Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-28 11:07:42 -0500 (Fri, 28 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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

CHECK results for epivizrData on riesling1


To the developers/maintainers of the epivizrData package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epivizrData.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 597/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epivizrData 1.23.0  (landing page)
Hector Corrada Bravo
Snapshot Date: 2022-01-27 13:55:17 -0500 (Thu, 27 Jan 2022)
git_url: https://git.bioconductor.org/packages/epivizrData
git_branch: master
git_last_commit: abfa958
git_last_commit_date: 2021-10-26 12:27:38 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: epivizrData
Version: 1.23.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epivizrData.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings epivizrData_1.23.0.tar.gz
StartedAt: 2022-01-27 18:52:24 -0500 (Thu, 27 Jan 2022)
EndedAt: 2022-01-27 18:56:25 -0500 (Thu, 27 Jan 2022)
EllapsedTime: 240.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: epivizrData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epivizrData.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings epivizrData_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/epivizrData.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'epivizrData/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'epivizrData' version '1.23.0'
* 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 'epivizrData' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData'
See 'D:/biocbuild/bbs-3.15-bioc/meat/epivizrData.Rcheck/00install.out' for details.
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'D:/biocbuild/bbs-3.15-bioc/meat/epivizrData.Rcheck/00check.log'
for details.



Installation output

epivizrData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL epivizrData
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'epivizrData' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData'
** help
*** installing help indices
  converting help for package 'epivizrData'
    finding HTML links ... done
    EpivizBlockData-class                   html  
    finding level-2 HTML links ... done

    EpivizBpData-class                      html  
    EpivizData-class                        html  
    EpivizDataMgr-class                     html  
    EpivizFeatureData-class                 html  
    EpivizGeneInfoData-class                html  
    EpivizMeasurement-class                 html  
    SparseEpivizMeasurement-class           html  
    ahToMySQL                               html  
    as.data.frame-EpivizData-method         html  
    as.list-EpivizMeasurement-method        html  
    as.list-SparseEpivizMeasurement-method
                                            html  
    createMgr                               html  
    dot-emptyEpivizMeasurement              html  
    dot-emptyEpivizSparseMeasurement        html  
    epivizrData                             html  
    register                                html  
    show-EpivizMeasurement-method           html  
    show-SparseEpivizMeasurement-method     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData'
** testing if installed package keeps a record of temporary installation path
* DONE (epivizrData)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'QuasR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'VCFArray' is missing or broken
 done

Tests output

epivizrData.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(testthat)
> library(epivizrData)
Loading required package: epivizrServer
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Warning message:
replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData' 
> 
> test_check("epivizrData")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 101 ]

== Skipped tests ===============================================================
* On CRAN (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 101 ]
> 
> proc.time()
   user  system elapsed 
  20.89    1.39   22.32 

Example timings

epivizrData.Rcheck/epivizrData-Ex.timings

nameusersystemelapsed
ahToMySQL000
createMgr0.030.000.03
register0.310.020.33