Mustafa Erhan Ozer
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: RELEASE_3_21 |
| git_last_commit: 8259124 |
| git_last_commit_date: 2025-04-15 13:15:07 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 2139/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.8.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.8.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SVMDO_1.8.0.tar.gz |
| StartedAt: 2025-10-16 04:14:10 -0400 (Thu, 16 Oct 2025) |
| EndedAt: 2025-10-16 04:19:11 -0400 (Thu, 16 Oct 2025) |
| EllapsedTime: 301.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SVMDO_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.8.0’
* 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-3.21-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.8.0’ ** 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 (2025-06-13) -- "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: 4853,5365,1672,4125,208,10269
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6445,57128,197322,2688,81033,2799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7428,836,4282,3685,7450,3948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27344,23410,4760,1601,84902,221935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2788,3418,567,5743,4688,79087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5644,57215,356,1672,5745,5580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4312,5277,5579,496,5740,3383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1282,54902,5723,5744,6927,23543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 409,1435,51204,406906,284184,4159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5465,959,4035,3033,4656,3600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2629,51052,2157,138050,3291,1646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8743,6788,3291,7320,5498,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,5122,2875,132,7052,5255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,185,407009,10221,200539,292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2944,113235,81570,3283,123283,5745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1601,2791,3119,3290,4709,275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55486,5789,22845,3995,540,4968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,5071,5346,5588,55699,151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 440503,79585,5195,477,51144,9997
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5728,7376,391051,54575,150,8862
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7040,10537,811,11132,6649,123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1339,4722,7388,4719,114814,7056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,942,5078,6934,285,7040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1346,255308,51601,5126,1812,5369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1650,3418,56606,1409,9382,407021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1537,2034,7345,9370,1186,6342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,3507,5828,84447,486,6897
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6550,1859,57818,4126,2559,7942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79731,1337,3304,3383,2890,6338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,8722,5445,6536,4609,768239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,84061,685,160287,84693,51176
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 440138,90624,567,3920,26191,9241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7056,9779,2064,8854,2990,153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10841,1582,3480,6521,23411,51167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197,407007,151306,958,6554,2678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23395,406922,221935,8841,63874,4684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26060,10059,4705,113235,10842,90624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6584,9091,7124,440503,9526,513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1812,868,940,9409,3054,79949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84300,241,292,2937,3759,51119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,54331,1203,4357,85446,406991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1312,8517,1394,6402,1605,118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653509,940,9663,9997,3667,5321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84062,2847,5167,7840,1769,388743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6383,5315,477,350,3651,2166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6888,9927,5255,387787,5369,768239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10,112817,5167,2786,2335,124454
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2155,1329,8642,22852,1584,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4716,857,27235,91452,340024,1582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201595,5255,51021,79001,162417,353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4609,55937,6535,4694,5445,514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27089,9607,1373,6772,3952,51
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2280,5052,3557,34,128486,6521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10457,644096,5255,440138,1175,440503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7157,1071,11131,6774,79144,1789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9692,208,6550,8772,37,124454
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51116,9630,87178,3663,652,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116228,6891,2280,3308,8818,407010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,383,51099,2119,9382,389692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104,6263,55340,627,27247,3692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 330,9076,8642,63899,1468,4728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 389,2864,1186,6236,285848,706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3663,89866,6550,84701,150,4758
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5175,11213,7030,347,57107,5054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84557,1277,27232,367,2584,2890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5595,3174,3417,2247,8195,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 175,3157,84334,10382,9370,1468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,4160,6647,2593,54806,137994
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3773,590,479,7319,64919,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406938,1514,5728,4125,25821,3172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1401,5824,4669,26003,92667,10686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2762,2305,2335,1786,100128525,23369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3939,2266,3930,8462,406934,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,18,55572,617,23474,51241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,3486,160287,2950,51422,5327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 293,133,1337,4715,26354,3482
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 476,5207,8560,5629,4688,2548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6319,1230,7389,847,407007,1356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10842,4712,6263,84447,6356,23556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,3329,200810,1621,338328,84947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2784,4915,387787,2712,1601,509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387082,150,156,2180,3141,3304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10577,1028,89866,3295,7038,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5250,7424,2475,27344,10250,241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 208,801,2693,65985,2820,5365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 629,4319,1807,567,383,5195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152926,4683,6720,3357,2834,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79783,6198,5345,427,175,868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1149,1813,6515,4125,9076,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10599,5538,4886,2147,3074,2653
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8504,1889,293,347411,2170,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3708,7124,1028,90624,79087,1543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,5329,4722,4720,6720,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80331,685,2260,4712,2203,27429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 665,355,6564,3643,1369,55967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5315,1716,123099,79934,3174,2937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 491,80331,2115,2108,3099,5191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2180,929,197,1583,26227,128486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55037,100128525,1393,1956,6908,6789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1629,148738,434,119559,26119,1584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 640,79133,4552,1559,9559,7471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4089,7515,201595,256471,3416,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9607,10524,23530,10466,1376,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 840,55331,9445,51611,4256,4594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6898,4015,2643,229,5660,160287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 249,90480,51092,90624,407010,5618
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 336,9945,10891,50507,7381,166785
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,57761,2180,5428,2984,10457
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9445,255308,6908,9388,5579,84705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790,549,3458,200539,2571,2591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,6772,2752,5236,8818,2864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56945,5019,6351,8639,54575,153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5501,8642,156,10157,79633,57761
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3339,56652,2788,6678,6536,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3710,10062,9479,10938,5860,116085
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
64.912 1.025 66.081
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.702 | 0.131 | 4.013 | |