##############################################################################
##############################################################################
###
### 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 4.4.0 RC (2024-04-16 r86468)
* 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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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: 5373,3728,7019,5967,486,4524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116931,5106,846,150,9807,8517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,6571,270,7852,8813,1369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5971,6272,10195,9498,53346,3106
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 155,1337,5476,119559,9437,5092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55937,355,10891,3033,9475,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3250,80267,1757,55572,9056,4843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3683,540,2690,347,84557,1345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 93587,376497,728294,27035,5106,137682
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53335,2582,2643,800,79053,1601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1807,10845,387,3157,1201,54902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,3577,885,3978,149461,27035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92609,3060,9382,4726,83854,6348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2731,1649,3032,2864,6530,5365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3600,3156,6576,1621,4826,10682
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2628,3991,6097,5108,8074,958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123,8560,189,3953,7098,215
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6720,51128,151306,3375,5970,3479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8462,4700,150,5313,3065,6715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 187,4338,10019,11232,79572,4171
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,152078,6526,2118,4852,200186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5236,55699,79796,7515,2949,2787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 210,3484,6523,124976,5449,80347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1394,11213,23706,10157,3295,7018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1588,5054,1118,51601,345,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 136259,509,2303,6441,79572,6492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5168,5161,100156321,64801,53335,2166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84705,6576,2309,5742,4151,4702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5184,3930,2793,686,5617,7100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8659,6901,54896,6915,51024,5325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8829,6716,3596,23400,4040,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4055,6833,5624,9104,7124,4705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,60386,2108,1337,5498,6183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1649,1113,191,51293,51660,640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57215,1182,6948,5798,2641,51
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4773,56606,10,6342,7226,1537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79644,8932,133522,1965,2695,1968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,1807,257313,6256,25805,7124
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26873,8473,10466,6447,3956,6248
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10269,1558,7291,2984,3439,283459
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27329,5286,10116,9409,2180,1606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 796,4055,1649,200205,8659,7292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5139,7345,1491,51024,2908,81570
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,8678,5743,6648,1786,401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,5828,7025,2677,1497,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 549,256297,2952,3423,10842,4880
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1594,2055,100125288,948,4846,5106
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10549,100131801,23118,6258,10062,3592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23576,3401,643387,80267,23436,9927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2200,80267,6522,2890,10295,6569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1906,1371,100132285,406906,5745,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3779,7220,6720,6288,56052,5313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57817,152926,170302,6343,1644,29843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2835,2746,3479,2739,79133,5788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7466,2903,4069,4702,8856,1585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2266,4704,4015,6602,256471,51738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5820,164656,5914,80142,9021,1956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200810,8691,56052,6526,6248,2678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,875,8659,94235,3558,2694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,5369,57085,823,51083,3502
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,1489,132,401,2056,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8462,130120,5971,81033,3117,3425
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7128,411,1807,9968,65018,1030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,64919,617,6097,10616,3767
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10400,325,1327,6821,22845,3572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9518,136259,6338,4567,27329,4803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5770,51458,3054,4744,53335,2932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 339,84705,940,54,6376,6915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,10457,114815,23436,55163,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7391,5792,55699,22877,1186,170302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4009,726,3576,467,2161,7137
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2752,55283,8431,4843,5730,920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2321,4591,5820,10845,3350,55885
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9927,28957,54600,5828,3938,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2950,4151,211,54575,51128,140803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1555,4311,2760,182,3162,6285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 207,27235,5315,2169,5053,1571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11213,7389,8742,51204,6392,355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9314,1182,8455,4171,10466,1361
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 51.455   1.174  52.607