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This page was generated on 2024-05-04 11:38:40 -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 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: 2024-05-04 08:44:08 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 08:49:29 -0400 (Sat, 04 May 2024)
EllapsedTime: 321.0 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 beta (2024-04-15 r86425 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 beta (2024-04-15 r86425 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: 121268,3280,177,2701,85479,51478
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23365,6288,7032,340024,8818,4214
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7057,596,249,32,9692,26580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6526,51300,1813,55829,4129,10279
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5465,3416,8682,821,7172,84705
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3315,2146,11222,1558,116150,435
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7431,3308,2952,4760,6583,8842
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3087,1371,4247,643181,384,6524
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23474,10320,6521,3569,3242,145264
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116085,55315,345,517,114814,11019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 121268,7010,132158,632,3383,3113
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6199,54704,7078,6387,9076,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6515,10845,79133,55340,27035,270
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2932,6999,3670,80347,7916,844
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 572,801,8029,3406,4650,1593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493856,4162,5257,9429,9479,1815
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 216,64788,6339,196385,6383,2937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5406,7466,57061,2645,2244,1118
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84684,4598,339,4094,50639,55283
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100303755,1033,9388,9056,5444,3075
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,50943,7421,2697,80267,3174
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6338,79585,10935,5447,51167,5293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8803,64919,79572,5346,131118,92609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1355,23118,116519,4792,4860,1185
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11231,10999,3638,54,6834,8784
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2166,203,5631,10000,8560,4609
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55858,6602,57264,650,1806,8722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54901,2653,1650,8932,3572,2786
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51181,1524,55024,56718,347411,56606
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1491,7128,435,79644,7076,406922
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2629,4540,5565,2799,316,56052
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4099,388962,11096,5687,5798,4128
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114548,4548,116085,64220,5368,5828
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1019,7384,54106,100128525,79585,5294
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2169,3690,3157,2717,9971,6929
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6722,1382,9054,479,81689,57016
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10991,942,5589,3593,4285,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5257,1146,84706,4057,10062,4668
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 644974,7345,10935,5116,2643,1806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3062,8651,3930,3295,9572,7381
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 518,7082,2475,80142,23530,3667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,2260,9409,1634,5449,57016
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387787,10999,4358,5728,10457,5730
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 104,642489,5167,2852,4282,3500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5891,3676,513,7350,2244,6392
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3995,2006,387,4826,22852,4694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 268,1636,2847,160287,64432,53335
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 619373,4544,6427,51649,3952,3500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4312,84062,57107,91574,10642,133
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4790,84889,63931,29968,6941,26088
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7389,6097,1200,5068,4285,285362
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 356,3292,2167,8567,7525,3159
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8945,3683,3623,1965,4925,10165
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6446,51117,10845,136259,2314,3240
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3670,2632,4726,3939,7852,54414
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7372,201595,10938,3284,1277,1186
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85569,2203,2696,5207,5806,2180
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57761,241,345,54822,1537,52
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,844,55858,57061,285848,5830
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 216,3418,29843,123,66036,4718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23516,3627,387787,388125,2155,3773
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407009,11093,3401,4855,5230,145258
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1583,2645,3978,4915,30061,5116
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3406,81704,6288,50507,1606,3931
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 38,1641,7031,55805,55885,27089
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6620,1369,10549,43,246,7253
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6888,5584,60528,55699,2992,9572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3766,6526,9672,7480,4719,3640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54575,153,23516,1583,80207,7026
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6752,3690,6199,90070,5624,6275
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2547,6786,8788,1565,1030,3658
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5243,4323,5077,10842,10135,462
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91869,4826,1813,57761,8764,2834
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8504,5105,7276,6521,3689,5293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 121268,2280,516,51181,119559,6556
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6007,1072,221895,3440,63892,123
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91452,1182,1147,3329,56999,10019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55331,632,79587,80724,3315,5826
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1869,8743,5787,9095,100133941,6248
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  60.35    1.85   62.28 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.610.060.75