5345,55750,80339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,1340,27247,3958,1312,56848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3141,64241,3651,10642,2159,4311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 156,1757,54552,2588,4973,4256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1374,22820,133,55503,84902,6602
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4015,2629,29928,57380,7390,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,4654,811,6715,5019,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3929,104,6602,513,8600,4126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 819,25813,3283,842,3170,10891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6925,2203,6821,9607,9692,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23395,1588,3703,55699,4860,6938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 539,6554,476,3284,6182,3489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2147,183,2115,30061,8803,26003
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,5445,5080,134,367,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4049,640,4040,1072,1606,7018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,8243,10524,266,5837,4233
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28957,4125,3636,213,2260,388585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7275,6571,406947,8678,64240,79068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114548,7084,80267,137682,7248,2571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124454,6891,5239,191,2334,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,6515,1718,2593,411,516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,7078,2984,8560,7350,407007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,285848,2904,6789,25821,8932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6391,4338,1281,84300,6403,79572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 210,6535,4713,4544,353,7048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4860,3991,54578,7350,239,4656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10352,27089,4286,4552,25821,8431
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
65.223 1.068 66.444
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.689 | 0.028 | 3.207 | |