##############################################################################
##############################################################################
###
### 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: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.4.0’
* 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-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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: 80267,1028,5264,5139,9512,64220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,7839,4695,2792,2990,9971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84239,5629,389692,54476,6523,4035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338,35,2638,2559,6354,3600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100131801,3316,6427,104,406913,326625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10559,3502,4153,9607,5467,1489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,4627,9882,2660,432369,9630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8471,2904,4162,5325,5891,627
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85479,2520,23706,4041,1435,2166
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64919,8471,7035,55065,6236,10423
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5320,1327,7253,80070,3630,4548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 821,599,57570,1909,9663,4938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2875,6721,6469,9817,366,10243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 590,3418,344905,3280,7167,85365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9971,270,6777,648998,5589,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4669,1509,3978,5116,3779,5327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1056,4256,9437,30009,138050,182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10094,5052,1277,1645,84334,79587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5586,79949,2889,10891,7368,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5296,435,1329,23530,117289,4521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5538,116085,4256,7480,4702,3636
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53947,6548,6464,2516,6357,6928
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 640,594,3081,11093,3122,7054
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7368,6833,332,2628,3172,3945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51004,2997,5581,6401,7486,929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 31,64122,7507,2548,197,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 201595,29843,9104,59067,79731,4567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9965,1401,162417,50674,5320,3394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3553,2335,1558,4012,55829,7078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2696,3574,9429,57017,6530,3105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5451,10269,3054,2876,3663,2584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4973,3099,27235,57554,50615,1950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6374,293,6097,3423,5428,1118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6287,4586,2314,5350,150379,10250
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57107,788,3157,7037,285126,1374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2314,514,3934,338821,7082,6198
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2488,5428,406906,3032,6352,6915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50615,4000,56923,64087,6382,2673
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6571,185,10457,79144,6523,3717
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25828,6550,3117,54331,8682,7389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 859,156,857,145264,3624,8517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1678,101180976,3624,5498,60412,643394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1869,8879,4277,5594,2646,117289
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4724,28957,10841,3709,241,55600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79191,200205,125170,6256,29926,629
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 823,84842,348,1645,2064,55768
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 411,1113,10842,28976,257313,23436
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5122,57554,11200,388962,1051,4938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84705,7025,4125,2101,4015,840
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10019,2787,83884,54331,1806,186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 59272,101180976,2593,4144,4547,148979
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5196,3356,5350,3778,23178,10666
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 185,23411,1509,6906,4591,2592
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51,6804,728441,2487,4137,4276
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2168,10423,2949,10316,1509,3708
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9317,1678,4159,23409,56259,5189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3948,2520,23479,3145,3081,9663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3043,2701,9370,8742,9377,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2638,1312,2762,4988,51555,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3658,2934,285126,4773,5950,10886
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6319,38,1185,513,84987,6007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2885,1591,6908,2804,91869,4126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4217,4891,2487,54578,8813,3375
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54577,6348,208,3417,514,2798
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,3115,27247,1499,4124,4088
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7384,4313,79585,6448,55600,84274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,2878,3766,3483,3559,1716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1644,10365,943,4656,119559,56945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,4609,124454,4714,486,4792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 93587,1548,3802,570,3406,8029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4886,549,3645,759,5802,54902
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4536,4780,2787,5331,80222,5507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3240,5193,1798,56945,3119,4023
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 117289,90070,1028,3117,1027,5189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1812,6462,55967,7084,132158,84277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 335,6492,3113,7345,84684,85365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54704,51094,3690,6356,10226,7364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2487,1072,28976,6248,210,3664
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123263,55024,9759,943,3615,8639
--> return NULL...
2024-05-30 00:15:24.721 R[26394:1974149168] XType: com.apple.fonts is not accessible.
2024-05-30 00:15:24.722 R[26394:1974149168] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 53.295   1.590  55.364