##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SVMDO.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.4.0'
* 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 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 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 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-3.19-bioc\R\bin\R.exe CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: 51167,7355,1030,123099,2118,9722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2694,406903,5770,7084,966,7097
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 496,178,3406,59340,2547,28957
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,7385,5207,4256,85569,1340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2308,7019,114899,3762,11213,203859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,84061,10128,3489,8942,5826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4728,84300,5230,8473,712,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2593,7515,818,3099,80339,125988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 540,5019,1312,7291,4041,558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2695,4337,5188,6280,80339,3708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1537,11136,2639,2944,1051,100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57761,100156321,3813,10965,217,1355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4843,857,2908,6775,3501,5802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6391,55970,643387,1113,7032,1348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8660,643394,5168,5313,3980,3992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6526,56623,599,3383,5781,7048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5306,65993,3283,5743,3784,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,136259,779,104909134,497231,6382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7916,779,5914,131669,728,4035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51004,7033,5629,3479,5346,4688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5409,55331,8876,4702,759,5191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7137,57761,3119,7507,201595,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1355,498,80309,1645,26521,6374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100303755,4552,3484,256471,1191,8195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1327,266,6814,10135,4540,28234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5730,2695,841,3623,796,6523
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,3034,538,55699,57016,7431
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1604,3728,10279,4843,5594,51
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 199,5325,29078,80207,54331,253827
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,2593,644096,51119,7389,56729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6289,150379,3074,3484,3489,6521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7157,406947,376497,2820,8604,583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79949,9507,51441,26060,3651,3351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,1149,121268,2597,6446,1369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60412,3425,56718,10999,54539,7297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4232,90480,23236,10559,406982,100126861
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64788,1557,153,10497,22877,25801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3500,84889,858,5331,11096,7128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3291,10644,2235,9619,6445,1601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407006,5176,5860,6775,4792,9311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1491,9997,2591,800,1789,6522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7076,5444,64788,196385,522,10157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2581,64116,6890,7295,1584,55526
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,122961,8659,23129,6564,3643
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3106,55644,4548,3574,6339,7827
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2146,2946,6648,7841,2328,23556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6834,80067,5345,10559,5507,6272
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1558,51181,54344,3949,2309,2512
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5971,9759,836,6657,9131,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11136,7879,1718,55644,10013,7037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,487,249,25915,1056,840
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6777,4311,117289,2677,4668,10102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 52,60386,335,2990,1950,81788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4162,6374,4688,1586,406947,3929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116985,3939,3030,6236,4017,2119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1499,3170,10666,3690,5837,23654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3673,10842,3690,4860,6748,23753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493856,513,811,5161,55805,23175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 211,54575,653361,6093,7010,6402
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2520,6337,729230,7364,79949,10279
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,943,5370,11035,6772,55343
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 706,51081,208,55829,6908,27097
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1728,8784,55586,867,9370,7098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 181,1606,4143,9241,3763,4137
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8455,7287,5744,64131,3759,200539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3481,81029,123283,2222,80347,5236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,10166,25821,125170,840,643181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6609,316,7424,4351,1369,2222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3930,5654,8862,2063,5968,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116519,4160,10874,685,8942,9437
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27429,1584,5551,7052,2310,29960
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10316,1621,7345,79144,4615,5106
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 867,627,316,4968,53947,1080
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64801,4615,811,9479,6329,3596
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9241,6515,6888,1491,7015,55858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,7345,5350,10013,19,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 359,28951,23101,5245,79068,83854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10874,5330,165,2548,1028,8877
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4478,3066,3122,25915,10522,359
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  60.96    1.78   62.75