##############################################################################
##############################################################################
###
### 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 13.6.6
* 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: 2875,8228,5288,57048,283459,6834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,132,79949,6382,3559,55283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,83884,4255,1200,51024,4728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 137682,4580,1201,3486,3811,121268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153642,332,6523,549,59272,283459
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4758,7025,7276,105372280,6329,9575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6337,51422,308,3062,655,818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25828,650,4790,627,3833,27247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1072,1443,81788,796,84705,85569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255308,4232,54,10842,7157,2954
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,596,6401,81704,5968,1329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1490,23411,2632,54982,7032,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 136259,2100,7035,1029,8560,540
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79585,2952,5743,800,145264,857
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4594,3566,145741,2784,186,3728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3115,5728,5771,538,3995,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2168,801,506,10935,55343,147007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728294,102,55805,5697,4323,8195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5294,2271,3291,351,6576,7052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5372,11231,6775,2488,3172,6351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84947,4860,23365,265,4012,28951
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29928,3593,10365,79944,6352,1345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6608,9445,350,2984,4914,9971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3664,729238,5601,1361,2677,5346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23054,388125,23446,154,10094,6406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11255,494324,22852,1565,1588,1803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5265,6362,54896,9512,25915,56458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 642489,308,6095,3596,7297,5053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116085,26235,7133,718,2696,4015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,350,4035,9104,79068,4855
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2717,64116,9882,25813,27089,2702
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1401,1186,383,5891,10279,6770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79053,5788,51092,801,3687,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29880,366,2115,1080,55163,3990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3598,728642,51052,1281,479,9414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 777,256471,3995,7052,3802,10094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3627,25821,1604,6374,476,5245
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 145741,6439,29968,63892,5270,6748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7025,7137,3030,2804,116085,9409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2512,1497,64131,57176,593,4208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55024,22796,1509,2937,6462,291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100507436,10549,11096,3554,5598,6462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3060,1893,401,5715,5055,3339
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8818,5740,7289,9054,2683,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,3162,53632,10686,9997,1436
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7076,4057,4537,2305,10686,3687
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9314,15,6258,7409,1636,4017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132,5551,1348,79689,64919,728441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51,5175,25821,6337,1066,2710
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2885,100156321,4318,114815,50615,4217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131669,7840,23516,4729,114884,7048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3417,3651,23516,9817,1489,10642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5116,6530,10549,347,3290,6948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1584,5742,5563,6329,51458,3551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27329,3569,3574,84274,2110,83440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10522,4323,91869,123099,407007,2169
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407006,91942,6722,4337,51441,10559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255231,9370,5108,2660,5571,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 291,80309,407007,410,582,9451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7385,476,644096,10000,9927,54205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80067,10667,3460,3570,104,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3077,54331,175,34,63892,788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51117,8567,30061,10279,3482,120227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26503,644974,624,574447,10352,4323
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2998,494324,9021,3145,5592,5595
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55818,80142,5515,84649,65080,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6348,6389,4283,1493,50943,51103
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8932,6311,2591,9475,2745,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8877,7498,538,7097,8560,5370
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,3956,4548,131118,2919,80724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1489,1589,51116,25839,867,353500
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7177,29929,5580,51094,9255,6279
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,54902,10599,255231,5023,5820
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29947,2169,9370,1118,4035,123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51316,2244,5962,84572,84684,2260
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81031,5327,4118,7253,407009,54968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9255,6348,5296,29929,3293,5443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,4688,2052,7139,5106,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2847,64135,493856,2645,57511,27329
--> return NULL...
2024-06-25 11:21:35.617 R[18206:83464489] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 53.246   1.013  54.597