##############################################################################
##############################################################################
###
### 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: 50615,23118,147007,2591,801,4126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23082,55243,51738,100128525,3119,6341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3565,685,1374,2524,4887,407024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,84447,7284,2158,51548,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56259,7355,1889,7389,3081,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51555,599,3684,3098,2034,10250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 140803,23365,5467,2990,9388,4502
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 940,5293,653509,5920,1601,54822
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54210,7099,2053,55586,5726,8682
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5261,3562,130120,6502,4338,253943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9370,1201,25839,8942,55034,23129
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 231,100132285,186,81029,4891,155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,111,348,3953,3565,7033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,847,3664,29843,1348,514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1789,10365,55699,7019,138050,7879
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79572,56259,6532,10599,3988,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 256471,7177,5728,406903,2642,4826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9054,10577,3099,177,1442,10128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,427,25915,56458,116985,208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,440138,10643,9563,5092,3304
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3572,338821,32,3658,1588,11183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 800,7528,6401,3687,54331,6531
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1992,1316,4217,694,7135,5168
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3764,268,2181,266,9451,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9512,9388,6582,30009,256471,3664
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 842,712,7390,55278,57215,6720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4323,4868,498,5080,6868,7941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,6280,6696,3486,6427,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6019,9475,11232,54704,51458,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23446,9498,3654,10116,100126861,3479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4159,5077,3162,7084,1208,5581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4683,2030,6009,5373,9518,2904
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5373,54,54577,7253,2101,207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55243,1548,2847,6199,3931,1365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2712,91452,5507,23564,64240,249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,406906,54576,3700,5914,221895
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5296,9588,5294,26762,1394,28957
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6505,6392,2992,4314,6814,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2587,4282,4671,728294,6521,1175
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1392,2584,10724,6301,109,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6340,6941,5445,80222,776,1329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3991,1571,51,9512,7018,23101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65018,7295,5644,6289,55970,54331
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4015,2936,2835,55315,3066,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7077,3242,3643,316,4925,585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5625,3292,93587,1444,2280,148979
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55600,4150,1798,84649,79661,1028
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81788,2952,87178,4057,5191,4099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51092,3600,5265,516,3710,5788
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29851,1056,401,169792,8742,7350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22868,1270,27010,6890,1232,10999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55805,6389,7941,5195,84277,3929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,6932,5641,407021,2260,1497
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23706,221895,2989,10221,7364,6648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51422,7351,5726,4887,1717,4232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 59067,8517,2243,2834,1524,712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2785,255738,7980,51649,2806,112817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1232,4041,55270,2157,57061,84572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54210,1718,1571,55829,6901,28951
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,3703,54658,54577,79133,80142
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 952,3292,4023,8202,22845,9969
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2947,55532,635,388372,537,57048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,60386,643394,3832,10059,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5245,4712,619373,7364,79689,183
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2348,7021,133522,3501,7412,6256
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2948,4547,57061,3418,3600,2919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4719,2348,3559,1649,2542,4988
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6289,6401,537,31,1351,1786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1490,846,1588,145741,91647,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1371,22852,1369,55768,8788,1355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80724,2778,153,3456,5551,1718
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3577,8877,2903,7056,284184,2170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26235,55343,9997,10008,4695,7408
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7381,7390,23516,5087,55034,1270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63892,84274,729238,2792,6929,1401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50674,5368,4669,54106,2876,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3507,83440,476,6256,3480,8639
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7385,55532,2683,4536,7376,63874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1588,1270,11019,51422,4803,2157
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 51.617   1.178  52.772