Mustafa Erhan Ozer
| Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 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 Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-20 11:32:21 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 2047/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SVMDO 1.5.0 (landing page) Mustafa Erhan Ozer
| kjohnson1 | macOS 13.6.6 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: 1.5.0 |
| 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: 2024-05-20 04:37:23 -0400 (Mon, 20 May 2024) |
| EndedAt: 2024-05-20 04:42:37 -0400 (Mon, 20 May 2024) |
| EllapsedTime: 314.6 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/SVMDO.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* 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-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 Patched (2024-04-24 r86482) -- "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: 800,148738,5053,3577,1604,56938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2688,65080,1203,3170,3566,5286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54205,6530,4656,170302,7840,358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26873,2539,10013,8772,5617,65985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84063,8660,800,2762,5241,11132
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1889,4313,7941,4321,941,79572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3577,54106,3670,3426,823,216
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5744,26088,8877,6932,821,51004
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26517,148713,3484,1345,8879,3358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,5087,91647,1116,64801,4285
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 844,6616,26503,4314,9122,22796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148979,3557,221895,53346,2847,2632
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3576,7297,3802,55034,9369,10165
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1033,56244,56458,9122,538,177
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84735,8842,192343,801,3689,59067
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1544,4773,23054,3292,83737,10279
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 640,337,4594,858,2673,84706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51738,91647,1443,1644,10730,1339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1555,538,6576,6929,5105,2952
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6007,5621,6182,3484,10379,1513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81031,22877,5715,6403,6401,26580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10094,6319,6275,1363,55970,27141
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3074,2266,9807,867,509,2834
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2592,5029,7098,1807,84277,440138
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 347411,10666,7381,5799,79001,1075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54809,51300,3551,10,9526,10745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3764,1435,6678,6821,7035,8455
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7289,467,6319,4040,55526,4255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7275,540,25839,1022,54,63899
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79587,3684,125170,5445,7879,6517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4338,64919,434,2055,7157,79158
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 759,81704,7841,3339,54344,10059
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2260,796,3507,192343,84239,5599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4714,9241,6868,80201,1678,10128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3558,10682,383,3995,10965,506
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26291,22852,5660,84342,2247,407007
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6775,497231,5563,5562,147007,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 595,10243,7276,4887,5618,1208
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4878,7225,9314,7082,54,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5571,293,1382,84833,2717,5641
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27035,55532,1591,90070,4694,210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11035,590,4718,80207,4860,51128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1717,657,6770,23600,2348,5190
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4318,5368,22901,27329,10269,2113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10628,6476,6248,5654,158,648998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3710,7919,10013,1401,10000,7274
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2166,1435,129787,5506,211,9475
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2677,2697,2949,100506742,9965,316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1363,2642,8835,5019,5476,4306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 115286,29968,4221,55630,407007,2638
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3101,5320,335,3425,2155,55005
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6492,6469,2539,2932,4162,3670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7177,4744,5228,4338,114899,9971
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1607,2395,1200,2989,8609,1043
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27329,595,57085,60528,3953,64241
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6357,84701,728441,156,3572,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 376497,7276,11213,148738,3157,51099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2495,790,114548,2776,9409,125170
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6279,50507,9692,4358,79158,3358
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3676,23101,3283,5826,6340,10938
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3625,51738,11019,406906,7827,50484
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 257313,2555,186,23062,5350,800
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7840,1043,51024,4099,406991,2542
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10935,3664,29851,3566,4868,84868
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4092,1573,5970,4548,8841,19
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6311,6182,7033,51119,1591,7839
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 257313,4217,383,147007,100125288,2790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9382,7409,1468,2760,6311,5593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4057,6387,1812,6609,4060,52
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8862,6657,28957,3157,91949,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4255,5095,85476,4726,6657,5087
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6774,5054,3251,122961,1435,89823
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 102,5108,7291,1337,120227,1992
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7046,1327,650,493856,8050,51293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4552,56052,2266,23590,265,134
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3489,7507,54915,6392,8714,846
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64131,359,165,776,406,1230
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 200205,5008,3640,285126,6530,55630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90865,4887,493927,3625,200205,7030
--> return NULL...
2024-05-20 04:42:27.334 R[58948:67001756] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
54.852 1.040 56.348
SVMDO.Rcheck/SVMDO-Ex.timings
| name | user | system | elapsed | |
| runGUI | 0.778 | 0.023 | 0.807 | |