##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* 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 ‘1.4.0’
* 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 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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.
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-pc-linux-gnu

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: 800,80201,10724,2101,84063,64919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26517,1497,4846,5257,51548,10559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55885,1604,6522,6272,1337,140803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 567,3811,8694,7021,142,3426
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2806,4792,57570,389692,10295,1514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2932,2944,494324,1444,10560,5068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11132,6649,90070,54809,5080,3172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 857,3074,5631,9388,55937,2582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2785,846,4744,7391,3990,84300
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,2885,1644,3081,51204,1555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 33,627,2222,1737,8202,5515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,6571,5190,81788,8228,4143
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1807,5078,1436,175,4716,32
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5443,1499,2717,5162,116519,590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8560,55034,151,2147,79644,3764
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,66036,28958,7167,5443,4795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,51,2628,2555,118,2194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9241,4312,9997,7442,5727,55805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2266,11222,6582,2876,7442,5261
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,4314,3066,6348,4982,51119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64116,4162,497231,3077,624,5330
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7084,866,7276,1621,114548,2746
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,4547,3710,51024,1675,1757
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3593,10686,3562,291,3992,5473
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4040,4017,255738,56923,496,6492
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23054,1364,836,4556,4726,27097
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387787,1889,2731,3658,595,5133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5096,797,2495,55630,8455,10094
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91574,51141,9572,3764,5052,1339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3700,51106,1490,7292,1435,2309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80331,2786,246,123,124454,3099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4709,407021,217,10874,134,5245
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8074,10730,5270,65018,5330,2006
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6934,388753,5644,6288,6392,51167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23474,148713,10497,10935,8942,4069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2875,410,3054,23600,10020,3552
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7084,3673,1135,149461,57192,84842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5580,790,1281,3315,54896,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7021,6583,1584,4887,2805,1634
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1601,5071,56052,6928,2539,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6357,773,80224,6615,3458,6342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9807,3156,54106,596,55970,2903
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,3784,5571,1208,5771,2034
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29928,100,5077,1634,1232,590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2647,6678,2167,51181,9255,55532
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5920,64788,427,4338,462,51478
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3784,10559,3077,3689,81570,5950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10243,4256,1491,6609,4879,6339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80201,8202,4129,50615,2731,54578
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8398,6232,5551,7852,4846,10616
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,5451,7430,10279,4868,3502
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3569,6657,3570,1586,7390,10295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8829,3174,5162,7177,9374,2776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2194,1798,5236,6915,9451,3293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3484,284184,3651,406938,5476,10008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6510,3643,28234,28951,2159,4023
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2739,10352,6647,406991,6510,23178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2948,6804,4760,55283,10,6609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6648,56999,255738,3673,1147,8050
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200205,5467,3598,2271,2548,55630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23389,5286,2997,3075,10938,5443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84557,654,27429,3691,5820,79689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1672,64801,55034,5449,479,3596
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57818,4982,3577,7422,10166,1605
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26517,2948,4722,50639,155,790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51555,55867,10886,6324,5728,56938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6531,5255,942,959,5329,4828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3172,211,56938,3949,759,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,487,84557,388962,406,5321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 316,2852,6469,2068,2752,3802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2119,3995,1508,130120,6554,64131
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10316,2539,2591,22901,3440,7430
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5428,10195,7528,397491,3980,8722
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55750,51004,123099,857,4508,81689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,54658,476,2702,1678,84277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3708,1352,5288,10000,25839,116519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 340024,3691,3479,846,7128,57570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5621,5579,11232,3956,23436,116150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6915,5837,338,686,7350,7274
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 53.933   0.924  54.837