##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘1.4.0’
* 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 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-beta-2024-04-15_r86425/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 beta (2024-04-15 r86425) -- "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: 3329,3316,29078,9512,7351,6564
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4684,7057,4288,8660,3304,1352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6941,10094,1471,4247,112609,5837
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28976,84705,2064,114899,3625,8517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,5360,5243,943,23163,776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5770,2520,1072,149461,6289,25805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 246,3426,840,427,54210,2152
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3373,23291,8945,1509,1201,2113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9572,4099,55937,2147,26762,165
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29843,270,27089,6232,5745,2203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1443,572,10999,4887,4247,1268
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55149,9997,123099,3394,2713,8784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84334,585,7177,53345,325,6462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4099,4536,361,1409,7369,100133941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3920,6382,6602,3764,3605,23600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84735,9619,7385,1186,118,2203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4792,6678,4277,145741,3091,84706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2520,1583,56623,64135,51117,199
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7538,574447,3813,6093,1208,9722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 847,7056,5730,4023,4973,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 52,7015,4973,409,475,5054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2683,2629,406938,5498,3764,5507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6929,3065,397491,6289,644974,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10062,7010,7021,5580,5029,111
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6382,9437,27097,9882,3683,9317
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 124976,92609,2321,335,2852,4277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6715,7015,3690,3119,3938,48
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83440,2695,4478,5106,27429,64116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6647,5563,6720,325,3606,2057
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,1200,5740,3054,5730,177
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6833,165,84340,2161,7099,409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4521,6608,4018,796,9241,5601
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 642489,2643,7515,941,9512,109
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 653361,79949,56606,6834,8799,5092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5373,9388,79144,2119,7325,4092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11254,1443,1582,7049,2592,3075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10938,1893,341,55486,51106,2820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,9104,57192,4489,2321,114815
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2908,25805,2547,2992,6615,336
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7220,2235,790,338,2693,650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2642,3938,5369,51316,2395,148713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4060,4009,5792,3685,6510,5443
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407021,23516,9332,3645,2820,91452
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8682,4255,9572,80347,5599,23516
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1520,5328,4129,26227,2683,3685
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3351,79602,4318,728294,8560,43
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54915,2135,2308,1075,7133,2335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 629,241,5593,126328,84239,6716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4508,5009,5589,89823,2057,640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51052,2158,5243,3643,57104,6833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 479,4544,6502,5236,6287,3394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84889,85479,6248,4580,7048,4159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22852,10857,4609,23411,4722,440503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728,6659,6814,388753,23175,4358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114548,100131801,123283,55163,3553,337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5023,55750,3958,57761,6548,3939
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 643387,5592,6868,196385,1650,6521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6833,2395,5787,6427,55243,1244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8398,79827,9311,3760,2006,84868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55788,2932,23082,50639,4478,64102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406947,3990,1606,4358,777,3625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9479,549,6329,8659,3995,2517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 841,5306,694,26119,825,341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1471,10842,4891,7287,253559,3099
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,1056,64801,2896,23291,54539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4868,3991,406903,4968,10243,89874
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9826,56945,6908,1033,10008,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51555,28958,1230,2778,270,4982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7284,10102,1514,942,1641,6340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57104,54982,538,4276,5962,23038
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 867,22845,2745,50615,4891,2847
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4150,25828,643394,109,2314,1889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55149,1591,10135,7295,6272,54578
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2166,91942,79087,6722,2006,207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116150,4040,27329,23178,1066,7124
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3784,406947,1493,55885,217,3687
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64805,5428,10094,5584,5599,1843
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1650,5589,818,728294,64122,367
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10845,84701,6530,5970,5860,5194
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 65.076   1.358  66.553