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: 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 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 2024-06-09 23:27:04 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 23:32:04 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 299.9 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 4.4.0 (2024-04-24)
* 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 12.7.1
* 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 4.4.0 (2024-04-24) -- "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: 3931,4726,2697,7498,1352,5588
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2710,25805,207,1737,3074,8694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 150379,3670,7133,6383,407009,80331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1056,51441,231,2683,2135,241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26580,79731,4217,6510,79071,5792
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4705,5787,1027,5806,3423,57107
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6522,4351,2992,3375,10195,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25915,1581,7035,1019,4547,1409
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2954,132158,361,79934,4358,6521
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56259,4233,3685,2587,4976,5631
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 241,23054,9619,3562,79585,655
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1113,57554,23118,170392,91647,779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10666,3551,2903,100303755,384,2720
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54331,64772,652,858,6199,3113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23556,5499,2593,53632,5565,8665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285,6890,5662,518,80201,246
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9619,57818,2475,268,8818,3483
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29968,4803,9370,1672,1409,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2949,4729,9807,92609,2280,54896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1116,7284,5571,1471,3991,10229
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 231,4353,1116,3460,4973,6448
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1365,2157,1491,4586,619373,51649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3304,9314,476,6183,2947,192343
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 840,4852,4700,54809,3383,4864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 165,4803,367,1071,10094,5820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4221,1436,54106,405,5211,7528
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 151,2030,116519,5919,27247,2731
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 551,2762,3502,5211,148979,1813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5213,1509,5167,2559,3708,7139
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80347,25805,6821,2806,1992,3764
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8764,2628,777,2495,5662,2885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1327,8799,1555,56623,9663,10157
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2936,406991,4694,2056,1185,406947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 583,50943,1409,7915,5256,182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 115286,3685,5860,23038,83985,2786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50674,9514,4478,23600,8218,6515
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3456,4668,2889,170302,3811,28957
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3291,401,64102,3030,387082,4009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5188,376497,64240,6406,7026,5069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2712,22796,587,4285,55315,3503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 793,2760,4171,249,2660,112609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4709,4099,10295,361,3593,129787
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7021,3833,7421,406,4728,53335
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 341,32,50639,7412,79572,4694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4524,7098,84557,4012,55768,8660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1604,5078,1175,3932,7827,406913
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5213,1889,3486,617,186,1135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 593,337,7389,1606,79783,8660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29960,6289,57128,10128,5274,7132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406991,5211,10599,4704,2946,2395
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4726,4124,7942,221895,26119,10580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5824,9180,6536,25915,8659,486
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 685,256297,590,5009,7422,3034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7031,2875,7172,3636,1909,643394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 818,81031,2890,5499,203859,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3439,4925,9365,3312,54896,5562
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2147,10166,131669,8604,4150,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 177,116519,2348,406982,1869,266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84317,1606,10911,4247,4323,79827
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2328,10365,55829,5160,84705,6519
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5925,56052,10524,644096,100126861,1573
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5742,2559,1514,4055,90480,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5230,4126,3816,6343,4548,5919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54414,3802,60528,6232,7037,9560
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5551,8862,5105,10019,196743,7225
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407009,1548,6521,3562,6343,10059
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 788,10000,3645,9969,7471,116085
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3501,10841,100125288,477,10165,10128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1281,10730,156,6890,18,5919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2146,3439,4035,81570,91869,2896
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79158,7386,2113,26088,5781,10935
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4700,26227,10730,2170,3685,5579
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1513,3690,4099,64805,1524,1910
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6648,5068,1409,885,2787,2203
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2571,22852,6510,1965,5837,1585
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3813,6608,6582,5499,29126,2990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2244,348,2785,22877,150,51081
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4036,7386,177,5451,23446,9131
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9377,130120,1499,3087,154,292
--> return NULL...
2024-06-09 23:31:55.933 R[13274:35292661] XType: com.apple.fonts is not accessible.
2024-06-09 23:31:55.934 R[13274:35292661] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
49.201 1.192 50.475
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.757 | 0.026 | 0.790 | |