Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-10-24 11:41:36 -0400 (Tue, 24 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4724
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4459
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4473
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 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 2084/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SVMDO 1.1.2  (landing page)
Mustafa Erhan Özer
Snapshot Date: 2023-10-23 14:05:08 -0400 (Mon, 23 Oct 2023)
git_url: https://git.bioconductor.org/packages/SVMDO
git_branch: devel
git_last_commit: 2cc7739
git_last_commit_date: 2023-09-24 05:59:34 -0400 (Sun, 24 Sep 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.3.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for SVMDO on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: SVMDO
Version: 1.1.2
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings SVMDO_1.1.2.tar.gz
StartedAt: 2023-10-24 13:55:59 -0000 (Tue, 24 Oct 2023)
EndedAt: 2023-10-24 14:08:01 -0000 (Tue, 24 Oct 2023)
EllapsedTime: 722.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SVMDO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings SVMDO_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SVMDO.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.1.2’
* 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 R 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 loading without being on the library search path ... 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SVMDO_guide.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

SVMDO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘SVMDO’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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: 10599,79644,2646,51478,283459,7056
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7098,10724,4286,1489,2244,51649
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 11035,79602,7289,84947,217,84987
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1075,100506742,6526,84701,8740,80207
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3938,5373,90480,4217,9388,191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7225,54576,23395,1672,6721,5584
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4712,9997,57107,90070,155,18
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8743,129787,7139,6447,3802,6517
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 340024,665,26191,1033,5116,7076
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8660,4543,8813,5077,3664,7291
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7424,189,8714,410,7057,4143
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1889,1118,9374,3673,341,4017
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3117,3988,5261,3636,2244,149775
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6095,3033,5538,6532,54896,4069
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149461,406922,102,1056,6535,7351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4035,6342,270,3295,2642,718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 728,1327,246,55768,2146,6383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8799,9369,3489,351,2161,643394
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4210,5588,5190,53335,582,1968
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 427,10195,6097,1201,10019,79661
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26521,2597,8799,57264,23395,1798
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 255738,51478,3802,6648,5901,2303
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2954,4276,4137,406938,3673,32
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9968,10008,3990,5820,7078,3596
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4826,5595,57061,1118,336,3356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 471,1555,10165,2321,8788,3791
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5078,84701,7372,100125288,23590,8856
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9997,2937,9317,3606,338557,22845
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 493753,55315,563,387082,182,66036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8842,116931,4035,1646,9095,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 31,285126,6338,145258,10549,3833
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3481,23178,2885,9122,8665,1352
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9563,4208,5176,54331,6715,4124
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50507,2280,3280,6523,5592,80067
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1361,7507,8517,3358,79949,868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5741,10134,1281,1019,1508,26873
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5581,10320,4171,6342,9377,3934
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,5207,9619,3484,797,5593
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,55818,581,6584,3162,790955
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 53632,90865,8862,5443,5740,54106
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6928,4150,3815,348,6868,1382
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 387787,3958,6198,407008,8455,344
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3479,6232,4338,186,6256,6280
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79783,56052,3293,537,5968,4312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5968,2157,9056,200810,3156,3373
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,1634,5476,51081,291,2712
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10686,1595,7078,10599,4522,55630
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23654,54802,686,3832,6696,80222
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7345,4160,25805,29851,7098,6615
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3358,51081,3082,3480,5365,10724
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6390,1316,779,6376,5167,80142
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3032,5091,27344,4758,5741,51021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 358,151306,366,5836,7839,2647
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2834,28976,57620,3292,56923,8648
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 152078,6427,1601,6515,79796,6502
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10935,8835,1582,91949,7430,55970
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6387,4311,5020,952,5967,353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 23600,200186,22933,10724,81033,4695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 432369,3738,2314,10522,549,7025
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6891,4556,1394,949,4722,9722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54575,1757,10857,7078,509,5571
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2100,7025,316,2778,9241,5901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 22933,5428,6648,1030,5214,9759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5176,3813,3417,84447,7249,5465
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26191,54575,8841,1672,5068,6523
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 131669,2731,8691,7412,1050,3557
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4012,54809,4712,949,1607,26580
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 83884,5257,4162,3728,4049,6337
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9095,5971,7048,493927,10062,6019
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 55937,4716,1734,4826,5369,56999
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5320,25821,434,2660,116150,6530
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4036,5313,7157,3762,5330,50507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4723,4159,4017,6584,1028,350
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5276,5925,3082,1571,846,353500
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1890,8682,9475,65080,4868,6868
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2235,64805,64116,54902,406991,55863
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4233,5571,256297,4540,8784,5027
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4547,1080,100529063,10874,440503,3460
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2181,3992,7879,406982,4069,59272
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 35.219   2.483  44.583

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.7780.0270.813