Multiple platform build/check report for BioC 3.19 - CHECK results for SVMDO on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4741
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4483
merida1	macOS 12.7.4 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4512
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4461
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for SVMDO on merida1

To the developers/maintainers of the SVMDO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SVMDO.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: SVMDO

Version: 1.4.0

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

StartedAt: 2024-07-11 12:46:18 -0400 (Thu, 11 Jul 2024)

EndedAt: 2024-07-11 12:56:51 -0400 (Thu, 11 Jul 2024)

EllapsedTime: 632.5 seconds

RetCode: 0

Status: OK

CheckDir: SVMDO.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 4.4.1 (2024-06-14)
* 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 12.7.5
* 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
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
runGUI 1.277   0.07   8.125
* 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

Installation output

SVMDO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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)

Tests output

SVMDO.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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: 391051,5255,388962,5445,123,11255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80201,91869,11255,118,203859,3956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6564,2642,3949,80854,7035,1589
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57818,348,3553,5207,10845,7056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4312,9415,5830,4351,166785,4009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3291,644096,10730,6620,3483,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7538,759,51703,5029,5507,8604
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30009,10135,3553,2155,7297,81033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4938,9868,2310,4247,4276,5228
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2806,6608,10379,5345,2694,1798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5071,1675,3440,4036,284184,768239
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,316,648998,338821,4826,2335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5078,1489,2646,549,29843,7297
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 475,3131,1605,1348,22926,51458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5506,266,91942,10400,3768,493753
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3339,6716,84061,3934,4915,81689
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,7391,5188,6522,2745,1337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10577,8818,6571,64087,91647,4040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83737,4040,65993,4828,648998,10466
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1471,7082,79934,84317,25839,8714
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1201,211,2689,6248,84947,3949
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493927,1182,4057,84063,1543,2548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2695,406938,10134,1910,5860,1050
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1027,7056,4886,7389,10059,54344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5617,55970,2547,1185,3664,54577
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3658,10128,5095,2395,6446,55586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3684,1608,10128,2161,2158,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8841,866,5327,2244,2167,2168
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8784,2582,2166,2688,643181,1232
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1890,7048,22797,5196,8743,7919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4321,5139,2710,2590,5095,5243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 640,2520,6319,347,5443,7167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1268,2539,8879,4854,376497,8609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6690,462,1675,632,55816,189
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55283,85479,488,81704,57817,432369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2694,6569,6319,6406,3426,4669
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3157,4337,11019,1798,2068,4009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2310,1116,8835,3283,130589,5586
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3131,2791,5449,149461,6301,2524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84557,8945,5744,25821,4159,7916
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 213,9560,5740,23129,2731,4854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7132,6531,1066,9588,2852,79796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9122,3082,4015,8517,3356,116985
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55340,6232,147007,2115,64087,486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406991,2244,409,3406,1893,64087
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2146,1514,2582,2158,4988,10466
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2936,3292,1524,2166,6376,3115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6890,7538,2026,1327,653361,885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 265,8682,6392,7253,376497,6524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6536,2932,1584,5962,152078,64772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2712,23556,10159,2639,1329,3456
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 191,3978,496,6392,7276,23564
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4864,1558,51660,6536,366,64131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,2834,51128,2101,340024,537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25821,5563,124454,3939,818,6569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338328,9311,292,5055,4744,1191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3990,517,5364,1401,285848,726
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1072,3638,7424,3481,112817,4017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1191,2181,81031,6602,4057,51
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2588,5345,6915,4018,2678,9311
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23082,151306,4540,7915,1582,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 169026,11132,6019,6339,4988,3593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2303,8764,3779,596,5020,84277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3574,133522,477,6019,2310,2203
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 339,401,23564,3426,2693,4318
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 376497,9968,2785,4055,85365,821
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51083,55526,1244,112609,5654,7048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10643,728,2937,11266,9382,54539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2785,164656,7200,2597,64122,6721
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10060,120227,6690,55283,137682,9314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57818,5331,8788,4976,116228,6535
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3703,153642,84342,51660,1634,2835
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5592,9672,7384,2155,5029,5087
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81029,7841,3685,4712,1583,23365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,4091,3948,4694,582,54600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 30061,6720,1906,726,4758,9498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6775,208,777,868,4035,1950
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9241,5270,43,142,2786,5588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 440138,54576,4543,4522,5806,5820
--> return NULL...
2024-07-11 12:56:28.581 R[50315:78176034] XType: com.apple.fonts is not accessible.
2024-07-11 12:56:28.582 R[50315:78176034] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 92.128   2.803 106.136

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

name	user	system	elapsed
runGUI	1.277	0.070	8.125