Mustafa Erhan Ozer
| Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: 7851a60 |
| git_last_commit_date: 2025-04-15 13:15:07 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-11 12:07 -0400 (Sat, 11 Oct 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" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 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 2148/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.9.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SVMDO |
| Version: 1.9.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SVMDO_1.9.0.tar.gz |
| StartedAt: 2025-10-10 14:24:41 -0000 (Fri, 10 Oct 2025) |
| EndedAt: 2025-10-10 14:32:41 -0000 (Fri, 10 Oct 2025) |
| EllapsedTime: 480.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SVMDO_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.9.0’
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.9.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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: 788,7879,8504,7019,29078,51608
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9927,1557,10667,37,2542,1910
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5825,152926,2100,4288,81033,3382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1277,51181,57048,51004,56259,656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4598,2475,406934,479,26762,3242
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,471,116228,959,10226,406991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 941,85446,496,858,4285,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2030,432369,55858,10243,4724,6789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10891,57017,6566,4715,241,3636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55270,57107,119559,151306,5406,175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27329,563,8862,629,57107,3290
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,54106,9409,2244,2645,10935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653,2487,5122,6550,131118,133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5372,929,100506742,5189,119559,629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1351,57085,51548,3458,89874,8665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5837,84300,81034,8862,60528,63931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6261,3242,54809,2876,2628,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4851,2584,1890,3082,2697,11222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7515,166785,5175,2064,10724,3598
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3351,5288,551,383,2944,729238
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5228,4144,5590,53632,4967,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7384,25828,4853,64900,4669,7466
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,5370,1268,51024,4842,9021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,2590,5654,265,22852,3779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55753,3101,10195,7289,7287,79087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1581,2235,10020,255231,3920,5105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2643,1468,2303,56997,2697,2752
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4700,6786,1281,229,57048,3931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406934,65993,4125,3684,3293,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,54539,7412,7276,100506742,5792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80331,2584,5501,5468,151,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2702,2235,4049,55037,11095,221458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51103,8932,582,26003,10062,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22933,5618,1585,7099,3952,5925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,405,5053,60386,4720,1672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64131,811,2314,7347,1270,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1340,10524,7391,3373,517,4069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7528,5970,4855,79736,384,64432
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8743,1277,5345,4846,27329,5445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4306,2645,5069,836,5194,57128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 345,26762,85446,100,1352,1353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51458,6888,4299,3251,10935,5506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1645,8722,5211,51052,1393,5069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,4879,8945,79736,2786,3554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353500,51458,89866,4049,706,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9388,9056,2587,5211,55532,92609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54106,8842,2952,3692,63892,6897
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347,7048,2673,1629,1718,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,2581,79001,6261,5330,150379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4149,7428,65993,91452,200205,26088
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51144,51300,4758,5727,2587,1347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81704,2052,54578,6821,84239,51004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,10891,55034,5167,23654,5291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55037,4886,2689,8473,23556,2099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1869,1080,1645,10195,7048,84706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1072,3293,34,221935,140803,27247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5189,9759,1201,29960,2890,999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51083,7284,4760,1329,5193,23753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53632,2064,840,350,3779,5644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11136,2303,133522,54968,1080,4744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3375,200539,7248,347,54575,7287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8473,2591,55937,999,51081,56923
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5617,2119,3251,147007,56623,9663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5428,6938,2597,26354,5211,55699
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11255,6389,3339,79144,10159,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1348,7056,3417,53346,50943,10730
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57380,23304,64601,3651,26354,54805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7384,2147,23054,80207,2539,57001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,8604,518,462,3773,10382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4069,4149,4118,57085,728,440138
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5444,2056,2335,51103,5286,2834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27429,3480,100131801,3458,5095,64689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 492,7220,708,795,6390,27089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203859,6868,1906,5728,84889,7325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50484,27429,56999,27089,3356,3082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,10159,7025,10229,1734,57192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6347,79158,10842,1244,26521,2348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51128,6182,434,3485,54802,3931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4722,2776,2696,3423,8799,6772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,3958,1232,53345,293,7840
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100131801,22868,10857,3383,3098,5444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2992,2303,83439,4852,1956,1769
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4143,8604,6392,197322,1558,3170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2244,2791,4719,2689,840,60386
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7077,1806,9572,537,79144,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406906,100131801,25821,7389,3988,5295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6794,6584,2487,55340,55278,344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3930,8932,5467,10935,1584,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152926,3952,199,351,201595,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5499,8675,7284,29078,11232,388743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148979,51555,32,51103,22933,407045
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 345,51116,1588,54931,3242,285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5175,388743,3991,5373,56652,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26517,563,158,3557,123,79087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2791,1373,55163,344,7841,54331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4153,7412,7351,79944,4502,3600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130589,4594,7325,9969,10644,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9409,3479,7942,29960,26175,5595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9420,3482,55503,1268,9021,4709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 138050,2108,7355,11232,2835,6571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57085,1471,3645,5250,129787,7052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347,38,7054,7412,1356,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51604,5625,2835,8862,1369,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,5214,3795,1027,80201,6721
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 885,5365,11255,92667,391051,498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 210,2740,2919,1968,3159,6198
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,6522,5288,3123,2932,7038
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,186,840,3938,1557,6464
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 632,2678,7297,6339,886,6492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,5192,2053,132158,5428,4548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1019,56259,229,5313,55863,23556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3440,80224,3101,150,406922,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,11136,57620,51083,5498,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84987,60528,142,7100,56997,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23129,6748,6786,7132,8803,92609
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
74.236 1.857 105.368
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.774 | 0.012 | 1.713 | |