##############################################################################
##############################################################################
###
### 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
 OK
* 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.
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 4.3.3 (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: 4609,148713,55699,216,7274,6794
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,10580,5092,1738,257313,8462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1147,54822,5743,100529063,2309,3375
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1807,2006,2876,384,5009,122961
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10643,79144,2645,23516,169792,6524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80142,211,2947,31,84902,1789
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23101,2946,3815,7450,1352,4852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200539,4162,4591,64432,2581,2990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353500,51601,79602,800,197322,116150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2194,3565,384,10616,25839,5660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7200,23274,55885,182,9563,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 156,648998,5054,23753,1392,10991
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3710,6891,2689,2798,52,104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8788,347,6890,2109,65985,5580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,3576,4598,148979,2847,3315
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5080,10643,8788,27235,5023,2653
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5562,64087,3032,84334,7941,5971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4478,940,4704,9807,5562,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3673,26191,844,10911,2170,8660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51099,818,3115,2677,8722,10423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 165,6620,116519,4353,4543,2746
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7021,467,5294,2835,57017,1409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 102,3565,6523,2878,929,150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3500,10269,5160,5365,4925,83440
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 549,28957,2582,6446,147007,6287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51478,6908,5726,23411,149461,1365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1588,2520,80309,2006,80070,23706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4323,266,595,952,376497,842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,4842,2950,4880,790,54344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8841,6341,29881,2990,11222,2520
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9314,7275,8431,84340,840,23436
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 170302,4288,6343,5745,345,4790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100156321,494324,18,27445,1027,64801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2159,6620,3033,5824,60412,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7915,7408,768239,1524,55024,1355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2006,1028,2798,3712,6352,2135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65985,7879,2787,182,5799,1672
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1604,6555,686,270,26119,2266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2792,7528,1116,3373,10724,3929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2314,54539,4017,55586,212,4535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7287,3242,2673,1807,9882,4055
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 156,7408,8504,3598,7097,570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3708,51094,2539,1806,6906,4792
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3484,4716,5805,2989,64241,3767
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7407,8455,2713,3479,2063,9420
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9663,6752,847,4716,10559,9054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7364,64900,475,79158,57761,79144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56922,4891,2548,859,1585,10667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347,56923,1281,55788,5451,79071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,5365,6890,23479,5193,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,57061,126328,1071,7177,5364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6275,23175,51293,1356,3767,2303
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406913,2119,551,7274,8678,5745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 627,6521,5096,3939,3930,7528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9451,221895,2785,7276,2247,6770
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55034,4694,2055,407004,2584,8764
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92483,1080,353500,6915,51604,147007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8829,1499,5265,26227,4162,2321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5629,821,1066,84868,3685,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2200,10891,8818,2309,6348,3688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3500,2731,6505,1363,10295,79071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3980,51119,8218,212,4159,10628
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6389,7139,11200,11254,84063,582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5264,9374,1340,7486,2949,1347
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7249,23291,6354,126328,6532,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8604,467,537,79689,4521,7295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9369,79934,388753,9941,80067,25915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6505,5126,8856,3098,6622,3030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5687,145741,8802,4089,79602,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64241,5295,3667,10845,5580,1565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51548,644974,5365,5741,6445,201305
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8803,5264,338821,10060,6530,3605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6279,54704,7128,5788,341,387082
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,133,4151,10935,2512,5728
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5328,59272,6608,7364,2998,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57128,406922,116985,1200,7941,3054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1281,121268,63931,5188,84868,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84889,2587,4891,1588,9965,7249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123,79689,1586,1798,5925,4125
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 65.159   2.034  68.315