##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* 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 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 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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: aarch64-apple-darwin20

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: 9437,2200,51458,6390,2113,664
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79001,7381,60,10221,54576,4914
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7391,79934,29926,6941,2547,348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57678,407008,55670,3948,7297,26762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10060,5798,54802,9927,5629,84572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,4060,91647,132158,10013,4017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57554,2992,59067,26873,840,5373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3351,1608,84735,8862,9122,170302
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6678,4925,5077,3615,3123,5806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2155,759,5740,22877,151,10599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7078,2166,8029,9414,6402,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26762,50484,79934,126328,51021,51293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51106,7980,2946,6715,5175,5788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,9692,5449,51099,5593,9429
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153642,5295,169792,170302,55340,8195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79068,2746,1812,2169,4126,5697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3556,5087,9311,5447,1992,5325
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,3556,2688,4595,79944,1636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6383,131118,5728,337,6287,6906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5160,493927,316,5106,256471,1906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22845,2745,9498,8942,5274,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1678,3032,26517,6522,558,1812
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6888,92935,5286,6097,83440,23446
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81031,640,7355,23556,2169,3845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80070,4889,51300,84300,63874,3658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4137,2520,3708,2896,3502,10059
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,1113,4057,5370,200539,9311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1113,64801,5250,6182,54575,1968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6401,2328,26521,26580,665,1490
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4337,875,4232,5697,257313,708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6579,336,332,56922,59067,3423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 170302,27035,6476,1584,2582,858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10365,7200,7422,2517,56652,1442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5184,7480,3658,2247,959,4968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50814,7515,5828,846,65993,10243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3640,3458,3978,3087,4719,7137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 948,5092,80267,2792,4982,4702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23274,7408,1351,54802,29928,1052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 522,6183,8050,1869,23516,5250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8829,6505,8876,6232,125988,6007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1442,6941,5588,406913,7408,344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,5730,5901,81689,3572,432369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,7480,2305,407008,8854,1337
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 170302,6341,6569,4314,6401,4988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79796,9563,5473,706,7376,3832
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79144,81570,26088,1537,6387,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51601,27232,1443,10886,4826,6678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11183,5055,3708,5687,7480,538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5207,4915,2688,7226,5306,10134
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7538,1812,9607,2244,55858,2638
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388962,3032,9409,145741,4914,6515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1019,8764,351,8074,788,54901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9882,217,9619,2321,5191,10549
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3157,9619,10019,6555,80207,9388
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5214,4214,7252,3308,3703,3687
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2584,5476,150379,8678,6248,60386
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65080,3503,5799,9512,8659,336
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64240,4744,10128,4988,5105,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,1497,130589,65993,7172,1717
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653361,5069,2597,169026,7040,3439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84902,265,51458,2984,407040,364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7442,66036,51548,79071,5139,353500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5365,22868,2588,4285,253559,6718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7098,2271,51117,4567,5009,7076
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,8722,9475,6515,5023,3418
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4712,26503,255738,9759,10730,123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2395,6714,118,5836,1244,3778
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,3131,376497,811,53345,8862
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51103,4337,2572,10365,191,4671
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10580,182,8829,6462,51004,811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,4552,6427,5473,3813,2115
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5654,2538,55526,1444,56244,406903
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,712,186,4099,2847,779
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 207,257313,85476,2984,5077,7128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10060,10,79944,6182,59340,23082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6584,358,1277,148738,200539,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,5175,493753,147007,3426,7037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,7040,4826,2639,1675,60528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,8799,374291,3440,440503,51649
--> return NULL...
2024-06-11 07:47:21.084 R[4575:39346831] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 53.173   1.377  78.882