##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.5.0’
* 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 Patched (2024-04-24 r86482) -- "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: 26762,5599,4091,116150,1185,6583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2547,80347,3062,22797,6550,1718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3401,407006,3043,2804,567,655
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2952,3575,3416,27247,6258,114814
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2696,3586,55600,8835,445,28958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1593,7350,9380,51703,55644,2548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7252,5967,79783,353500,3425,3501
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,5787,27089,9882,1373,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1734,1030,648998,9945,115286,64900
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7100,59067,599,114548,6690,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10842,3593,1444,5601,7424,26191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9927,3980,6199,7381,33,10243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7036,27141,205327,3401,51441,5662
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55243,9370,90480,123263,3709,5806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53345,5498,8877,7471,6288,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2628,3172,30061,11266,51703,4159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4697,51081,6891,644096,79001,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3098,7422,6414,5168,28958,5581
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9692,1019,2787,409,2581,350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1428,3240,9445,216,9374,57511
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1514,388372,1968,4153,858,2776
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79731,114814,5365,8877,4276,6531
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2632,3958,3106,6343,10269,4795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2155,6289,6280,5919,338328,59067
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5476,4704,3502,4880,6280,23474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 823,10008,80207,5294,5428,655
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3105,2243,11095,5184,3295,8218
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3654,197,1734,3351,6513,2310
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54658,7368,7879,201305,54577,2989
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54802,54575,64240,4126,11255,477
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116150,2950,3418,9563,391051,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2101,6447,3598,5498,3073,6446
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27232,4552,56922,6523,4536,5979
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2739,3155,26191,406922,1573,84868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 617,793,800,2271,7026,55818
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3676,2717,572,1803,6515,642489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 355,156,1672,2520,5230,5029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3638,345,1027,1066,7916,6774
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 800,7295,9415,80724,54577,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,6287,2235,7381,3760,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9437,100128525,7915,2235,410,51083
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57016,5428,79191,3308,54805,151306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 101180976,4548,7124,10457,64772,10466
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84557,5296,6462,5108,30061,6248
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,4128,2932,1355,1244,3406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 203,3316,8799,84649,348,5228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1786,4868,1050,8802,241,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6659,3643,10116,84684,3099,126328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1843,6609,6715,1544,6199,85479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2006,7056,6569,81033,23753,37
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3709,7386,10845,1118,23365,4976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5257,1555,4855,207,1909,4976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3552,3703,9630,635,496,1191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 909,2677,7424,3556,8788,3795
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4210,656,197,1028,2954,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7292,3577,6814,2992,7100,4864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9692,6007,6522,5264,4009,4338
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2555,57505,83884,6347,130120,3351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5330,516,2244,25839,3636,91949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1950,6777,7919,6515,7021,3394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79783,6340,1234,1520,7916,8740
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3683,5330,3759,2184,583,23586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 494324,858,401,952,3574,2030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55243,7057,7124,2260,54968,3773
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10666,3240,3667,4015,29126,5901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 52,406947,80224,64801,3032,6647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2475,4705,3572,5715,2638,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116085,3250,653509,54,3099,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9021,1537,2006,5325,1646,23753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 513,6657,7252,59340,655,1565
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6715,3645,90480,2592,11266,5255
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54414,2592,4012,84842,51601,7249
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5968,51316,1601,28951,5728,3845
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2690,2875,92935,91949,3978,2762
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7422,4868,406947,2348,1234,2309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4214,3717,344905,4598,57001,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5588,23530,5162,63874,6329,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55586,350,23576,1520,114814,22796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50639,2908,4009,3502,9451,3566
--> return NULL...
2024-05-02 12:42:32.744 R[98850:443818958] XType: com.apple.fonts is not accessible.
2024-05-02 12:42:32.747 R[98850:443818958] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 91.313   2.249 103.423