##############################################################################
##############################################################################
###
### 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: x86_64-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 Monterey 12.7.1
* 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-x86_64/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: x86_64-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: 4891,164656,3066,595,7076,9807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3556,29126,8854,3725,5950,1371
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3123,57215,3172,5168,5617,9054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9475,9332,92935,1281,26119,4843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79087,51,7325,5095,5327,708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56922,1585,92483,2524,340024,3627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3385,5654,7507,4792,712,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3062,6340,11222,1499,440138,229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4313,619373,208,23389,109,5920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2030,7345,3630,124976,3938,8600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1812,7466,1606,8202,57192,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23436,79944,5368,4595,5837,654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149461,1186,407024,1116,10019,6555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9131,5211,5770,5162,162417,130589
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2280,56997,3358,3658,5313,7287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 140803,54344,5295,1043,56922,26873
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 587,498,5971,55829,7157,4306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5133,10279,8639,9969,5476,5641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,952,728294,9722,2109,255231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55967,10423,8648,3303,2113,55829
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 506,540,57016,1200,51081,407024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29960,55670,2896,570,7471,4255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 796,1186,1893,5264,10730,5257
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51604,8694,5798,64805,5781,9076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3654,4012,2271,1118,6279,10577
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,4009,3643,253827,5697,3577
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1435,79602,2581,374291,93587,2790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5584,10745,572,6285,80142,2689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79191,8856,80201,2328,2834,26521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4015,50814,5192,51555,2135,65018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2180,3308,6007,4627,8567,1339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54968,6566,1717,5241,23291,6513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,1019,10886,4524,8818,84842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406982,1509,3574,9512,2200,629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4795,2696,6356,9722,5071,3481
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1588,5108,57048,3640,6659,513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9969,8842,7345,10135,479,117289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5365,1906,5069,3394,5891,1558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1490,5465,7915,8398,407040,5950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2760,3558,9971,488,5270,712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353,5360,650,6258,788,11093
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,410,164656,3250,10991,406982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51106,3700,8600,84684,3174,10166
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5588,3066,4668,1394,6446,55572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3992,3762,64900,23101,293,2152
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3554,9572,2348,9826,8648,648998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3356,5321,57580,3577,6752,64788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 648998,619373,6348,54,2752,2099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1050,498,1582,2695,102,54822
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,10134,6649,5277,1595,5313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10226,80339,54476,427,1208,572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10580,7431,3486,57817,105372280,51604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6382,4880,1022,84987,2785,1232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10365,10724,2115,2949,170392,3932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 138050,5787,1718,6427,793,1146
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2660,64102,210,7031,7297,635
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,5106,3280,201595,5571,1629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4744,406982,1027,9807,6794,777
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3456,411,6340,773,3623,1909
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1965,2159,1585,9437,353,152926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7879,594,80267,1393,64919,2335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5243,29126,2548,5236,4311,4137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2109,22901,8841,79827,3636,55818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3290,2155,1436,8660,4137,3159
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9965,8818,3623,941,7253,2152
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6579,208,6548,9374,162417,8473
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7852,29947,6678,5828,3762,5029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 283459,7077,4049,6329,1208,1364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92667,4780,4719,10842,4726,4878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148713,1557,3060,27232,340024,7137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63892,3992,23395,4868,8743,4683
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 249,358,6341,149775,3284,9380
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3417,10134,619373,6579,3575,23479
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 231,80854,1072,1364,6095,2791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4695,8841,3577,5330,9475,4548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 656,6439,729238,170302,5967,7082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1052,51649,51738,3074,3990,60684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4709,6888,4255,219,6775,2864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2110,91949,1394,538,5499,18
--> return NULL...
2024-06-05 23:36:53.013 R[5189:22427507] XType: com.apple.fonts is not accessible.
2024-06-05 23:36:53.014 R[5189:22427507] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 52.239   1.201  53.544