##############################################################################
##############################################################################
###
### 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 12.7.4
* 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: 26191,493753,2590,6347,3980,4128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2571,5213,5241,53947,1363,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,3991,7292,2135,1281,1071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2752,8854,84987,5106,7430,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 537,1789,169026,10938,5373,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79191,5019,51021,2118,5345,2266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 583,114814,114899,1595,8722,1345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3458,3106,6941,104,51092,5449
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 708,7177,2180,5293,5052,4709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6009,81570,4060,181,169026,5370
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2266,126328,3554,3654,2934,5008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3481,5091,8665,23564,8682,5806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 142,583,2030,5798,5799,64805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387,2949,4091,341,6941,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84947,9429,1803,6690,7364,2790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55630,4035,1363,53335,6390,6804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1584,4656,10134,134,5825,186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,4311,3440,1347,5020,93587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 208,55024,79827,52,1717,3932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,81689,81033,1075,6476,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4609,9965,10400,10891,6718,26873
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 129787,6915,150379,1374,5967,6199
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,2934,7167,10999,9945,5105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22868,356,10062,653361,22933,7384
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7137,5828,4015,1201,4547,4535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,11213,10134,5126,51703,27247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 183,100529063,5451,5255,1135,811
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 397491,10000,5771,5175,364,5364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2512,8942,2559,7276,10745,54822
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6550,54600,56623,4009,2582,23365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84705,114548,5367,57016,54809,5306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5191,1843,3106,29851,3784,200539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22797,256297,10157,53947,210,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158,79572,116150,7407,11095,1182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,37,5820,8841,434,54902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54344,2784,4860,842,2280,63899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 185,3767,2516,6351,4217,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6095,114884,9317,84987,3485,391051
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1910,664,516,7052,54704,22852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5274,7507,2948,2694,121268,643387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51649,7177,2310,5571,22797,1348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3958,3556,51099,2260,8813,1807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2030,2235,2170,3803,51478,635
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,51649,10195,2632,909,129787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6256,23082,54915,4714,66036,1601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,800,23600,5162,2638,7139
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 350,7010,4337,8202,3483,5971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51024,28976,25801,875,6890,57620
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2592,5087,22852,7368,1641,33
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4041,6414,6009,83985,1376,81570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5806,796,5697,857,8740,84063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2903,2992,407008,5830,2904,7030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4668,6929,493927,84277,9420,10250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2889,3115,7409,54982,3060,2990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23175,23600,4314,3284,1583,1080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63899,80267,11213,1371,3034,6406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 617,3351,867,27141,6608,7841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 841,5192,9409,5276,8678,6285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3489,1435,3845,3773,2110,56729
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3157,56718,3032,3956,2057,3439
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51117,270,29843,6556,5820,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6514,7369,1376,8473,1537,54802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2328,909,10279,79796,818,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3075,4846,177,7078,8195,200810
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,79087,5276,3991,4887,6009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5265,5618,114884,7274,445,5598
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 213,3640,3767,4779,7321,293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6821,407004,216,23446,4779,5193
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6927,130589,4357,4795,920,4126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5972,3569,5588,6280,3708,182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65985,308,79783,55065,55278,1234
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6550,2547,7128,3382,4150,8665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3482,570,10000,9475,116519,57570
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1893,9560,4780,115286,6716,712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116228,640,10616,10379,7018,5727
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8660,4712,4023,79158,2538,2784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 147007,170392,2889,1604,3115,2639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,1352,8740,23411,4357,3162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7030,54902,2115,7942,2799,100125288
--> return NULL...
2024-06-24 12:55:45.875 R[34842:1082209403] XType: com.apple.fonts is not accessible.
2024-06-24 12:55:45.876 R[34842:1082209403] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 93.094   2.217 104.537