Mustafa Erhan Ozer
| Snapshot Date: 2025-12-03 13:40 -0500 (Wed, 03 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: 2bc7e27 |
| git_last_commit_date: 2025-10-29 11:23:08 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-04 11:36 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 2137/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.11.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2025-12-04 03:31:47 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 03:34:03 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 136.2 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.11.0’
* 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/4.6-arm64/Resources/library’ * installing *source* package ‘SVMDO’ ... ** this is package ‘SVMDO’ version ‘1.11.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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: 8660,266,2184,64900,55331,434
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55186,407011,9759,338,653509,9076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3554,6890,4594,79731,28958,5009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3767,55970,599,4299,5579,100130015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5919,5364,801,3779,7421,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,54902,1401,2984,387082,4878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23530,5743,570,7494,10644,51081
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51,407011,498,1769,4716,5919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5590,590,2335,7942,407007,401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51608,2950,6579,10580,2548,4697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2119,84701,4889,4716,255231,203068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11019,1363,8659,7372,10008,5068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 31,3779,79053,2690,10226,79587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29947,6182,432369,55532,4688,5257
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,2950,57570,407010,51081,10094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4012,79783,8659,1801,7276,4035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728294,23411,3692,2310,5191,4968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5161,406913,8309,2949,6891,3978
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2804,1442,120227,1244,7052,6786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51079,5306,4878,28976,55644,6925
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 627,23409,63931,644974,84701,6928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3032,7388,4722,55532,859,51085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9451,1340,142,6648,9076,156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1869,2590,1327,2593,89866,50674
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,359,3490,55343,3480,183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11254,84705,5139,5184,1678,5723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3598,9630,10537,57048,89874,10891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9091,411,1992,2799,9663,6715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51079,152926,10019,3489,3624,2792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790,1992,123,4889,819,6389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4695,1950,5126,5594,37,3934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26003,8560,5498,3712,406991,8604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8462,7345,5286,2717,55037,4669
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,358,1443,1593,5601,3645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10845,694,83693,2834,2645,7450
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 166785,51611,24147,48,50507,477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64805,121268,4656,3954,9526,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6774,1582,166785,57104,23395,121268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10938,4524,10295,6928,1992,4128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 476,9759,8195,83548,1734,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 847,4502,5781,8462,1281,79776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,91869,3034,5315,8945,126328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2235,1801,347,79133,3710,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2110,3304,29880,9370,57017,9759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3486,11136,706,2729,80224,5579
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5970,5925,1608,7941,3123,10753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6182,55278,166785,4728,107075310,255738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5211,2305,642489,3489,492,7384
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 115286,23556,9672,54106,84987,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22978,3091,1509,6356,221935,2591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151306,594,4285,558,114814,1581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3440,4729,11232,15,142,6513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26088,10644,2791,2348,11096,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3486,590,79949,4143,124454,5745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1200,5329,155,55750,338328,627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7407,84447,6339,7097,2099,54902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84275,54902,6566,60684,3630,4306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3767,2946,4716,5444,9512,941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57817,7292,795,57761,118,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,4015,253559,4144,1346,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,23163,406922,9429,3949,593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,406937,1374,2805,216,27429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23600,1634,162417,5625,2052,9374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1537,4125,6383,6584,10243,4713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7498,2820,125988,6009,10269,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26088,388743,5330,10157,3483,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3155,3920,100303755,132001,353,54675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25839,347,121268,7480,2099,2642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84317,51548,65993,5276,3382,239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8462,125988,4159,3990,5195,23417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11222,6647,148979,26521,7347,1355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,1559,11222,8932,211,64801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3082,2495,2683,201305,5723,9672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,3559,4697,4889,153642,1584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50484,6354,2638,23129,51204,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23369,9507,5621,999,84987,5507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1717,51103,4358,10020,10642,7035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55750,3559,487,79587,5096,124976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,54915,29881,706,5364,3489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4887,6324,2280,116228,10128,1028
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6182,79736,51555,5207,5468,859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6548,51004,6402,10845,6476,210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10102,3557,5728,2597,1348,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51204,7471,7295,197,821,55270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2643,952,125170,229,5236,10221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3242,79736,338,5579,2100,2034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89866,51176,686,7295,3312,5288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26517,3351,10008,6183,6263,29078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,79944,2109,1355,5095,84987
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63931,5563,56999,113235,391051,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51083,6925,50674,3308,1080,6356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,3507,11093,593,6513,7054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201305,2584,249,367,5727,5787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91949,2328,64900,338,10102,6834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4143,55768,999,83854,4712,6770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104909134,1869,6774,5096,1374,54902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54331,7325,347,4722,293,4153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 119559,7480,341,2581,10382,1634
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,28957,2820,5167,387082,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7132,1605,7274,79585,6774,655
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1910,63899,6263,83439,55630,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51004,1583,34,57505,4012,6999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201305,4040,5571,2798,23530,24147
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5069,1738,4313,5068,1508,55186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,6531,54205,10842,4544,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5507,80270,3624,123283,56997,26521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9445,5328,590,1374,9507,27247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3284,406938,27089,729238,2784,2542
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3034,2740,4149,7390,2247,7274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4306,65080,2632,7841,728294,594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2591,4015,87178,4547,2203,18
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50484,51081,868,2896,8665,840
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56997,1594,23054,9388,5327,5321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6566,8879,3784,2335,26227,2628
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25839,55572,7225,84693,5919,55967
--> return NULL...
2025-12-04 03:33:59.004 R[24674:270700951] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
26.384 0.470 28.666
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.286 | 0.014 | 3.348 | |