Mustafa Erhan Ozer
| Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: RELEASE_3_19 |
| git_last_commit: 8015edf |
| git_last_commit_date: 2024-04-30 11:49:19 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-09 17:42 -0400 (Tue, 09 Jul 2024).
| 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" | 4709 |
| 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 | ||||
| Package 2112/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.4.0 (landing page) Mustafa Erhan Ozer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| 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: 2024-07-08 12:49:27 -0400 (Mon, 08 Jul 2024) |
| EndedAt: 2024-07-08 12:59:31 -0400 (Mon, 08 Jul 2024) |
| EllapsedTime: 604.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 12.7.4
* 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
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)
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: 25813,2034,5618,187,3764,3551
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 118,8876,80222,3615,3401,1442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,522,9380,1365,3557,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3458,3479,7350,7084,5160,3290
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64241,51116,8722,3690,2799,5742
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2475,124454,2572,2992,1056,7275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4285,6901,2100,23410,406,3929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4779,5551,7200,246,23576,6357
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 92483,6833,51092,29929,9475,3293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51422,2745,8932,493927,10845,5836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388125,6382,387082,22796,8876,654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10991,283459,6584,285126,9409,5288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 275,100,6794,4864,7295,3654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5824,316,6548,54205,9365,79731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64102,9945,137682,2159,410,3458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116931,3485,1634,5274,229,6351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2944,6948,54704,383,2798,9122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6521,6554,7386,797,6718,347411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 435,55149,340706,2653,397491,54331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22901,1116,63874,64102,1803,54106
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63874,9429,183,9314,4540,145741
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6329,650,7916,1149,599,8560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3458,55867,9672,203,57016,205327
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7049,3556,51106,549,325,26580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2639,29843,4012,6834,1244,285848
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54600,8029,4594,200539,5329,2108
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6093,2690,4842,5175,23400,3569
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3170,4282,285848,5644,6718,3312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5727,1843,476,2271,6868,10686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4256,51094,3105,10522,2947,1583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4286,26517,6462,5644,4758,6097
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3586,3676,54901,5261,1493,7515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,1621,406906,4128,91949,8694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 779,2108,81031,409,617,6285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 353500,4729,5962,1361,7507,1593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1030,407004,308,2235,4779,66036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1909,920,79001,84889,1075,84705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10365,54575,5122,2395,122961,4891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,2804,3485,10911,6351,6390
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10243,7100,6906,255308,9475,509
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54331,4773,7291,5618,4009,952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4313,7035,55788,2847,410,640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 624,81034,406922,11231,9927,2632
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 712,5274,797,2303,549,10019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7177,25821,6941,79572,4094,64919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,7369,5551,6256,801,2109
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84063,6356,80142,6406,185,22868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6476,57505,5295,9056,51083,7056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4719,9722,203859,6348,65993,54902
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 35,8195,55967,6647,2904,11254
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80854,10667,5617,100303755,10272,2146
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6338,496,65080,5625,4283,1369
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57620,54915,6390,7057,8942,7292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,7852,148738,153642,3375,57817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7352,3992,6387,1499,886,4126
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9104,6696,7274,5891,25813,4162
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80207,411,8678,11222,5771,3098
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2309,410,2542,23054,54575,5802
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 37,10250,5193,5744,81689,23564
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,4552,1051,2632,8651,7480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5029,3654,9560,718,2161,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5228,1716,253827,23365,4695,7032
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79944,1583,182,2852,8309,5009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6446,410,5625,6391,63892,2161
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388753,2555,3816,361,84317,23600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2520,5360,10102,9076,4312,57678
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1364,4864,1348,6891,3767,790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51316,6357,2677,6521,29880,1149
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4092,6928,2152,7369,79585,79944
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1185,5092,79053,2101,9971,9180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5167,8398,5770,3159,6019,50639
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,1369,7840,10644,3991,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2678,26291,2170,133396,1361,1645
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1244,211,1356,4700,116228,6182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4208,3832,1571,5837,4214,518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 158,5726,10466,6608,728294,8803
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2693,7032,10667,63899,6678,91647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9370,5096,85569,27097,516,1544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1230,5265,3931,1490,6198,132
--> return NULL...
2024-07-08 12:59:16.899 R[67410:2066371349] XType: com.apple.fonts is not accessible.
2024-07-08 12:59:16.901 R[67410:2066371349] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
89.676 2.178 98.432
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 1.283 | 0.062 | 1.413 | |