Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-07 20:26 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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: 2024-06-05 14:00:26 -0400 (Wed, 05 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)
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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SVMDO on palomino3

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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SVMDO.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SVMDO_1.4.0.tar.gz
StartedAt: 2024-06-06 12:31:16 -0400 (Thu, 06 Jun 2024)
EndedAt: 2024-06-06 12:43:51 -0400 (Thu, 06 Jun 2024)
EllapsedTime: 755.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SVMDO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SVMDO.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: 150,1890,50615,266,54806,3456
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100529063,5315,4232,401,59067,4337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4337,80331,64135,8841,4522,23474
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1022,26762,10226,1329,59340,28957
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 797,8803,6690,3688,1352,3426
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 18,51703,10667,7840,558,80309
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23163,7980,10682,726,51316,3458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1186,7498,3292,5507,28958,5105
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79827,197322,10365,57085,358,836
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1585,3978,8773,23175,4594,256764
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6403,51316,726,4277,84274,6554
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6517,57001,3643,3708,1345,619373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23590,55024,643387,5447,6548,6019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 132158,8803,1352,3375,635,266
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 155,3554,9526,445,6462,25915
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2786,4860,6280,5207,1355,361
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10628,7139,3034,842,3172,83985
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6354,84274,22933,1813,6340,2919
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1513,790,1118,4716,5346,943
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5313,2785,1312,538,3551,522
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55600,5586,6814,4656,5106,1607
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3658,5465,4256,54982,285362,113235
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8854,56052,112817,79158,388372,3082
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,23590,3507,3284,7941,353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 383,56458,79587,5054,7480,6513
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3077,1118,2321,4723,5250,9021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 63931,2244,1363,5211,4012,7287
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10577,1910,4982,5589,84342,29960
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 178,909,6258,2335,155,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27249,79934,51116,5771,29929,10560
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9429,81033,2180,29078,8802,9882
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7915,2799,1889,1524,4668,587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,1621,124454,5191,9409,3763
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50674,7132,1232,5730,7052,3623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23706,353500,2954,4779,2645,5444
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6097,5979,93587,132,7351,388125
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7049,11255,644096,6476,4306,90624
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3489,15,3087,4864,5660,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85569,2949,7018,1786,53632,1363
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 866,2168,8784,3558,156,4982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4925,5579,9575,10400,2673,7364
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57505,6510,48,4650,6532,3557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9374,5715,3484,10991,23600,1052
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2694,84705,1028,131669,27235,6280
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6929,6718,10643,6927,84902,1340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10842,6448,52,8856,79949,56623
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2937,2157,6569,3091,55034,6523
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90624,9314,1645,3803,266,3939
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3728,2244,93587,3425,6868,4891
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7056,9722,9965,87178,3931,112817
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8659,4318,92609,9607,4598,8050
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1586,3077,63892,6834,3062,7135
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7135,293,217,23706,728294,5590
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2488,2952,3105,5593,9512,6794
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4852,594,51604,23054,3667,3738
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 596,8604,1586,4149,3484,7289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3593,6258,1075,1605,1499,6414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4283,7287,1649,55034,57107,1890
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3623,3938,8517,497231,52,2167
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3066,4092,56945,3684,7037,6690
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,5641,4040,2792,2572,3778
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80724,5008,4049,3952,79949,1675
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7032,2052,4277,63874,51103,665
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5331,56922,5781,4715,644974,509
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2876,3483,4276,5360,5329,100125288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2908,1573,152078,3670,6289,64220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5188,5565,9526,217,1019,5161
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10229,55970,142,7135,8842,1815
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5467,114548,80724,435,1339,5068
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10379,5967,574447,10874,3489,4594
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1499,23129,8818,25828,2746,6427
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2584,64131,1608,4092,599,23389
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89823,9518,517,4654,959,462
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3358,23101,1428,686,5068,10845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84649,2159,3763,79796,2950,1737
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10999,10497,116085,5373,79796,3773
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2181,4684,80067,3106,84063,518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2181,1394,27141,30061,81704,54210
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4718,29078,4976,3945,4879,9445
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  55.68   20.21   76.43 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.690.070.85