##############################################################################
##############################################################################
###
### 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_1.2.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SVMDO.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.2.8’
* 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 R 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 in ‘inst/doc’ ... 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/4.3-x86_64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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: 3803,440503,4914,79602,55699,83737
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4828,10229,154,84447,3779,112609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4891,4247,1543,91949,3773,4353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,3670,6517,9692,8854,2593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57620,2584,5286,6248,3351,51024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5213,4598,153,104,2767,3803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25974,90624,116985,23516,10642,2689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6439,3316,407024,940,1524,6928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1583,6515,4547,5277,4842,120227
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5194,6649,640,8803,3250,7010
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2335,5092,22933,7139,8743,1650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 229,351,5087,8609,186,498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5160,63892,27035,6354,9826,54704
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 231,55340,54414,3077,148979,2101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8722,114899,8862,1428,2157,92935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8050,11095,6576,6427,7355,8854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2937,653509,3802,3551,6019,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80207,7450,9514,5788,10577,64220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5105,116228,345,1182,2487,5968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4091,64801,10128,2989,51300,10272
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80309,407024,4535,138050,3339,191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5901,10316,5027,22877,4899,293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2303,60528,7035,340024,5979,486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4792,4055,3934,2948,2710,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,1509,11266,90624,5328,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1428,5161,56938,4683,53947,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4878,57061,1493,4886,875,10845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2571,187,253559,124454,2280,92935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51024,6526,2694,1382,2034,2547
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23038,6777,3920,26291,178,6324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92935,3640,551,6777,5771,93587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7384,51099,3382,3803,9369,5345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91942,55937,2697,6927,3091,5306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5133,866,170302,164656,5826,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55863,7284,728,1644,60684,54344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,406913,84701,3054,9759,3956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 358,5009,149461,6522,3066,10157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1589,4654,56997,55315,5741,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3929,2852,406991,5837,1594,2688
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4060,5805,112609,6927,1582,9451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 563,1186,63931,51052,1815,29928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3312,5294,100132285,84684,4886,3725
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 351,10745,3486,4899,2731,567
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149775,875,80224,84701,5771,8856
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11183,4536,3290,5654,55699,11095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2235,63874,712,7412,4153,54344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5451,150379,1052,80854,5092,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54578,6868,5825,587,708,23530
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9388,595,3687,3375,131118,1444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,4143,8714,23178,632,6288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1050,7084,60528,4684,9498,2908
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2235,340024,6548,10628,1718,2992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7295,1738,3709,5654,2729,5264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2159,6445,6868,3709,6571,23410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55065,3356,3293,643181,9314,5687
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 590,2638,2806,5193,7220,54658
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7386,1992,7135,3074,4852,51167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 115286,4151,10730,51,7021,5428
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6571,3816,64102,9021,2517,4144
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 213,10999,9241,9131,126328,2538
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5116,200205,5161,57107,2787,54539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79949,109,122961,9968,31,5950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149775,338557,1339,9414,3054,2184
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54902,6834,7852,2697,1185,2591
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53345,291,207,4914,5306,3122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5291,55065,6571,5116,773,153
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64135,5190,768239,5745,102,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104,2310,4282,4521,54,6376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1583,1608,6941,9255,4716,29926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,2395,27247,1080,6462,6564
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6576,23446,387,23054,9429,4852
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55970,4705,51004,655,3087,5891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84833,4313,8560,2739,5055,941
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 166785,3418,7325,6403,10682,3500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,2170,4536,1393,8842,2791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84063,3242,1491,493753,50674,6387
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 175,2068,3557,9619,5726,203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7471,1601,1392,2638,4656,6999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8431,81033,56718,4715,5330,1365
--> return NULL...
2024-04-16 09:50:29.029 R[89988:2553250696] XType: com.apple.fonts is not accessible.
2024-04-16 09:50:29.029 R[89988:2553250696] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 89.055   2.061  95.637