Mustafa Erhan Ozer
| Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 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 2025-10-07 12:07 -0400 (Tue, 07 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" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
| 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 2143/2341 | 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: 2025-10-06 22:07:32 -0400 (Mon, 06 Oct 2025) |
| EndedAt: 2025-10-06 22:09:30 -0400 (Mon, 06 Oct 2025) |
| EllapsedTime: 118.5 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: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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-arm64/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: aarch64-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: 2864,9370,57192,9968,718,581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2200,56623,54576,2571,5962,1734
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56052,5069,790955,338,7428,5581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132158,6319,5265,51024,268,477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9374,5019,5741,10560,79944,25813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124976,79944,2806,149775,5080,1490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,7297,3115,10165,57620,3483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,84557,1582,650,51441,10382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8879,2998,100529063,655,3600,308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57511,205327,94235,5826,80270,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4716,178,3565,6402,54549,3554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1493,1629,1230,4744,2712,1347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3098,9868,4143,7078,79602,51021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4889,57511,4049,3482,3066,2739
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85446,1968,123,84833,940,219
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,3813,55818,4790,2056,4160
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7528,5291,590,581,4609,129787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,3098,133522,6566,2820,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84334,593,2847,63899,6901,3329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1859,652,1728,401,389692,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,51024,1608,57085,3251,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3978,55630,229,10466,113235,23291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,1786,2581,1022,8651,51181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57017,7421,1361,7284,1581,3663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3250,2786,1351,208,5618,5126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10842,3030,4709,2799,10352,5594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8678,4854,5054,2559,7040,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 594,435,1629,3980,3060,3074
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,7275,3709,490,5195,51119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4247,54600,87178,3576,5306,2646
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10243,388962,31,9131,51649,152078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5826,1489,255308,3284,11255,125988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151306,92667,2271,7471,210,26503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5592,4697,2109,5442,2628,56729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3312,498,1621,1672,308,2710
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 840,57215,4982,3784,1185,57505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 35,1543,57017,3170,2571,38
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1182,131118,406,4716,5370,3562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3115,1497,4683,92483,5053,11131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2628,5052,9388,291,2787,229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 181,551,51094,126328,3032,3358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8714,2587,10000,8517,1270,6789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5501,11095,4889,84693,518,84239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2194,56623,3066,3034,7390,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2184,3638,92483,574447,2203,5442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6602,6402,10891,6901,55343,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9380,5261,1738,7345,2642,3087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6341,23291,5189,6391,6383,156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4144,158,1586,7428,999,229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3290,2647,22796,26354,4311,160428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,440138,10682,284184,8842,348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1348,5255,440503,6522,51119,9104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,655,43,3490,10644,2799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493,123099,5581,1244,119559,2155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 432369,5255,6720,8648,107075310,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57176,5601,8694,486,583,8651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,347,7381,2646,411,729230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,3759,51079,4669,6519,1436
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388743,1801,10157,1312,1149,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3073,285362,3309,5625,940,2335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407024,114548,2792,2053,8879,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79572,26521,7422,84334,4726,4704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3460,29928,22978,4704,2548,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1678,84275,26503,125988,130589,351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79585,6389,3030,5789,3992,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 538,5329,64432,2947,6374,10135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1890,9076,650,51181,283459,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,795,7036,210,5498,3562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7840,112817,4704,5053,4729,51649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2847,1371,825,5096,101180976,10062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,28958,8431,84342,2806,5507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 958,3485,875,1394,1185,490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5367,6908,1890,445,582,6262
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2647,9945,9507,492,64788,10379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 19,5365,509,7351,54476,56923
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 43,51116,2271,4233,64689,5068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7390,1634,54805,6391,6609,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9498,1812,51422,84902,50814,27141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79736,10991,411,3553,63899,653509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 518,11035,183,493753,407040,338821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 587,1571,10580,2847,583,57128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 119559,85365,5971,5328,5770,23395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6390,793,23600,2641,4722,217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55863,9479,3630,8694,2588,3988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6401,3708,217,79158,4351,1185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2787,83854,350,768239,2244,55937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57001,7018,8567,3295,406906,5442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3174,133396,1717,6906,5250,6901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 538,4544,3988,22797,7381,7297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3931,3630,23417,2990,2348,5971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,3920,130589,5331,8431,1629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84572,1345,8862,29968,496,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,175,3357,2030,538,79796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 185,6329,4878,4988,5745,2745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2184,587,79944,6821,617,8665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6721,6696,6448,6786,2495,54802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 582,2053,7515,23409,2582,801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,213,3375,4247,7915,779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1889,7100,376497,51117,85476,3658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51024,2314,796,2919,3284,9414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64116,3170,2799,6774,51738,1718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9056,84701,10020,100130015,64689,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55670,6476,7466,80207,4803,5293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132001,55486,2673,91942,1650,9076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,9409,55343,2235,665,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,54704,7038,3416,4915,6721
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 138050,5191,768239,1116,409,6890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6248,5256,344,9131,1629,7515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1906,54578,958,4842,2760,2720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5618,4879,3309,64241,5625,150379
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2875,138050,8473,10062,5184,24147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5971,406913,10643,200539,3251,83884
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5644,2593,7099,3115,9498,81570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6535,7099,3240,2694,2643,27429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9971,3066,5288,50943,2888,1606
--> return NULL...
2025-10-06 22:09:27.357 R[79655:403595438] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
24.147 0.391 24.639
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.300 | 0.014 | 3.244 | |