Mustafa Erhan Ozer
| Snapshot Date: 2025-12-05 13:40 -0500 (Fri, 05 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 2025-12-06 11:35 -0500 (Sat, 06 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SVMDO_1.11.0.tar.gz |
| StartedAt: 2025-12-06 04:38:43 -0500 (Sat, 06 Dec 2025) |
| EndedAt: 2025-12-06 04:46:17 -0500 (Sat, 06 Dec 2025) |
| EllapsedTime: 454.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SVMDO_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SVMDO.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
SVMDO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SVMDO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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: 4855,1968,80201,291,50943,84342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,23175,6536,55858,3728,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,9945,84274,150,53335,308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9365,2235,64432,10229,388372,325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,4852,54205,100,885,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,50484,51021,4351,51422,582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,4705,51478,6925,8714,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3953,6648,4149,583,1200,138050
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1339,64432,6678,1027,1803,2559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 275,2936,5054,5176,1559,4040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3795,642489,5068,51176,55750,5588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5580,153642,3759,84649,10062,80347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1028,338,2303,2119,22820,4282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11019,43,6786,3159,5409,6647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2524,3606,51204,7077,7054,10874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8560,8879,1363,51649,51660,51144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25828,6341,8660,6351,23600,406937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23600,64241,29880,1182,54344,5592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,124976,2729,1558,27247,55863
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2778,5257,10911,57511,105372280,84340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,1435,4286,5781,54344,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347,4828,999,10599,2946,4524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2937,6517,4000,7295,8862,7052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203,55186,55768,3312,7297,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,79796,1116,5837,10842,406913
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8642,4049,11213,55858,5473,5345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6934,4700,5315,567,32,3382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1798,2155,1585,347411,9868,7025
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5592,183,54578,6351,23411,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,55034,2260,1605,57215,3645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,5631,4125,3551,83693,64788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,1869,54205,3295,2588,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,10857,471,5618,2937,216
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54931,5255,941,388372,132158,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3117,353500,162417,3284,10524,1734
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3945,1608,4312,2119,7040,2936
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2729,407009,80207,1182,4803,9091
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29843,374291,4502,9409,121268,81033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4299,2804,1185,3115,10195,1543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2587,10229,3157,3087,5581,567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9377,10383,2063,2678,80347,2200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6356,5581,4232,4126,2937,6374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,516,51300,84572,54344,283120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 793,83985,1571,1950,56729,27141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1208,51181,142,208,8772,6775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2006,185,186,5501,5315,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5967,1353,1789,5373,1646,10128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5538,376497,10724,5498,57511,51293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56302,5901,79585,50484,8675,1537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 594,50484,166785,10643,8714,10842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3717,10753,8803,55863,1347,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 107075310,3308,56606,54552,1345,156
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11254,51119,79644,1234,7076,60386
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55037,6383,7132,9968,54896,407006
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,7528,2717,35,148738,1607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3624,54331,8942,2729,23556,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3295,3115,51241,6571,211,6901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4887,3383,7386,8243,6519,25813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148738,5713,3551,27329,10102,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64087,9076,1571,79633,5631,100303755
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55024,5967,3351,4358,1571,3978
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4311,718,694,205327,2767,124976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6565,79587,367,6775,3630,79633
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 150379,4357,391051,4543,9559,100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 18,5467,3145,2740,5805,3066
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29968,51555,5744,8600,5331,1393
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5581,64788,388372,56652,351,5139
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84833,26060,8802,5009,51083,90865
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8722,5588,54896,5580,5447,3423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 540,5744,6521,341,51167,50506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84062,10577,788,26291,2487,5601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,8567,3373,4337,4524,5230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2984,51103,9663,79944,9969,1471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 275,4137,2155,3174,6565,6387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,2752,50814,54809,51082,148738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51608,57001,411,10580,84342,1268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89866,54205,123,1803,3123,2878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7077,10379,10019,1340,11035,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406922,10686,2799,7424,4594,54675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85569,51608,4967,2271,8813,123283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79934,51081,186,3667,5826,2937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9607,4314,5592,24147,4976,55163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84693,8243,6576,54210,5498,25828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2310,22978,54896,4709,3081,948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9498,3569,2937,6678,23530,10667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6198,4968,3673,2548,7052,6199
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,84275,8642,200810,23038,132001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4842,790,51092,6929,1621,2767
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3034,6715,3703,574447,211,348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4714,27125,10020,5428,6339,8560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91647,1859,8660,2166,6678,5189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,795,479,266,10875,83548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3710,563,6932,2984,5191,116150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11222,7172,1893,7052,6464,60386
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 335,6392,3356,10243,4889,11222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,55970,2646,3483,7018,728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,10269,3250,57620,10008,2170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56923,151,2645,79949,22978,3113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,4715,6616,54802,5329,407007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5264,4780,6576,4351,200810,4723
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388743,2597,57001,3339,7056,266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91949,7157,11222,2548,8567,367
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,2588,64087,10577,2702,2805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28958,10891,1636,587,125988,5654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3329,11035,51176,10599,54805,51083
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5584,5211,84705,6403,2161,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,7100,51300,64116,6263,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,2034,6579,857,6519,9365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10159,2642,7941,6714,728294,2101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79602,2740,2110,51601,23410,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4716,85479,1581,440503,64116,200186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80267,2487,10686,2159,4137,2673
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 941,2587,4729,79934,5741,3934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1716,4357,10682,54578,7297,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,79087,407021,64241,87178,1646
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
215.158 2.528 217.852
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.696 | 0.070 | 3.682 | |