##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SVMDO_1.2.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SVMDO.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.2.8’
* 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 R 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 loading without being on the library search path ... 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SVMDO_guide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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.
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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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: 2762,5468,10730,100126861,9076,2572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8818,3816,1208,4773,23479,85479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3784,572,3032,642489,7391,3709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8740,3760,842,3113,3980,55816
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4069,55340,4151,549,952,64116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55970,2488,131669,7287,158,1608
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7033,79068,3759,51204,4286,56052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84833,5715,5644,3778,3833,6804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1634,3556,8813,5108,2235,4018
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6584,10159,64241,5806,5194,197322
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79602,1043,26521,2167,55644,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6403,5329,1471,1893,6690,10559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9563,11136,3418,338821,57176,6095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,83985,158,55149,26762,3938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6446,4208,29126,3766,6352,1992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,85365,148979,4864,3123,2587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4478,1489,1352,23274,5579,708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56458,583,54210,5054,7276,10886
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4015,23654,3956,2629,256297,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,205327,80309,2792,3117,7376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2787,6536,326625,3077,7135,5901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 336,2834,84062,29960,4914,9588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3654,3630,3291,4889,6403,52
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25915,6356,5080,57107,84649,231
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3283,384,5365,29968,170392,406922
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3385,7422,192343,9868,10841,7031
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7879,4864,3593,51099,635,79689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,2348,3034,51094,64801,9451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4790,2512,1113,5264,6721,4282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2064,2760,8835,5191,2303,3416
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4069,4318,132,4149,5161,51316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5346,2694,54931,51167,158,2944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5601,10522,4712,7287,1595,169792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3439,56848,1524,2752,7442,57048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6093,51458,152926,25813,7084,3293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6288,1135,253559,6678,80067,9969
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6287,9317,5320,84705,63899,1327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131669,56945,347411,2590,55863,6948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84300,3101,3290,2745,2063,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10423,10221,116150,9563,5277,126328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,326625,3439,11266,11096,4591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,53345,156,2161,338821,10580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23163,11019,406903,29851,79827,23654
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5728,1956,81034,1589,7287,7172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3418,25805,6301,2167,105372280,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7409,6362,65080,100126861,5788,51079
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 657,5563,64135,29079,23400,1268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8309,6523,10102,26873,255231,2271
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5565,114884,4357,253943,90070,7253
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 119559,23411,54809,8029,2146,2798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,1646,3845,29926,11255,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2785,5176,114899,54578,79191,6548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4656,10874,51316,3383,59340,5350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3350,5372,1843,4654,10886,4760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3833,4854,120227,189,59340,23600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 337,9374,1337,10524,1376,9369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1524,114815,7082,1675,29929,5744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6447,7424,3401,205327,4718,405
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7525,10642,54806,79133,7430,79783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3759,2203,4277,2673,151306,1869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,4915,151,650,2720,361
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10497,29929,4544,8682,2488,2524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,9365,801,2990,54205,51119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133,29079,57818,3242,1493,4887
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23038,8455,4976,2099,8722,116228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,54901,285848,4535,790,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,7369,348,79053,26235,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9807,7352,846,1807,7980,4160
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,2591,7372,2847,486,407004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,5599,6777,7031,5286,1537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3978,29929,1786,1649,84342,8842
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 538,84842,8665,10577,5213,5589
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5584,3630,9437,55278,406982,2517
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,6391,7248,5077,6608,48
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1508,3643,56997,858,574447,1641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5330,6232,23590,50814,4702,5291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8714,51441,6523,34,30061,11095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3394,59067,9021,84274,3586,54205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5798,6834,6329,207,54931,4988
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 51.119   1.114  52.209