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 11:39 -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: /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_1.8.0.tar.gz |
| StartedAt: 2025-10-14 11:22:36 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 11:34:03 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 687.2 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SVMDO.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.8.0’
* 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 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 ‘1.8.0’ ** 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 RC (2025-06-05 r88288) -- "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: 10094,80222,653509,9241,3673,2992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 411,4851,1352,3875,768239,3813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653509,355,3054,1595,3784,4722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6908,6248,5053,8813,1327,487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9560,203,5442,283459,8195,64689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5009,8651,7274,5365,7048,582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 359,51181,25915,8639,79001,10938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5270,6347,8195,150,551,5728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353500,83439,93587,51660,51117,388372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9919,55768,2693,617,2904,7284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9479,8854,54798,3978,51103,55486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,22796,4311,6535,2643,7035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81704,63874,3242,5498,1353,4125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4702,7287,2152,8818,1340,4889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7289,7097,6352,79133,130589,7351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,549,1906,388962,1071,5274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4684,5798,2099,694,6901,51204
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 35,2642,10295,55503,10062,3375
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27249,2271,406938,2147,29947,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133396,2720,7424,6556,56652,5230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 427,51144,90480,10116,3308,28976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1728,6319,2919,7037,7919,2760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5830,3482,4144,23062,10537,493753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407040,27344,7018,9672,407011,6347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 166785,2713,8879,55753,84947,2834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51206,217,113235,6868,26060,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 572,4851,4758,6932,175,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4878,5019,5740,100529063,1843,6678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,3440,5584,151306,84557,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3283,50943,4351,186,407007,10008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4153,9969,150,9498,7297,56052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2678,3383,4125,100303755,3939,4846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5264,10457,5191,7276,3638,5009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 326625,1581,7056,1509,23304,5787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130589,53346,57128,2641,80201,3423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2729,2950,89866,5836,435,1444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10159,54806,1786,8854,9997,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,55037,1634,1175,6775,3710
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 517,256471,203068,4035,5264,23291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54806,411,33,51167,356,80207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5409,388,655,54210,79133,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3767,9180,2539,51144,2063,80222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2919,256471,2582,11095,5091,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6536,5792,1608,10102,54968,80270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4312,4695,84239,2158,84947,10686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79796,2305,55037,23395,32,4729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23417,51099,4716,241,686,3099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,2108,7172,952,1769,2305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 359,3309,79087,10000,3304,64241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7372,776,790955,56923,5594,5743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10457,27247,51204,9021,3486,795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4716,217,8471,11213,2784,7391
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,79144,56997,2147,5161,6519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5644,824,2792,5264,200539,5971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11019,9377,57511,5019,514,6888
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6339,1369,7480,3283,51099,115286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644096,5428,54802,23530,239,211
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1019,7345,7376,3576,57761,3600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5789,5444,9241,7124,476,1906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4702,131118,84275,2834,123283,3700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55005,221458,6584,7320,8694,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2946,84693,653509,160287,1352,4128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51117,51021,5364,2731,632,2169
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6248,339,1471,5195,6908,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3440,6932,9559,1232,1909,7480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,1443,6716,846,517,6391
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10991,158,4744,50506,65985,1968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2908,131118,2524,23556,1992,1544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2712,2639,685,155,5409,7038
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,79602,208,27235,6009,29881
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8642,2739,9868,1409,118,2200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,563,51103,356,4118,9409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5594,4925,79783,401,9180,57104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407021,6678,6492,79087,84274,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8714,51478,1544,5370,125988,2984
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,2934,5625,5214,1394,6009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4040,4118,10423,26003,875,3251
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100131801,28951,729238,1634,1327,64116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100,4968,7480,1906,4040,6351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3795,1499,7916,387787,1769,84334
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2717,4609,9526,51738,335,91942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6571,4852,51649,5740,2395,27125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151306,3423,5406,435,124976,199
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5618,1559,2115,27249,4306,5654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80070,572,5950,6448,80224,9131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,285126,200539,8504,3458,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92609,6519,5250,4656,23516,7052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,152926,654,203859,1185,6582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100128525,3034,6564,2702,158,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4160,353500,2683,4982,5824,1644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 221458,11254,26060,1812,5562,7431
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,488,54805,340024,6248,115286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57176,406982,4524,23304,653,6571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2713,5053,8694,847,655,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3930,9380,6714,55967,3709,7350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28957,10938,10642,7350,3482,3065
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,5727,151,25839,10316,514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10250,432369,29880,9971,1586,54567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,5193,5444,1232,132158,1393
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,189,51128,2305,124454,126328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5727,23411,91942,177,3991,11136
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 857,9054,64131,79633,1645,5950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5214,617,231,6521,3375,836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 186,7220,285126,79644,5445,6391
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1027,563,29968,7372,10135,1581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54575,2064,1230,2752,64689,90480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,183,7466,7276,656,84947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 38,656,3920,83548,3779,51099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,3645,640,4722,5830,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80224,8694,640,567,51293,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6714,1634,493,5584,7351,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 339,6833,35,90865,3953,5781
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7916,55331,57818,2517,1401,114814
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 196385,948,91452,1201,92935,9180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1544,51144,406991,4695,153642,1401
--> return NULL...
2025-10-14 11:33:50.314 R[21876:8174047] XType: com.apple.fonts is not accessible.
2025-10-14 11:33:50.315 R[21876:8174047] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
176.393 2.333 182.955
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 1.268 | 0.067 | 2.030 | |