##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SVMDO_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-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 ‘1.5.0’
* 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-3.20-bioc/R/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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: 5364,10134,5350,9817,4688,5799
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7287,2696,5096,840,22845,7295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 316,54,23516,51458,60,8862
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27141,150379,56259,3768,3339,3625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4718,8854,1339,10549,635,8813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,1604,10229,2629,7225,4695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3816,187,4489,84447,215,9241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2590,2702,2520,3795,2729,90480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100507436,84274,148713,2517,55937,3938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8567,486,9332,1382,111,2683
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5330,3725,2184,1906,5080,7941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2712,388125,10316,4828,113235,1401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4285,2548,1607,2746,6339,2944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 800,3507,388962,9241,1116,8228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51548,291,2746,479,217,1022
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,3676,104909134,8877,55243,63899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80724,64220,6554,5295,23400,200810
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23411,4282,2790,197322,26873,111
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4255,5369,200810,338557,4729,10842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8228,51004,4729,2147,5092,3816
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,1586,84902,4716,29078,203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 581,85365,4594,2180,23516,5071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3123,5467,7226,83737,4524,943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3292,5624,26762,64900,84340,285362
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84274,6564,5662,8665,10857,6505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11093,3565,5592,2053,941,347411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4535,51293,80724,4615,90624,55331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 18,7128,79053,51116,800,3101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6402,1182,186,11093,5095,2064
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 332,51099,6296,5330,5293,9056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84317,80224,6609,406903,3592,8788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22796,54806,3105,54344,2572,7409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2310,1589,3172,9420,493856,175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9512,29881,5176,7100,2949,7019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 617,3141,440138,7839,80854,3417
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9518,7030,339,6337,1608,3605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1056,11095,6821,2539,356,1051
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 796,9560,6649,64241,65080,11095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9380,54822,2581,1606,1544,54539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 909,84701,3615,1428,655,197322
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9451,80854,2919,3242,84889,5641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55278,124976,151306,5473,158,3480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 59340,338328,8942,283459,6182,4221
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8942,5095,249,1186,5364,4314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3636,6357,55005,347,51116,2321
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4092,2696,3738,23411,4314,1080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6492,1351,100,5071,1337,2642
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8856,4337,3091,56938,949,3654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6649,6915,435,5108,5802,25813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,6402,1382,796,84706,4795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7352,467,836,27429,5160,92483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6324,7049,2875,4744,3816,2271
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,3664,5925,2056,3484,3773
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1493,2475,1909,1489,6569,191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10938,7431,9388,54704,80142,27445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5228,1672,1444,686,4502,2950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5825,210,10423,2591,3077,2101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9365,7010,1589,1401,9997,583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,7980,942,3075,779,3651
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2055,3759,2539,5971,50615,3157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 823,8473,2053,94235,6383,643394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1270,10243,85569,6280,7021,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1316,79144,7941,2266,197,629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 875,3690,166785,7036,8743,3030
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,196385,27089,32,11222,1543
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 112817,4700,124976,3990,7494,10497
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55486,7466,23038,7249,79602,7177
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2101,29880,9475,28951,7276,60412
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5581,432369,5465,55805,79191,29926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8764,3308,4973,5054,6402,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6934,3930,81689,10841,7010,81031
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7480,22877,6391,4099,178,4171
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 121268,5745,859,10365,1149,4855
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8803,3938,5196,2937,2646,7840
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5091,8029,5920,7077,5828,2584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6550,7840,148713,253827,718,1116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3766,6439,4129,11254,1393,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56606,3460,1071,2984,6678,2170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7350,5296,316,1028,125988,2222
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 52.594   1.527  54.103