Mustafa Erhan Ozer
| Snapshot Date: 2025-10-15 13:45 -0400 (Wed, 15 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 2025-10-16 12:08 -0400 (Thu, 16 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" | 4867 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4655 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4600 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
| 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 12.7.6 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: 2025-10-14 13:26:49 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 13:33:58 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 428.6 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: 8471,100529063,92483,1859,2260,151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1558,6901,27329,56729,3717,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54798,434,3030,857,9630,1738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 256471,23129,84947,5781,857,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387082,1514,10599,3485,6833,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,1075,83884,2303,10938,3145
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 154,84447,4524,53345,4878,6901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56945,84334,2271,490,4000,3242
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7056,3122,197131,496,170302,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1789,10013,11035,1268,10599,5105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4233,5442,161247,5078,11093,6833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1345,1443,4695,3073,8050,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5967,64801,23543,54805,10062,90865
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3174,57017,123,1593,2984,7389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51103,8639,2157,347411,2717,55753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79731,3948,3290,10999,5799,54675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11222,54476,4502,51422,2053,6565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56923,2147,83693,293,5071,3283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6351,26060,10423,2571,132158,4694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,5161,7287,84902,5122,1282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9630,4023,26503,54331,1208,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3251,9445,29929,2170,5188,123099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100529063,51119,5741,1056,2632,3570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1716,2673,55970,1116,488,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1802,358,3123,7840,3480,293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22820,5167,51,8714,432369,2157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,2348,2785,55858,406922,57128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,1607,3952,4288,2310,1356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5443,6352,10938,7057,5728,6720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6897,3638,1493,7384,3990,2642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84239,22933,6794,355,5581,2052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 516,5740,5506,558,2729,208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6341,26119,407010,57380,23389,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3995,824,655,5444,5826,4314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6338,490,5740,387082,84701,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79661,1182,6462,43,728,6775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55005,2309,7384,150379,367,10999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22901,2948,51176,229,5967,2713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 105372280,1950,2745,5230,10128,122961
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6834,5176,5950,7372,1329,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4695,1595,1956,5798,509,10842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,338328,5499,4968,7036,153642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60528,92609,2697,27344,4852,10094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4149,4627,23417,1629,56922,55526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7350,3308,7431,10911,5345,55750
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10682,1798,5194,9374,1363,79644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2063,80339,51167,9414,868,326625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,1075,80347,2752,1371,6772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1203,51117,84300,10382,10229,2791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4899,54675,9091,7287,2542,4285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51103,1186,3308,3779,5162,7347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1581,5950,2590,518,3479,1786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,10559,1185,1312,3953,4852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5295,1234,51458,387,640,1555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3101,7422,8473,477,54577,6382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,3685,652,55902,2745,6569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7220,4282,2159,358,2310,5207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3953,406934,5167,3489,285126,26517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,28234,5617,100506742,1807,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4143,203,10559,952,8862,9388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91942,7048,10577,148979,3032,6928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 516,4012,7297,92935,10667,4724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3098,2643,57620,153642,79944,23409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,27344,388372,115286,3098,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,54798,29947,55503,92935,374291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51081,1471,728,152926,2052,3930
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2052,84706,186,22901,6772,55503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4988,2591,1968,498,151306,221458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7352,9091,3162,9692,2308,25974
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5562,50506,7099,133396,84557,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 549,4854,407011,54675,4089,2100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3351,58528,54798,191,7386,5618
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25828,51611,11136,154,9380,490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90865,5276,6347,2266,6999,3813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6492,131118,1591,2158,1909,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3482,4143,80347,51099,57678,1493
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23409,948,3283,6720,25974,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51601,1352,4627,7284,6263,7494
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7252,239,1080,4790,8651,434
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3066,2052,9091,347411,105372280,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7345,55753,155,84705,152926,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55283,4502,29968,10875,3312,2990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,490,7428,2946,5331,4716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7078,80070,5139,118,5781,85479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51144,80224,4942,7295,2767,1339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285126,1075,34,1678,5213,56922
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,28957,3062,6925,216,292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,51144,857,79572,3728,3375
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2653,138050,210,51079,10842,1956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57085,10383,29968,11136,5194,7040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 513,407004,3123,80267,3489,114548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4790,54539,5971,84317,201595,8803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5313,1582,5562,2934,51176,1468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6352,1803,4712,200810,57570,84693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728,5515,6714,11231,388962,79949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9672,2629,8818,374291,4306,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3098,2638,8932,2785,6868,85479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5277,6448,5824,7388,471,27232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,387787,2934,4286,8471,513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,2890,212,644974,929,2110
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,788,4720,89874,2752,3606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1641,3565,4744,51241,54805,23274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3485,7320,32,115286,28234,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60528,56302,471,4760,10599,1537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64087,4035,3073,338328,2792,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5295,138050,844,2159,50814,7325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 999,140803,183,2118,4000,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9374,4153,7841,84239,28951,1356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91869,123263,65985,4247,364,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1182,7421,58528,50484,4714,87178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2767,15,2642,9927,83548,471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 952,4654,3482,6579,5265,5321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7172,958,26175,6392,1497,388372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4149,5288,840,23304,2908,4780
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 205327,87178,3156,54567,4137,11255
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
77.669 1.722 79.769
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.733 | 0.027 | 0.999 | |