Mustafa Erhan Ozer
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/SVMDO |
| git_branch: devel |
| git_last_commit: b5eba63 |
| git_last_commit_date: 2024-04-30 11:49:19 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 2052/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.5.0 (landing page) Mustafa Erhan Ozer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2024-06-10 10:58:12 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 11:08:17 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 604.5 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_1.5.0.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
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 4.4.0 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: 2889,100128525,1050,55034,6383,7386
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,7276,1340,81570,79144,114814
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 208,155,91942,4938,6441,4282
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1678,3551,1468,285848,2542,80347
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2555,182,3502,4702,3303,7368
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6285,407007,5409,1555,7840,2068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4478,790955,825,5139,9965,133396
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3559,1361,9518,4722,7369,341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,7442,7498,6649,1606,407008
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197,8517,63892,229,4729,7480
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3978,7248,6340,2934,308,8195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2628,316,4040,5901,2694,387082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3768,241,51099,1591,6678,7919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,55586,5654,7135,151,407024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7010,3638,5580,2876,1056,6584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10886,1499,50943,81689,1051,8074
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23389,1737,6890,50484,1374,4982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51738,653,6566,6448,10019,479
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3358,1493,7916,23129,7538,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9056,3383,6441,90480,2673,5660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 712,51092,55829,140803,5805,10935
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100131801,1435,5257,2937,3554,344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4760,29947,5092,1393,26873,125170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4712,1043,350,2896,2119,1956
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11232,7852,3791,340024,6289,6505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 558,6579,23516,4938,8660,407040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3766,2321,6554,6389,3481,2539
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,6352,3596,79144,9479,2720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5020,112609,56997,56606,4256,169792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 253559,3625,8856,2990,2778,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1591,1582,387,1559,339,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407006,364,5175,7135,5919,51004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5270,493927,7386,3630,9180,1080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5770,7291,57817,7019,10229,2852
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,56923,3172,26235,4925,255308
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2878,9095,84987,2673,27445,9941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,999,2788,316,1191,1348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8050,7507,1135,1555,7289,5019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7942,1789,1646,5590,79587,6288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 509,80854,2919,6289,5175,3172
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3717,3251,9317,8879,54600,64801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5740,5080,5126,54575,2767,728294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8682,51601,558,2639,3592,6620
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3728,25805,9965,5593,5108,4000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5195,4671,23409,55532,2520,54575
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644096,407004,2181,5538,7409,64919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3703,27247,8665,1968,84842,338328
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2694,6279,10911,1201,5029,8195
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160428,5406,2786,152078,581,1052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5745,3802,7026,3763,54106,1716
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10135,952,54809,3760,5108,3654
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9332,3486,3766,2778,57580,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3685,23118,83440,9512,3295,124976
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23400,3339,246,6198,1789,8560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644096,84902,407024,5728,4522,4855
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57128,1649,5091,5054,5787,407021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116931,7466,54577,4023,3119,4973
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57580,1346,2475,79949,9526,81034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79783,10522,2745,1027,1493,10667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10842,1559,5950,2520,1815,10841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3667,2792,5971,2056,1605,1348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51106,518,2677,2739,5368,340024
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2235,43,1382,3280,51293,6748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64788,57001,479,6256,388753,5194
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1030,1950,2820,694,9370,823
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4891,337,2135,25805,4671,3779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7498,115286,5805,1443,5589,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4973,1027,64122,920,509,1376
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,10102,55816,23600,2572,2314
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79661,1807,4069,347411,796,9826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6391,5741,2158,2542,5624,5598
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4247,2266,64102,11183,3458,2992
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3624,64788,27010,50507,347,3562
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6256,2548,4982,405,23163,100
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5160,397491,5825,64135,5592,5009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9388,56938,29926,2787,643394,285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2184,84987,54578,23706,9255,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2547,9311,3295,2989,8600,54576
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1716,407024,6696,857,2146,1738
--> return NULL...
2024-06-10 11:08:01.743 R[47043:489614532] XType: com.apple.fonts is not accessible.
2024-06-10 11:08:01.745 R[47043:489614532] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
92.791 2.145 101.490
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 1.273 | 0.067 | 1.447 | |