Mustafa Erhan Ozer
| Snapshot Date: 2025-11-21 13:40 -0500 (Fri, 21 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 2025-11-22 11:37 -0500 (Sat, 22 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" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4567 |
| 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SVMDO_1.11.0.tar.gz |
| StartedAt: 2025-11-22 04:38:59 -0500 (Sat, 22 Nov 2025) |
| EndedAt: 2025-11-22 04:44:58 -0500 (Sat, 22 Nov 2025) |
| EllapsedTime: 358.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SVMDO_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.11.0’
* 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 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-3.23-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-10-20 r88955) -- "Unsuffered Consequences"
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: 54982,85446,5346,5052,836,4709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2305,7284,2006,2696,5161,169792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1355,48,389692,2746,92609,79068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2804,5277,26227,64919,582,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2101,129787,2790,2147,4654,4968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6445,1244,1606,34,5105,2539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,718,1281,7879,492,2247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5962,9498,5370,60386,2395,150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,79068,4089,84649,6582,6868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9779,540,2152,23038,6182,2888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,6582,275,7167,119559,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23274,1351,200539,2146,4695,4803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8675,4319,384,178,4968,7035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 846,7018,54576,54805,3460,23175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6868,1807,56652,4089,84649,7036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2688,2310,6929,7528,56938,2597
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29968,2495,3159,4318,161247,3643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5789,1232,2030,7421,7157,118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,142,50506,4854,383,1268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5499,84239,55937,27344,407024,492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3712,7220,6714,249,407024,54931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4790,123263,1950,253559,4697,26227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 836,4609,2006,51604,2694,3170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9131,51021,2587,51660,2903,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,3920,64240,6566,3099,5925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10195,5257,285,9759,79633,6352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6402,253559,3930,3988,29926,56606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84987,9927,91452,170302,54968,63892
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 463,8642,4852,57678,55163,4715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1281,539,57128,57505,10537,54539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130120,5971,5730,407011,776,148979
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1582,142,2646,3600,6584,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,1234,7412,124454,1203,6932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6788,6647,1443,152926,1356,463
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10537,3630,4023,3569,4842,999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3930,2767,1641,570,796,388753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7035,3930,7289,3624,84334,5723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728294,405,5188,6789,54344,38
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4899,1499,5468,4126,55503,5792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,4942,79572,6571,64131,388962
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54968,35,26191,10938,3490,7350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,7036,84701,1571,9429,56729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2158,65985,10842,6897,23274,3562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5617,5019,4988,351,3630,1348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,5830,219,1629,22845,10019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2990,587,7942,7424,7941,6602
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3156,1645,6515,5571,5274,7297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,9559,4543,7026,2798,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23291,275,389692,1356,8659,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5442,859,642489,7040,90480,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9104,3030,51422,2834,3091,4285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,85365,1636,407010,256471,84317
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11132,3779,1435,5207,25974,1351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1815,572,8665,6182,26235,5925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,7037,9409,1490,26291,4853
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10580,6938,1737,840,427,885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,140803,3553,6341,2559,7124
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2328,5590,2303,52,788,6462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,338328,509,6908,3081,6576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 640,38,80222,4286,1028,55270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,54931,55278,3795,54476,3170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197,2064,3995,10382,63899,6513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2689,3425,10135,10724,158,7471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1468,64601,8648,4118,55863,79087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,9927,50484,819,4864,160428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56302,6382,150379,5364,166785,3159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26003,3643,1345,4318,137994,265
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,266,1716,353,4312,9927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4128,4143,463,55818,10891,11096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,3952,1442,3663,4702,27247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1499,7252,6531,1992,1608,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10560,11035,4288,2266,1353,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406913,1497,51052,644096,119559,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2587,91949,5188,5139,26354,23753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4247,7350,6439,10991,7471,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9927,51422,9968,1607,7320,221935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1807,50674,6464,50814,3562,116228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,150,7084,2998,2235,201595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3953,207,1544,3373,63874,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55526,549,6464,846,1803,5741
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7385,186,5621,358,2184,10965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79944,81034,3240,79776,84062,4338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81034,29843,29078,5078,2646,56997
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 471,10643,10466,353500,5176,1634
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406913,999,5962,389,2524,5345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2790,80222,2006,5476,54931,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3339,10577,23556,335,8517,1812
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1409,4803,132158,338328,1890,4049
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160287,7076,200205,253559,65993,9076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1634,1080,2729,336,4803,5228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152926,5092,15,388753,2720,2799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9479,27125,6927,23400,9374,5277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60,166785,1906,25828,8659,6347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,5291,4714,2247,387,153642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54577,6374,122961,23304,2683,1585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221458,2896,6199,64116,8818,256471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23543,2992,1234,3684,203,4846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1346,51021,51555,5189,1493,84889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9370,10000,1584,2693,2760,6999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7480,111,6182,1230,79068,6392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1716,64087,1361,160428,8659,4700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4744,3624,57104,353,335,81034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2876,3554,3931,1802,114814,6602
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406934,4337,29960,2572,5176,2950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3562,5175,6897,175,80331,7292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203,2793,387,2590,57570,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 265,1649,1595,10991,6356,3795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,6999,6609,7385,2946,56259
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 819,10644,84275,2947,7494,4705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3054,867,6556,133522,81689,644974
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7252,56623,6789,8942,5617,3791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79572,3552,8659,55343,6342,3077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6356,1906,2936,411,201595,84701
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7025,23236,4137,3600,54552,9759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8660,26235,7919,83693,3283,81033
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
115.858 1.622 117.647
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.701 | 0.044 | 3.786 | |