##############################################################################
##############################################################################
###
### 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 4.4.0 (2024-04-24)
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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: 6659,2690,6348,23178,3688,3503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2555,100133941,3708,10642,4889,4586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3440,1116,2762,9619,55034,57016
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3423,54331,10497,1950,7841,4828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29079,7032,5727,2158,130589,3768
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57048,5588,2309,10243,3778,4160
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79133,10457,63874,6446,7098,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1051,435,6464,29947,5967,57570
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2790,6441,2538,1601,7135,4337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5095,123283,654,29929,3759,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3811,1649,643387,4171,8604,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9369,23054,886,6522,79689,9969
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2989,5008,9498,1508,406,11095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2170,6834,7018,8665,2717,3551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 256764,6647,6566,119559,5360,5162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7226,2806,121268,23446,5243,4780
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10008,332,3683,6343,2161,1558
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 34,3689,4285,55768,1737,338821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9475,3658,11213,7100,10682,10667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80854,57176,6387,3939,50814,54806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1365,8660,57620,100,8879,83854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10013,5601,9526,10549,3766,3034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9365,257313,5621,30009,23400,401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5836,196385,5369,627,6382,54896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3624,4580,3802,64432,3766,6356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3401,27089,7919,2992,4171,79144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4792,170392,3670,255738,5588,4860
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,3816,361,7048,2720,1369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6566,54414,1672,55644,6716,2804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51004,10320,6515,1393,55816,11019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27097,64220,5188,9180,91869,2878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,6513,355,5328,3574,6391
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4864,79068,3932,2798,285848,2697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3099,55065,25974,3077,3145,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3640,3627,84572,3992,203,4889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3833,4124,80224,27429,5629,23365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,5069,1621,391051,773,7291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387082,3956,6555,79001,706,54
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2200,7430,51703,1815,1113,217
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3551,1815,1200,1607,340024,966
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10965,151306,83440,3791,112609,6622
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55750,124976,1588,5096,355,7172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1548,7422,6390,2115,8803,811
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25839,3586,5188,6279,23129,27089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2053,55005,54658,50814,29881,5447
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2308,10020,5950,3784,3309,23590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,80222,1200,6659,3953,79689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4982,1339,4321,6232,35,2057
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2984,43,1508,506,80070,648998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,4724,3784,3106,7350,6183
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3664,23082,11222,10059,6722,7408
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,11232,80331,3426,150379,361
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8742,5116,5741,3768,5979,9868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92667,2875,116085,4795,89823,79949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 366,867,7919,100125288,5160,875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2903,1678,3557,10745,1072,5618
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25828,3674,796,4552,6647,151306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10965,55858,4137,7082,2006,4878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114815,407024,229,5967,1718,1738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2113,2137,3062,10616,4128,55885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51081,55630,8462,3945,6522,617
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56244,1582,2950,160428,57215,3932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 776,64087,29960,4852,3304,51024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10497,7980,4069,156,10599,2919
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4233,4323,6891,51103,5571,4780
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114814,2804,9377,5105,114884,91452
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2180,51703,119559,90624,868,4915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6615,949,104,790,23175,10060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3625,3773,8714,8195,9451,9826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6348,84902,29960,3636,4092,7021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6403,644974,51141,30009,150379,3087
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55005,5726,6447,6337,3708,6275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 140803,79133,1493,51092,356,1491
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,4057,3507,10250,85479,6389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9380,4118,4864,4780,4718,5369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10295,4722,1312,63899,7025,2170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8694,4057,90624,2878,3113,7253
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6354,60386,2937,1812,5621,10135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406906,30009,6414,3760,359,256297
--> return NULL...
2024-06-28 11:43:47.120 R[58434:92938481] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 52.931   1.031  54.349