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 11:38 -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: /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: 2025-11-21 04:38:32 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 04:44:29 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 356.5 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: 3570,55331,6649,364,3980,94235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7376,6774,8195,2548,11093,83884
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1351,57678,2645,4311,55902,4598
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 652,3930,56606,406922,2395,5315
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124454,3283,2588,2820,255231,2745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1559,558,64689,4723,1801,10730
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51316,9479,1497,4683,7528,5506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50674,56606,84701,23543,6341,3357
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5160,6616,5327,54576,55902,80224
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29947,5315,401,4780,55818,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2056,3458,7841,2159,8639,2695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51052,6403,10226,5730,177,10616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54549,4318,3339,3875,3784,2571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 185,6932,6550,7077,57128,401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,10911,2787,1435,3991,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22845,3795,1559,54552,5052,3636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50484,181,518,8309,3081,859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3643,3159,79949,570,200810,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54901,51478,6566,55937,239,191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,2303,217,5787,3283,58528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3416,3423,5365,7054,51478,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1361,5189,2786,627,133396,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22852,3939,391051,56302,796,6009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5962,92667,11213,6556,28958,55788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27232,2581,1376,79001,6811,221935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2739,6715,768239,7424,821,1593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2710,3700,27249,1208,4705,2475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387787,3636,90624,4973,5019,9091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,113235,64801,1646,56923,9968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6582,85446,54896,51092,216,7422
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84447,1346,2712,7084,10991,91942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 410,57001,6374,10682,2109,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7252,5080,4790,4976,5967,1593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,2309,253559,2834,3576,2559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,1352,1956,10062,4973,1268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,4035,23400,4160,330,55967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 249,79736,3440,1906,4855,54805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3663,1813,2952,84705,7098,6519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,54549,942,1812,3034,57678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3795,5443,5175,2677,22901,1524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53632,51,4688,3700,10382,51293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,10094,3667,5160,80070,27010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3440,643181,1589,539,1493,3949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1182,3643,84557,2328,255738,64801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5346,4853,338328,183,5257,4137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255738,7052,2847,10724,55937,4864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51094,5080,3489,405,5364,1282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3773,6389,1558,23654,3945,126328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 563,5274,1608,388372,686,570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3157,5799,5442,51181,2628,4684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10062,5824,6199,84705,51117,6811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 275,4543,1149,4358,10195,2790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55486,1769,27235,2517,551,585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9131,3703,10316,2739,3490,3312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4925,3373,8932,57215,7428,253943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9056,23417,5580,185,3651,8694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4719,6383,6934,8642,11222,348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,3356,5350,3174,55340,4860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2695,5265,7840,54931,376497,3060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51608,52,50484,2876,137994,5068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2653,4137,801,2118,4719,338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84833,2784,9607,9429,65985,5213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6183,23304,8471,4712,5162,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5702,1606,406922,5364,859,6476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4319,3155,1559,81704,7351,26762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79572,4973,5828,7019,203859,56052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2690,3773,498,7077,203859,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51601,1340,1442,55486,3251,5654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54931,91647,55503,2548,4668,1807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7098,10559,5824,4715,3767,2998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,11232,26291,2694,7471,2052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347,4627,8841,79068,4035,4149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285848,490,57761,50506,2696,1813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84061,1327,9420,2303,492,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3939,5019,15,2629,7048,5618
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1605,54982,79944,34,3586,11035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2100,6648,55065,23175,1646,3486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27010,652,5264,1801,8932,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,1444,3172,9692,5276,3553
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,153642,2946,4627,1559,335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,6774,58528,1514,266,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,1906,22978,4153,1678,6774
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,2170,4976,407007,338328,5824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5631,229,7350,10195,2118,389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 339,54798,3507,7319,57048,3375
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10686,8639,7057,9968,6535,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,2990,10642,7915,2581,11019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23129,1558,84557,8722,4128,5372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 115286,3709,5243,84693,10577,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3482,23274,5078,4719,2200,1392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51092,5465,3773,60528,1369,2745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2052,28234,200810,80224,9572,3060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 216,2697,56259,7292,116228,284958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4851,7038,4855,1757,3949,104909134
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132,4851,5078,5071,4232,6584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27232,148738,283120,55670,558,3791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4311,3600,79087,7036,3717,5270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6901,3251,6390,6531,83548,7385
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7056,2740,3145,121268,6775,599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347,4049,776,1509,112817,4853
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8803,9091,3309,9779,6324,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3576,6938,23409,1497,3949,859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1337,5798,35,3990,5592,9779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1716,2203,84062,1537,6341,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9945,1351,886,3117,338,9180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,51099,5372,1807,344,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 583,54205,7450,54806,3710,6948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,5443,51119,6521,2539,1649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55034,54806,6515,471,84061,197
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 486,3562,25839,2629,56923,6897
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2641,191,26175,51660,5167,407021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 665,5214,2155,9868,7038,5230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,819,28957,113235,6403,7019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9969,3651,8942,104,1019,2890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4040,627,183,6925,10166,5967
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
116.296 1.608 118.046
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.691 | 0.054 | 3.781 | |