##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SVMDO_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.0/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: aarch64-unknown-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: 640,7381,9826,3728,1369,6095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10935,4795,7276,80207,796,3845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3315,7827,10842,57128,55805,54809
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6288,10857,3081,8945,2653,2820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5654,6401,3250,9945,2776,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1312,3598,125988,155,6834,23236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2889,3980,3375,644974,3060,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1337,4232,66036,4351,2713,1594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7276,3670,18,3502,9131,1030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6097,5771,4162,7040,10135,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5236,84842,10745,1244,27429,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6232,406903,3483,11231,5055,9607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3115,1910,1557,7409,3627,7076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4088,123283,84701,2271,728642,3684
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 217,4126,5365,7124,3105,643387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3630,7100,6462,5598,1191,1066
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5715,2166,1798,124976,7407,4852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 166785,7032,5571,5190,1392,5372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54205,54901,644974,57176,4938,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27249,5191,3460,100156321,2638,100126861
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6582,4938,2776,4057,4012,5979
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406938,83884,23365,23411,2099,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9255,4151,1050,4591,9619,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4247,241,1030,4723,5744,629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1346,5580,27089,5188,11093,1075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1557,6341,5629,7409,7355,4049
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9180,3949,50674,8431,5106,1869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6775,8942,341,112817,54576,1555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5190,5294,4009,123,7919,9180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5313,407040,326625,2159,10560,3119
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7133,3811,2762,1361,1910,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 265,4842,3623,1339,9415,55670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80142,54600,3423,25839,1316,7220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3145,84334,7369,1584,84239,3956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55586,790,3416,4973,2645,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100506742,8932,10128,2948,2057,270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1893,81704,5167,5069,7167,596
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2952,942,2395,38,2588,201305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 401,5306,231,81033,8648,51004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91452,3099,3710,5367,79689,4700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2639,7352,93587,6532,83854,63892
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10379,582,10272,4057,6774,51
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2006,4144,2119,3605,4709,9095
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80142,9420,7052,7321,1208,3929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10134,1443,3293,6715,56922,3123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55863,57264,51548,8841,22852,2475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 326625,11231,212,3439,7052,3667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6256,9382,5331,6915,1337,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60412,6183,57176,3385,10102,4878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8651,54414,5108,4283,64788,686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23411,4773,4162,2950,25974,4313
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 355,7528,1806,1645,1409,801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1490,6526,3481,54578,3703,3484
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6941,1573,147007,5428,1728,3425
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80339,6531,5601,5891,2653,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4000,2247,3553,5621,55340,326625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6786,4688,6648,9588,1355,3803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1559,9314,51099,112817,821,5139
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5820,3815,836,79796,1351,6583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8945,6356,5194,728441,55867,4852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388372,4040,2110,28957,55967,55270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2702,2908,9445,10221,599,246
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5055,212,4221,5828,3482,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3032,2731,3099,5506,316,9514
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60,4338,5116,6447,9572,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1717,8471,4548,55065,5562,654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5160,5586,124454,7376,64788,7351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 494324,2947,3700,8802,4306,9512
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4668,8803,2055,818,6564,80207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51024,648998,4720,1312,2643,653509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83985,7021,3978,5595,3479,23474
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2539,3929,3586,999,5972,119559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4854,5189,9512,142,7841,4091
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 183,100506742,5538,3172,5315,101180976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25801,1893,150379,9104,255308,1558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 216,3309,256764,119559,11035,5294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5193,6941,23389,779,3034,256297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148713,2135,2997,26762,79944,54931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3350,7442,3394,2235,2161,648998
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 62.966   1.023  64.062