##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘1.4.0’
* 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-3.19-bioc/R/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 (2024-04-24) -- "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: 137682,63892,643181,4656,3811,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6382,5565,6093,54344,3425,5087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1646,29078,51181,6616,2798,8651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3482,7289,1029,768239,55526,1636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54968,2590,7480,6821,51079,712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29947,6287,2787,34,1019,4540
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4089,2271,4925,26191,5095,10457
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7291,5781,57818,28958,4988,5256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53632,1803,5188,255231,3717,5184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8504,26191,7048,7036,10379,109
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,84274,9588,197322,1728,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,844,1409,4256,2235,5330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2161,3131,80347,653509,3119,793
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27445,26521,162417,29928,4695,1965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,3106,5194,5662,122961,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26873,5828,7128,81031,57016,9122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83737,2760,2303,100131801,2793,6236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4128,10020,2203,2057,27235,3479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,2643,7841,60386,4709,5515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3401,5192,57192,3485,2099,2243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7442,7498,4609,51052,3423,7525
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5662,9095,9131,537,265,140803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56922,23556,6524,7097,23479,4069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 59067,215,5321,2936,57017,3931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,5345,655,5465,51555,3833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6555,4288,101180976,256297,4118,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285,1312,3992,1718,8660,2643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,3795,8862,9507,3077,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 494324,790,1436,81689,9663,9560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 118,54802,1371,1270,6576,54
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9414,406938,25839,3630,6648,124454
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8600,5740,2147,9868,1027,728441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,10320,3290,26291,5744,164656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 326625,10159,387787,9575,1201,219
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2538,3995,84277,2889,164656,91949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60386,7381,8932,80347,432369,6009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10599,1072,2806,51478,2997,7133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54902,55805,4338,7056,8932,2170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3551,50943,2806,1312,6934,27035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5116,773,154,1591,5770,80222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10524,3115,6530,56922,6777,84833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1608,239,5641,2784,81034,4069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 59067,10559,5962,4255,10965,26873
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55818,207,1116,6908,51422,55630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113235,79689,2542,9588,3304,6464
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 182,1968,7350,2101,84684,4221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,57580,4159,29929,2110,8431
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5581,10497,56259,6556,25805,55149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,4843,6786,5781,929,7025
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57104,467,200186,7352,11096,1339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4357,7372,3762,326625,6275,10316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 726,2903,5830,56718,60,6402
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5641,2030,10522,5241,23654,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5825,6519,9056,1022,80201,8228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 432369,1734,8665,6941,665,54539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 257313,79949,3651,2235,479,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23054,3486,5950,85569,5445,100506742
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6948,6182,35,7226,5837,5802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3691,7100,11095,8818,6348,6009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1312,4868,6374,4615,54577,22868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5970,84572,123283,55805,540,79068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3350,133,5654,3572,80267,55867
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64788,364,10379,2167,100132285,7408
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,624,818,1588,2244,1489
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4521,7026,8945,5697,7385,6576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4036,54575,51649,1051,10845,1200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2034,9370,291,1270,51441,8609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7100,432369,5188,54809,10226,728642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9076,5506,7942,5214,87178,54902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5581,3155,4232,51128,3636,192343
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5914,55750,2584,85365,2710,498
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2063,3240,825,8835,406903,1584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1312,728441,5071,2628,1444,178
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3283,6657,6514,54968,55586,3948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8473,338328,7325,2555,10020,2587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6401,100,5321,85365,54578,2335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7030,10320,104,4973,5562,5055
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2948,2135,1232,3596,7376,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79144,8202,56652,6347,5824,4724
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 52.133   1.456  53.568