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This page was generated on 2022-12-05 11:05:50 -0500 (Mon, 05 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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 GenomicScores on nebbiolo1


To the developers/maintainers of the GenomicScores package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicScores.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 779/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicScores 2.11.0  (landing page)
Robert Castelo
Snapshot Date: 2022-12-04 14:00:12 -0500 (Sun, 04 Dec 2022)
git_url: https://git.bioconductor.org/packages/GenomicScores
git_branch: master
git_last_commit: d78fec9
git_last_commit_date: 2022-11-01 11:15:32 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GenomicScores
Version: 2.11.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicScores.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicScores_2.11.0.tar.gz
StartedAt: 2022-12-04 20:35:13 -0500 (Sun, 04 Dec 2022)
EndedAt: 2022-12-04 20:40:55 -0500 (Sun, 04 Dec 2022)
EllapsedTime: 341.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenomicScores.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicScores.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicScores_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicScores.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘GenomicScores/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicScores’ version ‘2.11.0’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/gscores-template/inst/extdata/.gitkeep
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicScores’ 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘hdf5Backend’
* 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 ... WARNING
checkRd: (5) GScores-class.Rd:129-160: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:166-168: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:169-174: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:175-177: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:178-180: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:181-183: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:184-186: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:187-189: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:190-192: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:193-195: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:196-200: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:201-203: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:204-206: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:207-209: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:210-213: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:214-217: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:218-220: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:221-223: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:224-227: \item in \describe must have non-empty label
* 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
GScores-class 13.877  0.724  14.604
gscores       10.168  1.981  12.616
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GenomicScores.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicScores.Rcheck/00check.log’
for details.



Installation output

GenomicScores.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomicScores
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘GenomicScores’ ...
** 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 (GenomicScores)

Tests output

GenomicScores.Rcheck/tests/runTests.Rout


R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> BiocGenerics:::testPackage("GenomicScores")

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, aperm, 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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'GenomicScores'

The following object is masked from 'package:utils':

    citation

Loading required package: phastCons100way.UCSC.hg19


RUNIT TEST PROTOCOL -- Sun Dec  4 20:38:57 2022 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicScores RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 17.709   1.479  19.180 

Example timings

GenomicScores.Rcheck/GenomicScores-Ex.timings

nameusersystemelapsed
GScores-class13.877 0.72414.604
availableGScores2.8370.7353.799
gscores10.168 1.98112.616
igscores000
makeGScoresPackage000
rgscores2.4660.4762.942
wgscores1.2860.1261.792