##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/SVMDO.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 Patched (2024-04-24 r86482) -- "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: 7226,3250,654,11200,4543,4283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 788,7139,351,1113,27247,55037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407007,6341,125170,3932,55486,3990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10667,635,9377,25839,81033,94235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81788,60412,25821,105372280,7471,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,7941,1548,9722,2588,6535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,7036,5194,590,6351,23082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55024,51,23479,5728,1444,7157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,7100,3280,6915,54331,3624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2712,3507,4548,8945,2643,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79944,54600,7289,93587,7384,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1435,2798,7018,338821,3988,4537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1737,55967,83985,54600,5257,6311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5970,7515,3240,84572,10524,121268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1345,7287,340024,7345,6774,4716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90624,84447,28951,2952,80347,11254
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6382,2984,6357,158,7422,5744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4092,57817,344905,1815,1361,9255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8228,6446,55149,9868,2696,23101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1678,6236,2110,80067,10560,83440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 777,3174,644974,1337,6722,54982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23590,7124,56729,624,6287,3485
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5009,347411,4714,581,2762,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64772,11232,64087,4128,5467,9314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55644,255308,6383,685,407009,3115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9507,1565,6821,3673,7026,3351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4795,2944,55532,84705,3291,2875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 154,3553,84063,2305,6901,57104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5740,6097,2745,123283,7097,5290
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6280,2194,2896,10682,4854,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6804,2701,54331,777,388962,54915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10935,5105,6690,5286,5598,2591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6319,2068,5447,3670,1716,11093
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57620,1052,23400,2717,1149,3710
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4150,55644,7389,2713,6906,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6647,7077,6340,25839,5624,4694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3717,8309,239,9826,6256,4828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9374,130589,5743,9518,23474,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7486,8228,2740,5824,55532,942
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 117289,5970,1593,2745,9317,406922
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8691,1672,3240,55163,6715,2746
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2115,90070,3710,5080,23236,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9941,4627,116085,1544,2516,351
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4795,216,800,55283,138050,64801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1675,2571,823,89874,1514,3931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653361,4760,26503,5360,8784,10166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1734,23590,29926,6382,6324,56923
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9122,2762,156,6427,3486,4715
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79661,2889,2752,1537,1027,1393
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1890,79087,2113,150,5189,729238
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1608,148979,26517,10102,355,4709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,4214,7291,2056,909,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3593,1019,4233,54704,4210,6183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8218,5108,50615,56052,153,3159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7226,3251,3250,4153,2788,1191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4879,37,3676,23586,3958,8074
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2547,2936,55572,407006,488,80067
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6464,54806,5507,572,3460,256297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3779,6536,8742,759,406938,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9332,9095,5192,56997,10272,57085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2180,23101,79001,836,4547,486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,51649,54414,91574,1066,23590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10599,8504,6390,53335,3458,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26521,5771,3557,5329,221895,8455
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493927,4149,80270,5372,358,7852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 599,23082,406922,219,397491,4508
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6948,3479,64135,3075,51167,3615
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6447,59272,3073,487,3576,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2934,54578,6550,50484,590,53335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406991,217,9514,6347,3483,196743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55024,3339,249,26873,1392,7471
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2516,4214,5970,1789,4040,54822
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,3930,1815,2030,9380,3684
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9429,55829,4277,5631,8818,4171
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3155,5565,123,6770,2068,3141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1200,54476,3439,5191,9572,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11132,1508,1075,4879,3766,10682
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1524,2487,1329,5360,83985,5499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1200,6492,1636,10020,5743,57580
--> return NULL...
2024-05-13 04:58:24.383 R[59814:55600185] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 51.982   1.071  53.462