##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SVMDO_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.5.0’
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘SVMDO’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
`shiny::dataTableOutput()` is deprecated as of shiny 1.8.1.
Please use `DT::DTOutput()` instead.
Since you have a suitable version of DT (>= v0.32.1), shiny::dataTableOutput() will automatically use DT::DTOutput() under-the-hood.
If this happens to break your app, set `options(shiny.legacy.datatable = TRUE)` to get the legacy datatable implementation (or `FALSE` to squelch this message).
See <https://rstudio.github.io/DT/shiny.html> for more information.
** 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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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: 7941,5306,1909,84300,10320,6555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3670,4255,3030,800,407009,1394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6584,3667,4214,9498,5970,1789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1339,9514,3615,50484,7225,435
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2110,3815,137682,80070,3043,506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7916,3676,7538,5054,5270,467
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51316,79796,332,7840,842,4015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,9518,8195,133,5805,2555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3501,2804,5919,102,136259,3423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1051,4521,2793,1588,2697,3312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2952,427,516,776,440503,3572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197322,1548,2739,23400,948,1509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3329,2524,3980,5914,2247,9255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1052,117289,79602,3816,5625,4683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4842,1555,11231,3417,9498,27035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2889,22845,2740,2852,23479,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,148979,64801,3949,3658,169792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,6311,51316,54539,114815,53947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 516,2739,9997,9759,6469,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,5296,4826,948,4312,2673
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80070,9377,203,1644,5160,2488
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64102,148713,114884,4151,155,1382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3762,2712,27141,3091,8604,7026
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,1234,5971,513,4321,493856
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3339,3768,84833,366,5745,239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 999,50484,6897,1608,6339,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2740,4714,51604,7137,4018,821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1593,3674,8829,5962,6007,1717
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100303755,10999,7139,7172,83854,7321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,514,2799,2055,2305,9514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,11136,22933,3623,1436,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,29881,53632,2693,64131,4914
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7528,181,6554,5261,3503,1392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10020,56945,63892,405,4535,6576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 581,7084,79796,55340,285848,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3394,5618,4567,6289,410,3075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55586,2593,51119,467,84063,8691
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8764,842,29851,1586,50484,7980
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,355,4868,54809,5962,56997
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26762,6948,2950,940,51167,4151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29929,191,64131,2244,1428,5586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100506742,5745,337,33,3934,4282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4017,10,943,2949,6390,551
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2180,1606,712,1573,1471,3938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3833,3551,1490,3557,2834,644096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8609,51094,3174,868,10250,5167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6232,9927,54344,3043,479,790955
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1591,8660,10166,635,4744,7355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7528,84987,858,4860,1601,1499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,9479,3596,4282,3081,5621
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7157,1910,60412,338328,5498,493753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4255,728642,5189,617,8659,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7177,3664,4627,1786,2260,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4208,3691,340706,3284,1443,3122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 205327,55768,8678,11231,3155,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5192,5369,26119,25813,6391,3949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6007,3054,51004,2068,2006,493753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 112817,138050,2954,149775,5968,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,57016,788,3099,5824,7407
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5837,57215,3043,9560,7167,2495
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2538,875,5364,104909134,840,4715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3574,10580,432369,5598,1678,4055
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 940,1605,4729,4125,1443,2271
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26088,83737,2767,1436,387082,2776
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4489,6721,2954,7507,2517,57001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3654,5236,1499,1050,5837,1066
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2147,2068,265,8665,6786,51703
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,5601,4089,23082,7276,1812
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9377,5563,9882,1594,5091,4153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3174,4017,4773,5662,6554,10999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9619,9882,3934,3502,4968,2936
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,729238,6383,629,2673,4760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 587,79949,3938,25801,6775,10857
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406982,4357,3312,6999,187,3033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3351,8600,10195,64772,54931,145741
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80309,1524,55805,3576,3623,2487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 656,5008,91869,10062,2055,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54539,3803,3623,1442,2542,5507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,4088,3156,797,3315,51316
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 52.726   0.997  53.714