Mustafa Erhan Ozer
| Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 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 2025-12-22 12:05 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4883 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 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. |
| Package: SVMDO |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.10.0.tar.gz |
| StartedAt: 2025-12-19 12:31:10 -0500 (Fri, 19 Dec 2025) |
| EndedAt: 2025-12-19 12:41:15 -0500 (Fri, 19 Dec 2025) |
| EllapsedTime: 604.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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: 5329,2314,4828,10128,1270,445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6616,51119,5184,1607,4153,330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5563,3791,9607,3099,10226,2992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5275,3645,29929,178,124454,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5727,5228,6789,4976,27125,4704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5970,2629,8694,1409,640,5824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1175,824,54600,197,406913,2677
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,4700,4851,4256,80224,4541
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123263,3098,210,5250,64241,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 587,51081,7376,79944,1080,199
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,629,92667,2908,5250,3708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2864,54575,8408,1893,2303,1802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1355,7030,952,4541,2034,4843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10229,142,23590,941,83884,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,7320,8050,6772,387787,7942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 121268,7052,85569,5162,4718,7528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26521,1409,116931,51738,5445,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60684,729238,5194,847,55788,387787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,2798,1757,23054,10379,653
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84300,1022,847,2591,201305,4338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51608,84833,29929,54931,84275,2495
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,3073,2888,26275,4524,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8309,7036,10008,89777,27232,3082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,3643,7289,5268,344,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 383,1281,57085,2581,1869,3309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116519,147968,80270,5654,2778,55340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4718,2710,6462,5211,5646,7515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8802,3930,197,55630,6696,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2804,445,2099,10965,57570,1738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4728,6324,432369,5313,196385,2693
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57017,9382,1586,51117,6445,407004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7466,79949,54539,7389,51300,178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30061,50814,427,3651,26235,10599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,10195,3293,130120,7412,10560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10580,4702,8945,406906,498,2689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91647,3773,3482,407021,3813,23062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1605,9131,147968,3141,688,388585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51181,4544,2878,51085,7941,5228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55753,5069,4860,728,1675,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3779,284958,3375,1348,3489,53632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2110,4716,1489,26521,4153,7450
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5799,3115,7078,3074,92609,384
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,10686,3949,2688,8710,57570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,2987,51604,5207,6515,3242
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 111,3295,6928,348,4023,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 558,585,6470,10019,54576,1584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,3558,7480,2194,407011,509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22901,9388,80339,92609,4886,1636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3667,253559,57678,3122,55630,87178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5188,796,3312,89778,1355,100506658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 351,4860,5562,5443,3489,54511
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4878,2786,6391,9095,2778,5313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,4726,2495,23129,5594,9997
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6696,9380,7276,2875,131118,5214
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60,51660,26503,406938,253943,6906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84701,3934,4502,819,64087,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3065,137682,91869,3425,4704,28951
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54331,10165,100128525,2559,2693,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,407010,4149,1369,2729,55630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 145264,9513,11019,89874,3458,51079
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51083,7040,207,8842,2146,6556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2745,3250,4548,498,54575,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1149,5019,3284,7515,7376,3099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4694,51085,54806,549,5330,617
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 128486,114548,7248,2987,89866,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 18,384,4724,7096,1346,2639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3784,10857,55699,3953,3034,8309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3460,4319,866,1497,391051,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 145264,80201,411,1281,55503,5925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6262,9575,293,5599,2678,160287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,3559,3054,2584,407007,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3562,10965,409,10935,728,2166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6932,2539,5069,2799,25839,440138
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54148,4524,8813,5194,55753,63931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 12,3101,8560,5372,84833,6770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92609,291,197322,6821,28957,83854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54896,5191,2934,51478,8743,1149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,5970,10667,241,2932,9969
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,140803,9607,8803,5078,9919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7386,10159,4089,23654,5161,9091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2784,11035,407024,161247,1116,6582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,11232,6382,7030,26354,476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 157848,6319,1471,5447,22978,79585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7376,181,8818,4864,7078,4843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22820,3373,2101,2113,1182,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,4537,10221,4886,152078,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2571,3489,56729,3155,3630,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 111,407011,6821,7389,1890,23516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203859,570,60684,10333,338821,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 654,283459,1208,133522,2629,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,28951,3291,440503,51103,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7284,3700,152078,11213,2538,2101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7840,6439,4285,3784,5019,25828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3636,9415,5370,410,959,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1340,335,89778,5184,9498,100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5971,358,54205,10000,6521,5571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10643,2785,27232,2876,170302,2539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406934,6901,7274,79633,84769,3673
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1757,8651,1608,1345,3929,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8560,5515,643181,9332,2194,4318
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6794,347411,1789,9692,284654,8678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 583,51167,1071,26060,5428,29928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2101,23530,11019,7431,867,5288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1593,3373,3507,406991,462,91949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2334,6402,5830,8694,6514,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51099,405,11213,2731,6929,177
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10316,2588,23556,79087,5306,5054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4684,2099,4843,5588,6602,3813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4502,3638,4540,51103,4232,5268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56997,599,4089,1734,6317,388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10295,2990,79087,3145,7225,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,1909,3992,6898,493753,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5211,1893,9945,123688,4314,129787
--> return NULL...
2025-12-19 12:41:01.547 R[82306:145240082] XType: com.apple.fonts is not accessible.
2025-12-19 12:41:01.548 R[82306:145240082] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
98.941 2.098 103.743
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 1.349 | 0.065 | 1.824 | |