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This page was generated on 2024-05-04 11:41:12 -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 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: 1.4.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SVMDO_1.4.0.tar.gz
StartedAt: 2024-05-04 12:35:17 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 12:41:21 -0000 (Sat, 04 May 2024)
EllapsedTime: 363.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SVMDO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SVMDO_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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
* 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 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 ... 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:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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: 6348,28976,7297,7054,5092,3725
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 567,57505,3303,494324,3482,4036
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2064,91574,3767,23576,3122,2696
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4842,5080,3598,4323,4544,4137
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84701,4217,7450,4171,4792,8772
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2852,22877,435,57215,773,4247
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50507,5019,56606,90480,10166,341
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2597,2752,35,367,6446,6566
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10874,2109,3131,3240,6356,57104
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84572,162417,91647,405,29947,26873
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1524,6999,1281,51099,4716,6319
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 125988,5970,5925,2588,35,6248
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5069,51703,2712,3667,729238,22901
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8682,8560,3651,3106,51024,2555
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51703,55331,2584,6696,126328,4773
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27235,1056,538,339,4000,718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9514,8842,10643,90865,92935,4255
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 648998,23365,29926,522,216,5194
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8462,4255,4718,10020,1806,644096
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5697,1585,635,5029,7442,4306
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 56652,51083,5802,9572,5189,164656
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3802,5195,4595,3077,5054,4722
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1738,5230,2200,7351,7289,1312
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116085,5644,35,4232,6340,347411
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8202,64900,4688,5290,1513,10365
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 91949,517,5728,7421,4124,51099
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2788,29881,6343,3574,116228,2937
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 197322,7099,3929,51601,5291,22797
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5369,2280,5467,92609,2936,55243
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8854,54578,5315,1444,2152,51181
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10845,4276,3643,3032,23274,51548
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 949,119559,5023,522,3098,100126861
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10221,4283,1559,92935,56606,3122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7919,6342,9512,729238,3416,407040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 374291,3293,345,2701,366,54331
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 114814,6505,5662,113235,406982,79602
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 51548,23389,5825,1244,6772,8743
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 308,7167,3418,3482,867,648998
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5328,1565,2752,150379,5325,3489
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8195,712,1201,2885,10599,4695
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5328,3815,10128,55937,285,401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 27232,79602,2244,4535,25915,3458
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 116085,5241,55630,3980,256297,29078
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 617,54577,84649,2006,3703,2864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 497231,266,648998,1351,2159,2760
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2992,3658,148738,3645,5742,84572
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5193,1605,4286,4128,2639,1201
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2778,2793,64801,728642,8691,5053
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6097,79191,6715,55343,6339,65993
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1376,79944,6941,885,23474,4351
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 125988,5193,2653,93587,6555,3060
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10,1956,80724,4886,3503,3101
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2572,10841,6582,374291,4536,1356
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4217,6532,4543,1339,2919,5122
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57554,1869,7916,255231,1493,3503
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3640,10423,231,93587,63892,5108
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7369,6616,7030,30061,619373,2876
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1565,7124,145741,221895,3684,4171
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 64087,759,92667,7048,4128,1815
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 50814,55005,8218,388962,3033,102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7167,5592,4055,2056,407008,53346
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10295,100131801,270,2713,66036,3670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6362,4012,1728,1645,8218,55005
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4049,4012,26191,1203,4489,11222
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 84340,84447,6777,55867,409,116931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3676,10599,56945,27232,7098,23236
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1595,4714,51094,840,1716,3640
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5288,10320,4521,7369,5295,4773
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6519,115286,1376,3157,22877,2694
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 33,55867,5029,54806,5168,718
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 149775,8773,2026,65080,7538,79144
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 632,3565,10845,8772,406922,7097
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7032,1489,253827,7422,56244,5962
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5662,3329,3663,3600,6183,55163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3691,4803,1734,155,6402,3485
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4162,7385,10628,100506742,6403,5451
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5507,4724,25813,84889,3945,80339
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 148738,5621,2167,2146,5091,2713
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 90865,6341,364,4323,599,7019
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 65.351   1.802  67.253 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.7520.0320.785