Mustafa Erhan Ozer
| Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 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 2025-09-25 12:06 -0400 (Thu, 25 Sep 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" | 4831 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4618 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
| 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 2136/2334 | 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. |
| Package: SVMDO |
| Version: 1.9.0 |
| 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_1.9.0.tar.gz |
| StartedAt: 2025-09-25 00:38:32 -0400 (Thu, 25 Sep 2025) |
| EndedAt: 2025-09-25 00:44:13 -0400 (Thu, 25 Sep 2025) |
| EllapsedTime: 341.5 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.9.0’
* 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 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 ‘1.9.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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: 1185,406934,4311,6536,388585,255231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55699,2101,5243,3033,8879,6714
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,7424,2890,54704,26354,212
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5962,25821,2998,5745,158,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3291,2696,2903,1557,587,51144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4886,407006,3304,211,7319,4351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5594,65985,154,43,4313,959
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5207,496,2597,9479,84447,9927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2876,57570,1807,9997,2806,492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10383,124976,4729,7037,3375,728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4609,10013,4137,26088,6938,5447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5329,79783,5584,2280,8841,51241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 150379,2697,23410,1019,153,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5702,3954,5730,6897,5798,1327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5465,1581,3554,8932,5230,54806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,10243,169026,249,4149,5295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407011,2524,6714,1869,10991,5078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5631,84274,54539,7372,3480,3172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4358,2110,2948,3155,84701,37
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8813,293,23395,9779,2517,5293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 239,10250,10730,6262,3290,2760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 432369,1594,10537,3692,2118,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5270,6891,212,265,5409,6934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7355,79144,3034,6602,3978,729230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6505,26291,213,1644,2834,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6833,275,5595,4548,221458,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 213,212,51085,79001,11213,582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353,5295,7376,3558,6770,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1277,2155,3554,79949,2653,11019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51649,125170,1555,79949,6564,231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5327,2247,5962,56919,57678,84340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64788,23516,3562,2328,793,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 291,7840,26503,4694,1890,6927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3145,275,84334,51316,51293,63931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4728,9365,2632,200810,2677,858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,23291,55788,5594,81033,1893
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5373,4843,80347,64601,551,8678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1581,140803,84317,79068,2516,6402
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 326625,2597,1056,345,2739,1607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4358,4702,4728,2539,283120,7274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5950,23753,3554,1601,2712,6775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3170,5799,4669,326625,10935,191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23062,4700,1339,10159,3290,4878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5584,10999,7391,2180,11035,345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6236,886,51601,123,6401,5239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5617,23129,65985,9971,5194,513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79572,842,364,11232,4656,432369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29881,2694,6382,126328,858,3712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79572,5243,10457,2109,9131,1490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51024,4144,91452,387787,4351,133522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388372,2266,6897,406913,7225,389692
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3030,6522,10857,137682,57107,2314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100529063,3141,4337,2099,116085,779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5306,3087,80347,1737,6770,1230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,5256,5265,4720,825,1757
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27125,138050,5972,3073,55818,844
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153,35,4299,5175,4023,79572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5740,3065,4779,55818,6891,57107
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,9415,133522,64919,4143,10667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6356,406922,486,10999,28234,9095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5367,2646,2305,23590,1392,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3123,51116,4716,886,3684,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729230,359,7076,6720,3357,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353500,107075310,79731,51300,57511,5364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3483,2244,130120,5476,6576,1027
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1352,84340,4286,1182,5727,2767
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10965,2632,7038,81033,1116,116228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 199,4803,2653,9672,26227,10059
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5901,54982,5860,2792,407024,26175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,158,169792,6576,7352,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2642,54931,4654,7941,2752,3062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1340,54896,2099,1992,137682,5824
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2787,2677,846,11231,2158,133522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2592,6009,384,5122,4860,5192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9370,5315,283120,9380,5644,64900
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,2101,3899,6582,685,4548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79736,8802,65080,5406,5105,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51083,1646,5184,477,63892,492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6938,7052,4846,10008,104,1149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4780,124976,5321,790,2118,463
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 48,2638,84902,7390,199,4351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84833,22933,2739,6248,79661,596
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54476,5288,4709,847,6748,118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6609,7431,1072,1201,8504,2998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54806,3710,10382,8659,27232,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3304,5331,107075310,5744,6748,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 216,9968,2948,8517,51300,181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1524,2152,1589,208,285126,1234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 145264,90480,54331,10013,124454,28234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,84557,940,8604,56922,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2767,155,6571,4351,2628,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4543,4125,1444,219,5828,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54575,3784,81034,4654,6389,8471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51241,2835,55486,627,57818,23753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,2495,1468,1956,347411,3339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2805,253943,3759,3117,3351,5213
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,5126,23163,4683,23753,23175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2592,7840,3066,776,795,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 999,51649,629,79133,388962,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,1436,54576,57104,51604,3784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,2247,201305,55937,55037,384
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64805,2169,5789,56922,5584,8945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80070,4285,3382,2834,5406,406937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3034,351,406938,5971,2157,6521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,570,56945,3073,356,6716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1806,84947,3295,6515,85446,4982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5330,5950,5370,79934,1815,3795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,359,2694,10991,4159,23543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 126328,7941,7422,7384,4697,1591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79587,211,51128,57380,84701,51082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1361,5295,151,462,340024,185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 558,1339,134,1559,26003,5837
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6794,868,116931,1621,19,563
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,4702,1605,3930,5592,51081
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3073,7372,7840,5499,80339,115286
--> return NULL...
2025-09-25 00:44:03.540 R[89499:375405095] XType: com.apple.fonts is not accessible.
2025-09-25 00:44:03.540 R[89499:375405095] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
66.259 1.429 68.415
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.787 | 0.042 | 1.161 | |