##############################################################################
##############################################################################
###
### 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: 3292,5373,80067,9479,123099,5728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1524,728,291,4843,2852,866
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4854,3931,203859,1509,5069,4232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3795,114548,4598,4973,1191,6510
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153,57817,2034,3664,28958,2516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9437,4552,4041,350,8517,100125288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5914,7486,27445,391051,3484,5641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5106,5091,5728,6357,57017,84684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100126861,51083,9965,9314,3458,2786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1734,7291,5370,43,10991,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1365,29947,5781,131118,9997,23411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5465,6515,10577,132158,8799,6357
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8473,2835,4988,5096,1593,2804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 941,100125288,2798,63874,55858,3034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,1649,90480,7916,8431,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27141,7841,2806,407024,9514,79001
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5444,2778,149461,3098,8835,7056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3159,10886,6446,7391,1365,1650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1543,1373,409,154,265,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4615,383,56923,56997,79001,57085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1499,5538,2629,4118,9969,5584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54331,3932,4700,27097,23564,3676
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84987,4035,55805,2559,25813,4760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,114548,91574,8879,83854,28234
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10560,344905,3784,9382,6716,1588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55788,4671,3575,4323,3507,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,2701,858,79644,496,1428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7274,4221,155,2538,2713,55818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 113235,6794,1376,4312,59340,6515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2688,4878,23129,84239,9619,5290
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57176,3990,5788,3638,11132,4286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3832,7525,57017,2820,1072,10724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6770,3373,9630,3738,120227,4094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4057,116519,3948,6622,338,8567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2806,23291,4057,51004,9479,1232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55149,3503,338328,344905,6402,1340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7422,4508,5350,122961,2806,37
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3779,249,1030,3570,5624,10891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1992,7538,2395,4719,91869,6517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57761,6714,3356,4852,348,4351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8854,7048,27232,407009,6690,7097
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1146,3425,5468,1116,2878,2645
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23586,497231,4288,3503,253943,5080
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3575,1182,5192,1509,5962,1672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5715,4842,27010,1392,55829,1571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64805,4306,10666,3802,2588,308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,8772,407006,6445,4502,1544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28958,55278,7430,4338,54896,3401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6354,1364,388125,9507,1376,1806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6339,1524,51422,367,9498,1019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5345,4357,91949,2184,64801,123263
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,4669,6338,7052,959,5820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80724,3934,1051,790955,6556,5095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5730,2524,2834,9104,122961,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10497,10666,1645,2632,3043,462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5507,4726,55902,2157,79587,4159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4129,55149,29079,1351,790,130120
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 582,132158,406947,55902,1374,115286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406,5476,3315,4976,5277,2989
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,23054,10365,9968,100125288,22797
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55867,7225,4719,7019,89874,3503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,6584,56718,10166,8829,1146
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 257313,6770,3991,3815,6648,23365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5920,1352,3712,5901,6678,2280
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11255,9317,5293,1442,596,10013
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,728441,332,7919,5078,1497
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55748,10157,85365,5331,3119,4552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 350,4091,4217,4017,514,3502
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7515,5027,4338,6285,23038,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6289,7364,23101,9817,6890,10008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3802,2495,6382,4724,185,5190
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,8877,1185,344905,3155,594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2184,1340,712,6362,1244,51083
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,6696,1234,1230,23274,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8665,5116,64900,356,3709,7137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23163,4709,9498,7350,7019,10891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10642,4000,340024,53346,7287,64772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7498,387,9507,1593,2947,28951
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114815,5091,200539,486,3768,2495
--> return NULL...
2024-06-27 13:00:30.325 R[30306:1290384698] XType: com.apple.fonts is not accessible.
2024-06-27 13:00:30.327 R[30306:1290384698] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 91.856   2.281 104.877