##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SVMDO.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SVMDO_1.2.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/SVMDO.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SVMDO/DESCRIPTION' ... OK
* this is package 'SVMDO' version '1.2.8'
* 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 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 R 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 in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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: 25821,6519,1634,55005,5372,6182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4099,6897,26521,4744,131118,51021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,3791,25805,3481,55343,29928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2548,538,253827,2786,10157,55816
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55526,6602,3768,5598,3251,6376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2157,348,5243,6722,116228,9475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 256471,2798,3953,406991,22852,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406,391051,4286,387,23590,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3115,3988,9054,64220,558,119559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,285,2788,2778,64432,10745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1312,3113,9560,10891,2695,65080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149461,6347,2053,5891,10019,100128525
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5409,3141,3615,6515,57818,65080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,79587,5449,3624,3552,4124
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55768,79602,338821,686,7275,7031
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26580,2834,26517,5290,84947,57085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55005,686,4899,80207,653,7321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23163,4283,1230,712,60,84239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84061,23178,83985,1071,5728,81788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5168,5195,2053,2739,4313,4288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3725,181,4338,729238,6362,10365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54809,1584,65018,1028,2303,10616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 801,6258,9317,9332,3316,4654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11096,79071,119559,1056,886,3565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51116,3762,5320,1588,6097,3292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406938,7421,7368,203,1509,124454
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2642,55829,4650,4695,5618,4283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2694,26119,23706,3439,6576,3303
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,6772,8818,793,2788,55885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4277,22933,91949,50484,6566,407024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1869,9518,6868,9369,4017,7839
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 540,2678,5449,152078,27232,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5571,23600,8517,57511,9415,949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8455,53345,3763,23291,1232,6502
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55805,7049,1645,10599,4828,516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1737,8742,27232,6319,56244,340706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285,407004,2155,3574,23054,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4323,1182,55768,9122,22901,38
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113235,7471,3460,6602,5325,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2157,5594,2702,388962,80070,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6941,2593,8714,51099,5192,84701
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54,9021,4128,10379,7915,29881
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1815,79661,2694,57554,8764,6833
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1327,6280,10559,1608,5836,574447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55340,6502,5950,2697,2792,2555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6772,8788,6517,2053,617,80347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5580,3658,125988,3691,169026,1571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4700,5256,9054,26191,5770,189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1340,1339,340706,909,5799,6517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7980,5962,3240,9507,4129,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10891,131118,52,79644,5096,1728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1992,22926,79689,7015,28234,115286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 397491,150379,5306,23409,7450,4060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5184,5370,9927,9255,5019,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6548,4357,4323,8309,1072,4478
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79087,7839,55748,643394,80309,22901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4860,6696,292,3703,3949,3630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,8682,10019,55670,256764,107075310
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2677,4704,6340,2776,3456,4722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7351,6555,4522,656,55937,6390
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 59067,7297,842,53346,2632,3458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 196385,23556,3043,10667,8818,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729238,6804,2063,8742,3122,54539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3073,6929,406,7879,6446,5020
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8788,53632,9332,4214,4036,1636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5213,358,2200,5188,9560,3553
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3303,2584,2310,9672,3703,152926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7408,2919,79158,53947,4544,57761
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2157,55024,4151,3172,25805,2645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1641,80201,3600,5443,6256,85476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2266,10935,55163,6324,81704,332
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5820,4524,840,2588,5730,28976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3553,9588,1499,23436,57570,231
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10466,2559,2696,6696,54806,55750
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7031,8651,3416,1646,3382,4868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3773,121268,29843,790,2109,551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 216,6446,9255,388753,6319,1728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1548,10466,885,7220,338328,6649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,4722,821,55818,627,6403
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  57.76    1.21   58.98