Mustafa Erhan Ozer
| Snapshot Date: 2025-11-14 13:45 -0500 (Fri, 14 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 2025-11-15 11:58 -0500 (Sat, 15 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" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 2025-11-15 05:01:34 -0500 (Sat, 15 Nov 2025) |
| EndedAt: 2025-11-15 05:07:28 -0500 (Sat, 15 Nov 2025) |
| EllapsedTime: 354.5 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: 517,644974,406913,7915,2266,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2835,5579,2950,4125,4023,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51117,729230,4704,4337,1555,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4684,51181,8942,55283,9365,4713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,57176,89874,4069,3663,4143
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,2784,29926,150379,129787,3087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8714,3074,51085,55768,3767,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6788,1606,2064,64689,1468,5071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55526,2888,2310,5009,3562,5579
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 212,64689,15,6721,1806,516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6402,6374,114548,2588,7220,5644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2720,2647,4779,1394,15,3240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790955,6927,3490,79053,5789,2495
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28958,6720,350,54539,10,3483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2581,25813,6868,58528,5096,2944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7841,203,5445,2055,4089,7098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,2034,4780,1717,405,7320
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23411,6720,5214,55283,7386,3978
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81033,7466,22933,2888,1182,2591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5228,9365,55283,491,493,35
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 137994,64788,1019,84705,847,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5291,1471,26191,5214,3700,4976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55902,3948,3934,3482,5068,3458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10524,3596,3991,10874,152078,79644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3557,132158,7252,5373,540,492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2161,91647,91942,55788,84889,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3460,5105,6513,51604,4524,27010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,2786,8722,196385,2776,347411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5257,1557,114814,2947,9919,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2793,1843,1594,490,9021,183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4035,200539,2161,23395,1348,5770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1027,9374,84061,5194,5188,11096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3034,51604,2678,57570,1813,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11131,570,113235,5053,5255,1435
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 640,517,3375,183,2487,4846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54600,9779,3708,292,1028,1244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4049,1812,407008,1376,140803,2155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6929,51083,7409,285126,85365,1558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,2695,11095,4878,35,10226
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5473,26354,1361,5315,84300,4023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79144,2729,1716,3685,6263,5592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2203,1738,7098,3356,8560,9415
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 199,5009,2904,1393,5293,5467
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4654,5213,793,5792,4247,79572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4502,491,2948,5329,2335,197
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3978,3638,219,1621,10243,7157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5805,64241,4878,491,27429,55937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10159,9560,1401,18,582,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10667,1607,1075,5207,5161,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,79644,84833,212,19,85479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,5743,8932,2984,52,3643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3658,3251,3240,189,79087,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5562,2896,1815,1392,4285,1230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81689,1369,407040,6390,3425,8743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55699,8642,1347,81033,8932,8862
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91942,476,1581,406934,9388,23543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,54798,57128,5313,29881,6248
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56623,10229,4256,84705,79934,1355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2937,29960,79053,51611,6329,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 686,1175,79736,55283,4779,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3290,5345,4718,9969,940,1672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1444,1544,3692,8942,2584,26521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,9056,7480,8818,11132,330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3551,9969,2110,6339,1230,654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 199,6579,123,10599,51082,25839
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2244,2776,686,5052,5306,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388585,3992,6890,4925,2591,197131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3667,407010,83439,9409,1394,3651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 581,5207,51081,5971,5069,2702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54802,116085,158,4780,1956,2784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53335,4718,5276,10524,25813,6582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,85479,3295,84334,793,23530
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,22933,5621,3875,2266,56052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,54915,3091,56923,8309,1346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84947,7386,50814,7076,137682,1442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3077,87178,2063,6354,7030,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22978,1203,1537,51099,55768,3295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5830,1409,9698,56652,3559,4728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1353,79796,11035,4967,7347,6339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10383,2180,8660,5270,10013,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5315,57678,91869,92667,58528,5595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5078,10537,1175,388,123099,5837
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,132158,389692,51660,51144,153642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1234,2271,1019,80070,2944,388372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6556,387787,4159,3293,1606,3113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 350,3636,340024,55967,51206,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89866,729238,3115,8743,6389,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4864,79587,5315,23304,83439,5826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7292,51079,60528,1789,1585,316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91869,29947,152078,125988,84705,92609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1072,3795,7385,7040,8473,2495
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5306,112817,4864,2688,7494,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1514,407004,1544,7422,28958,6439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8560,409,1080,1244,90480,10382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27344,5787,6716,7248,8050,9365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2717,8560,7100,80207,1027,8813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 291,1555,51176,1992,10686,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,3980,79087,55858,54896,768239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6403,15,3295,729230,4887,506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5228,538,25813,6898,54901,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29926,1268,18,81704,219,513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2904,150379,5270,3954,2328,3558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 836,1644,1353,5053,2903,2159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,10295,84572,3700,7431,5288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7099,3417,513,4715,6868,51293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6789,1471,2760,2876,201305,3115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57620,5167,2308,5506,185,4712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8675,27141,51128,4594,341,8854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5515,3939,55024,63931,5631,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5255,2305,9663,2115,788,84701
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55503,6462,6445,6476,55768,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84706,2628,643181,151306,3779,1557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 405,10165,10599,54675,5293,79053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4358,169026,1595,3489,4285,492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6934,6868,9559,9698,2696,7915
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
115.549 2.389 118.136
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.667 | 0.024 | 0.851 | |