Mustafa Erhan Ozer
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 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 Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:46 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the SVMDO package: - 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: 2024-05-07 01:21:39 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 01:23:19 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 100.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SVMDO.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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-mac-arm64/meat/SVMDO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘1.4.0’
* 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-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)
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: 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: 2660,51094,8813,3596,80267,3920
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10559,57017,6616,3074,5979,6329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3663,51081,4879,26291,3766,4744
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6097,5369,1524,1471,165,6532
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200810,2280,350,8431,3569,3663
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3131,6556,1509,522,55937,339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22797,7916,84735,3356,7225,2244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54805,1186,123099,5261,4049,54809
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7515,3643,5078,875,5160,51117
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1583,5792,7287,83884,6556,7033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1392,5192,29929,6441,23516,9475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 316,4702,4351,56945,4129,51738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 487,7200,3460,9997,10845,9512
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27097,5106,6901,2642,23274,11200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 388125,2820,427,3687,9420,867
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6502,79191,5914,6324,387787,22933
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9619,338557,7364,4057,11136,5806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84342,2629,4543,9518,4669,10000
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 285126,2904,2793,5296,2787,55699
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 160428,6341,8678,3700,1019,1071
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3240,8398,55065,7015,93587,2875
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3145,6182,6531,5257,4803,7167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57678,7076,197,23556,51083,6182
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10116,55278,728441,57570,5971,81029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29947,10682,54476,3280,5579,1022
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3486,64772,3760,3251,118,38
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7082,5236,51083,23118,407021,643181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 133522,2539,51083,54344,10134,1583
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23236,149461,55572,51478,8567,11222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3778,91647,285848,11266,4088,4221
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55283,9382,6351,540,8609,7408
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51478,2984,256764,92935,5373,3554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1393,79572,4671,2063,50639,8945
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1080,6258,80339,142,6097,5161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3953,10379,6716,2745,215,11136
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54600,213,10116,3615,3250,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7372,28957,207,3643,4868,7442
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 338821,619373,3554,5080,23101,326625
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2542,1672,4151,7486,599,8764
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 153,203,367,7099,149461,292
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4695,5968,388962,7052,8309,844
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9826,1606,2559,84572,858,5467
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 142,29881,54931,5211,7421,8660
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6524,84063,6526,2989,10560,2934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6908,64432,1491,10423,4337,2115
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9380,51052,2932,5860,2063,9968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9415,212,54344,2335,514,1361
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2582,1786,7364,4057,4151,582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3401,9241,1029,54575,56997,3779
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8029,3106,7078,6932,2584,56244
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8877,3795,145258,344,9941,5274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5584,1524,2720,5802,23291,5080
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3122,149775,10965,406947,406922,2056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4276,84701,1351,50814,5805,4151
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8799,1584,91452,114884,5255,11035
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2776,3766,2161,8309,219,5444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,2678,5250,2161,84063,55748
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2593,6448,93587,53345,23038,885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 712,2157,55526,5660,7480,3624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2487,5741,5595,7133,153642,29947
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25915,5243,169792,6804,10019,54901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8029,10524,4803,4544,5860,6775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3593,9588,4537,388125,175,84705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9563,2597,54822,8228,3958,2990
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10730,10365,2591,7525,182,7284
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6519,10008,886,3456,7841,109
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6898,23564,23446,3155,5295,2548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3401,4714,50507,3115,1608,5563
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2155,2793,6556,138050,858,27235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2244,5968,3062,3156,6319,92609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7852,1813,51649,91949,196385,2108
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50484,292,9076,7157,54658,55644
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4744,54802,80347,4860,6821,6524
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,7010,1520,3640,3703,196385
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2101,23038,9971,3667,54331,2784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54576,6521,51649,4880,80267,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 65018,151,3032,23038,109,57511
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7099,292,361,2776,726,686
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4338,51441,3141,3507,54896,6390
--> return NULL...
2024-05-07 01:23:16.020 R[43569:42246763] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
17.000 0.320 17.325
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.569 | 0.005 | 0.575 | |