##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* 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 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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: aarch64-apple-darwin20

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: 9572,3577,2056,7253,1051,178
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8932,4855,5787,7538,2308,6441
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114814,5728,53345,1815,2739,3383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 476,6019,2638,7295,388372,6521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51099,5409,4041,7078,1548,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84684,6530,203859,347411,2944,496
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388372,6620,1027,55867,3358,122961
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23479,7408,7430,151,54344,64135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3101,2308,7368,25828,8862,5625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 112817,29851,5590,4860,10643,1030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55340,836,4144,3486,1806,79796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4318,3945,1493,191,11136,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 435,9420,3938,1147,5617,10400
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3101,55034,149461,345,4286,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4914,344905,275,3759,3625,90070
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407008,471,256471,285848,4722,55586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3932,471,7036,191,2944,3479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3174,445,6009,4524,57001,51703
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2524,80224,142,10159,57678,9056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6232,4540,8818,5328,5629,581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7297,8803,84705,7507,6720,7036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1548,5406,6329,116228,217,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51106,3875,6721,133396,54896,66036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3691,1757,79644,38,23054,6772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 624,59272,6351,3382,64919,2593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23054,285848,92667,3875,538,617
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7139,3920,4843,5726,3978,5592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4580,38,10560,1409,84684,23654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2660,253559,11095,1435,10157,2203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5106,7352,4162,5095,51021,411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285848,256471,6376,8560,1594,1373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7078,2030,8799,1361,57817,9332
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4938,2271,5096,7915,10295,4860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4035,3640,653,3156,29928,158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 847,1605,728,54802,100133941,1392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5276,10644,3767,133,6515,3032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6999,401,55586,9759,2739,7355
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7390,23101,6351,55270,25974,55805
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23178,4023,8218,25828,213,4125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10845,4015,726,3119,4285,26521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53346,1644,6445,50484,9518,10965
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5590,2989,3663,5193,1348,80201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407024,7097,10379,5325,51092,2235
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84300,2788,111,793,201595,37
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3759,1581,5236,2998,26119,10644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9095,84902,2119,5824,51004,7177
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 212,210,51119,3663,7480,54576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4306,10628,148979,5467,5189,200186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57818,79783,53345,1890,9927,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5277,1033,844,9563,1200,6821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5133,2109,9968,3385,3293,9526
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65018,10229,55699,4668,7839,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,51052,2653,54476,2729,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54896,5447,51660,1716,6183,11266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7442,7915,653361,55283,2597,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 28976,4705,361,80854,1728,79661
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4357,1116,7252,8398,3710,1565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91949,5277,4017,4595,846,653509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50674,4879,1499,3106,920,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3562,4092,909,5364,10938,5972
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6389,11255,522,3074,151306,1815
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55644,5190,89874,101180976,4094,1555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51103,9512,6523,5968,4126,10
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 706,2068,8604,336,10911,63931
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,6715,5245,26119,80224,858
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10320,142,3358,9722,2762,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3507,4855,1268,84649,1468,1644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6007,4323,100156321,10580,10497,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6927,2524,1444,6510,2710,5255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8740,23436,29851,7157,9365,4017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5325,9475,497231,7295,406947,1737
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 434,859,6340,4233,80270,1071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 215,5236,81788,5740,3995,3316
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6523,4552,10497,3091,5687,3762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,3087,2194,5350,2169,6275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3636,7025,5175,11232,54344,9663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,53335,7248,3636,1644,23654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 624,1468,1277,10320,3598,6464
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4162,1329,8854,23291,7498,7486
--> return NULL...
2024-07-09 11:22:23.832 R[54357:122384361] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 52.420   1.055  53.888