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This page was generated on 2024-05-04 11:37:16 -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 nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SVMDO_1.4.0.tar.gz
StartedAt: 2024-05-04 04:13:07 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 04:17:58 -0400 (Sat, 04 May 2024)
EllapsedTime: 290.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SVMDO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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/bbs-3.19-bioc/R/bin/R CMD INSTALL SVMDO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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: x86_64-pc-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: 1629,3569,2222,1200,25801,33
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4668,644096,406938,3932,55970,79191
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3553,148738,57215,6616,1499,117289
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 229,5919,1738,140803,8842,3674
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8455,125988,1392,9451,596,2806
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 43,4726,6928,4276,6714,406906
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6446,100507436,5660,2520,5053,1281
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7345,3290,197322,1052,25828,353
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7409,2260,79602,203,5802,793
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3811,5108,2632,6374,55867,3700
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 79661,4091,162417,91942,3312,5468
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6183,6338,4522,476,4221,3670
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1208,55750,1909,115286,4548,3931
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1497,840,51660,3991,7507,1029
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 406938,3640,2889,29851,842,6272
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4319,5295,4744,1509,7274,93587
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1369,27329,2260,2592,3507,773
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10911,9104,57678,6280,9255,3077
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 57001,4153,56923,5009,2516,2790
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1316,116519,1757,4724,5781,6535
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5920,5331,1513,2639,3875,4143
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 344,5468,10682,7325,3569,84277
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5071,23753,26503,5806,8398,31
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6531,116228,11266,2992,22796,6505
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4792,3106,151306,4715,1051,6374
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 7026,2309,9498,5191,1376,759
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123099,64772,116519,4129,1636,11254
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 229,4609,55788,8742,1557,3667
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 257313,10666,3033,8799,81034,136259
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6535,2643,686,22845,9241,7350
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6657,3401,8835,3485,3066,7048
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6338,643387,285848,10935,200539,1340
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3815,3598,64102,5830,2776,7385
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 85569,8784,23564,10577,3684,5697
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 26088,6183,79934,3638,91869,4854
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 384,9560,7200,2792,3339,6941
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 123,462,1075,7052,55867,3033
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4712,5276,5175,2068,1369,5092
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 10165,3690,6550,4886,8854,4288
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 175,5406,94235,18,353500,5967
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4017,3566,37,406938,407021,9095
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5972,1956,5498,706,4069,2954
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3569,344,3292,1208,3557,5590
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3934,186,9518,8228,23365,7507
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4548,406922,3574,50674,3292,256471
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1843,136259,3625,5274,84557,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 100,10116,10886,2152,54414,1030
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2115,2559,5860,5920,563,10102
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4704,8788,1491,2587,2946,1650
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6492,4580,10991,642489,1371,9518
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5599,6351,3385,6535,4285,64220
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 130120,1789,648998,90480,3284,5445
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 275,1806,2791,203,5294,407021
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 1968,2896,83985,1270,54575,8813
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4586,2166,5641,5080,55343,200205
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 336,5586,1394,83440,4318,7841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3356,5726,5565,6535,1565,3990
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 120227,9507,1382,5468,64805,859
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3934,90480,7025,4609,55065,582
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6342,353,10116,821,4852,114884
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2950,5836,265,84868,8471,4889
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6182,959,8202,25974,3119,57061
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 8932,200186,5346,6301,6583,410
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2155,1033,7942,4544,3762,643387
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5077,5277,25974,8803,6548,23163
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 54806,104909134,516,6584,9722,85476
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4729,1589,5792,9311,3485,10559
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2168,79068,7132,3624,3250,1807
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5255,3426,8462,5071,7325,10599
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 5826,2806,6492,111,6392,4709
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 6616,8029,100133941,221895,10400,29960
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 2697,8462,8609,50639,57085,6401
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 643387,50615,4547,7056,6232,57176
--> return NULL...
No gene sets have size between 10 and 500 ...
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 407004,5515,116985,80267,4879,5406
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 89823,23291,4489,4723,1508,54982
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 80224,3242,2791,779,6718,4040
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 9575,6620,213,56244,8074,57192
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 4914,496,6821,215,10116,8841
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 3759,3725,4552,4938,4880,3815
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 52.063   1.134  53.177 

Example timings

SVMDO.Rcheck/SVMDO-Ex.timings

nameusersystemelapsed
runGUI0.6190.0520.674