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This page was generated on 2024-05-04 11:40:05 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 2112/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SVMDO 1.4.0  (landing page)
Mustafa Erhan Ozer
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 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)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for SVMDO on lconway


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.

raw results


Summary

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: 2024-05-04 01:19:09 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:24:41 -0400 (Sat, 04 May 2024)
EllapsedTime: 332.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SVMDO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 beta (2024-04-14 r86421)
* 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


Installation output

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)

Tests output

SVMDO.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-14 r86421) -- "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: 5618,6532,1650,3479,341,138050
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 192343,1329,486,1270,2308,2559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1347,6526,7097,10965,6392,64900
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7498,5291,1113,6948,2642,5820
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6927,4988,3687,353500,1327,3559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51,4852,7031,84557,8659,1277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5329,5594,23101,3570,9965,494324
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2244,367,7026,3952,779,4548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 196743,867,84061,7200,3766,3099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 790,593,23479,27329,80201,10522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4009,4716,56458,6999,112817,27329
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1608,10560,2776,25801,1363,1118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3593,6868,5116,51167,2791,23411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79796,7252,92667,6383,55024,5116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7056,6289,3577,217,5584,6093
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1435,3645,5176,56606,246,1605
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 477,51167,409,7840,2590,1340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9377,6524,54796,10020,1019,3034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 60386,4035,100529063,1672,9588,6093
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6301,1601,22845,5581,7046,100529063
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7097,6531,2147,23178,80309,6659
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1345,23410,2026,790,2168,1737
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55163,54577,1401,4650,55600,197322
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,51703,3074,5192,2762,316
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6794,5193,4319,1394,3768,796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64116,165,1080,29079,64788,5662
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3119,5095,2954,4311,2702,5745
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,6770,7021,726,1428,836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56729,22933,54704,5444,23576,1056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1029,2169,6720,3738,4522,4758
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84833,132158,5053,493753,6550,825
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,54539,4312,551,10457,3958
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81788,6340,5245,8029,27010,23706
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27097,4160,2948,3995,885,9380
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4151,7226,5581,84701,7049,4137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 81570,27089,5625,4318,3576,796
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4548,107075310,5621,51106,4233,7295
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 191,6571,54796,1906,29947,2746
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4627,5589,10682,406991,148713,8609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6280,57061,51119,134,5320,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5621,84705,10013,5139,5468,84062
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9526,8813,148713,4126,5274,2034
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104,2702,26762,1582,5087,2161
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407021,664,2903,9382,7137,8856
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 29881,6678,8639,3098,4160,5771
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4283,1043,6338,89823,4712,2591
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55805,7057,2592,6337,2875,4556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54931,10379,493856,1208,5837,104909134
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 648998,3767,51649,4792,642489,1348
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4151,958,796,353500,2137,53345
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4357,84868,200205,4720,3762,55885
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104909134,55630,87178,1312,57620,487
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4143,4276,91942,1558,9021,594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10134,26119,26291,4968,4650,7471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 38,33,7124,9969,5962,6341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3383,5291,2203,4149,29881,196385
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5743,84061,64788,3932,132,115286
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10497,1910,4723,7248,3763,1537
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6009,3586,2194,132158,3291,5264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7421,25915,341,825,10886,2998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54600,26873,65985,27344,9056,7498
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1634,387,1268,2266,29880,100131801
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3676,51,5321,9663,10874,100133941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5598,3958,5321,8932,909,1329
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 59340,2161,55867,3630,4319,6514
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 129787,22852,5730,406903,6868,3418
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 217,875,138050,5020,102,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1022,2731,3423,3577,10549,55600
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 25813,57001,3383,407024,509,4842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2517,440503,6609,5193,57761,5742
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84868,3576,8639,10559,3766,4282
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1636,857,875,5515,3953,57761
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 567,9317,53947,3988,549,6342
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 268,84342,5741,1716,3356,1968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6311,6093,65993,3688,4843,5161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116519,200205,387787,2767,249,64432
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1118,26227,84649,48,7486,9927
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1043,54205,79133,5365,4337,4009
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4041,3995,768239,55805,3674,4088
--> return NULL...
2024-05-04 01:24:32.420 R[41568:1727723262] XType: com.apple.fonts is not accessible.
2024-05-04 01:24:32.421 R[41568:1727723262] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 54.813   1.590  56.877 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.7700.0370.828