##############################################################################
##############################################################################
###
### 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 4.4.1 (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 13.6.5
* 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-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: 2885,4615,959,644974,2055,8764
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5971,4878,57570,4700,5590,79071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3283,1436,10524,10644,55858,100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2538,367,8799,11095,5629,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54982,200186,9965,776,5473,10165
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3155,65993,7352,942,11019,8567
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6275,100156321,4017,2119,51141,7019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51555,6389,7035,594,3501,9095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51116,958,6439,3795,5770,132158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6256,5802,406938,3439,4151,4318
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57192,4843,10549,2159,64801,109
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9076,5068,6523,4726,6554,9941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4720,5592,3606,27344,4000,867
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,595,1232,5315,1392,4878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 31,6584,80724,6097,1591,3875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3627,85569,1019,407006,219,3875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 256297,26227,3553,183,79949,3105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,183,55572,7381,2778,91869
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27141,9365,5629,773,4535,3576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10559,7942,2729,2889,664,1678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3759,1277,1428,498,1281,6804
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7507,6999,1232,90624,246,6648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1033,3766,2646,3636,81033,4285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7139,338328,6389,6289,4656,285126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8567,54806,114884,1135,90865,6510
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3931,5476,54896,657,116085,8803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5792,2677,3931,105372280,1493,94235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4976,79689,8835,10891,10644,2335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6462,341,8660,65985,79949,347411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285,114899,79587,5365,118,3791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56997,5241,868,7124,5565,4489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,2784,9672,187,81029,3952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1815,6198,3934,1813,9619,7275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3054,4023,3570,8609,51119,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4544,217,4162,23038,5451,57048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81570,7287,4728,445,5967,22926
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7056,6566,8660,2266,4694,152078
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7249,2712,246,1382,9526,8802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1491,54577,175,4968,4744,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407040,22933,57620,811,9971,6948
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2739,2305,5962,23564,3651,9451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10874,1499,80267,60,5052,3952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 265,10094,2335,83854,664,6868
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2997,2101,3304,729230,9451,10666
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6696,788,60412,5116,26521,2932
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5176,2992,10965,8309,1789,2919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3978,10316,7376,1678,80222,3284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23175,2026,7249,5095,54344,57620
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 551,1393,11136,197,2180,3155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6514,406982,5660,51604,102,1033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 59340,5195,1340,1585,4311,3551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84735,51316,4925,1401,4040,2308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3091,7049,5176,1185,2950,6354
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 196743,952,56244,8675,407021,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81031,56606,6622,2896,124454,129787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,1968,55024,5360,4092,1537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2639,5629,27247,1607,2998,23479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7049,558,5443,4000,80309,5068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 145741,3416,759,54539,5617,55024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6602,9076,5274,2875,9512,2247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51106,85569,9941,27235,63874,27232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3030,3551,8455,5468,80270,6556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7321,54344,63899,2395,6383,6555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3375,170302,3426,2989,653509,655
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1382,100132285,7015,718,199,55315
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2702,66036,10724,2740,79602,6615
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3569,4864,3764,10295,2100,4009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,1346,57001,4609,81029,5052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2947,5968,2303,59067,3551,7372
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,7421,5241,4864,84334,3815
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1352,7369,83440,1649,9388,54600
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6446,51092,1889,5571,207,3507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84277,7351,84735,840,5428,23590
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29078,1582,51141,94235,776,26291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5293,5788,1555,593,7345,2990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4256,4860,1581,27141,5726,5116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5837,5053,4247,7025,5214,594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55586,7389,79158,4855,8682,166785
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2280,2542,1316,1514,1636,4144
--> return NULL...
2024-07-16 00:34:40.352 R[70845:157261871] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 17.573   0.323  17.913