##############################################################################
##############################################################################
###
### 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 4.4.1 (2024-06-14)
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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: 5328,3458,197322,9451,1352,3060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6287,5328,5744,4891,23178,1544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 476,8651,79644,4353,388753,5499
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79602,90070,3141,23054,2244,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2932,6582,27232,1019,64087,10730
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3845,275,10457,55343,1644,4092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9122,54982,23395,712,4092,256764
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5901,5644,9104,10062,3043,150
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7128,3308,4855,54577,5195,10965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338328,29926,2903,5770,138050,4015
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3303,2243,2158,5950,7325,54901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 836,2495,8675,1329,132,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2984,5806,1641,2146,6403,844
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5052,3712,29880,10559,5799,1443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6722,788,5914,4489,54931,56938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1571,339,801,5599,9607,1401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28958,8740,6324,3240,178,57104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3738,123099,54476,652,6275,9311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2989,624,6948,3065,7177,1468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5588,5971,2944,2593,407008,56999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22926,114814,3643,1268,57192,4700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80207,9382,8813,55816,6007,4879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4842,5770,356,1806,6584,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2643,4891,494324,64135,3638,3691
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 846,249,2137,1889,51,6342
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 619373,114548,1565,4758,3460,79585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2677,1147,3554,1646,4697,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,5230,4094,1337,34,27010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53947,59067,132,105372280,130589,123283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4318,51106,9575,4556,23082,841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3845,4313,23530,57620,4543,114815
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6620,367,23564,80270,152926,2932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3375,11254,27097,3565,6519,356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1033,1815,3990,11183,148713,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1374,6009,10020,407008,1337,2587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 111,80347,5580,9377,84947,2697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 196743,116228,493856,5296,8802,644096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2990,2271,55867,596,210,84572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6199,2889,79689,629,6275,1607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6248,81689,1992,114548,6348,3690
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 391051,6721,81031,1589,7049,23291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3251,2740,6898,132,27429,6576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,11232,4868,654,4556,112817
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7291,10549,3553,1601,8740,4567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6441,5293,10365,7372,249,5467
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 332,145264,182,2516,6009,80070
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5069,10352,79587,4595,8218,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10423,8813,177,145258,1340,9722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10423,57107,462,497231,64240,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23410,55750,84649,6718,64122,867
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8682,84572,6446,4722,6620,599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7391,686,3725,3295,10019,6932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11222,256297,6550,25813,7916,2713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1544,2055,10644,5228,7431,3658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5192,793,3615,572,706,5291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5176,337,2799,51024,5196,5447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,6383,1789,2950,5595,56938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5742,4714,2937,7275,117289,8560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10243,7424,90624,6868,65985,4478
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8560,8784,1489,64241,55343,80270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23753,940,4017,51181,8639,6441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,84705,2305,79144,1392,55829
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80067,55037,6448,3934,6280,5327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4724,3773,29078,178,23400,8803
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5662,344,51300,326625,7442,1588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4040,4702,9380,10730,79087,292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9241,4887,5697,5369,6339,10686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2194,3778,7372,6357,5805,1965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5740,1232,54576,5580,7049,1910
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3113,79661,5631,51083,2305,56244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406906,100,1351,4709,4125,2168
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3406,79053,2717,8813,23411,60528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4854,376497,2572,5962,2516,6515
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5188,4887,7385,2804,3811,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3645,2804,10667,348,4214,2876
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,7054,3663,4758,3980,2740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1645,435,1675,3312,728294,64900
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,2673,391051,6095,35,59272
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2590,5315,5660,60412,23411,2934
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 52.843   1.681  54.496