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CHECK report for CexoR on merida1

This page was generated on 2020-10-14 11:22:53 -0400 (Wed, 14 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CexoR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 256/1930HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CexoR 1.27.1
Pedro Madrigal
Snapshot Date: 2020-10-13 14:40:34 -0400 (Tue, 13 Oct 2020)
URL: https://git.bioconductor.org/packages/CexoR
Branch: master
Last Commit: a9b251d
Last Changed Date: 2020-06-30 07:24:53 -0400 (Tue, 30 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CexoR
Version: 1.27.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CexoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CexoR_1.27.1.tar.gz
StartedAt: 2020-10-14 01:19:59 -0400 (Wed, 14 Oct 2020)
EndedAt: 2020-10-14 01:26:28 -0400 (Wed, 14 Oct 2020)
EllapsedTime: 389.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CexoR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CexoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CexoR_1.27.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CexoR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CexoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CexoR’ version ‘1.27.1’
* 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 ‘CexoR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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 ... NOTE
cexor: no visible global function definition for ‘subsetByOverlaps’
cexor : Stouffer.test: no visible global function definition for
  ‘qnorm’
cexor : Stouffer.test: no visible global function definition for
  ‘pnorm’
cexor : Fisher.test: no visible global function definition for ‘pchisq’
plotcexor: no visible global function definition for ‘colorRampPalette’
plotcexor: no visible global function definition for ‘par’
plotcexor: no visible global function definition for ‘points’
plotcexor: no visible global function definition for ‘abline’
plotcexor: no visible global function definition for ‘legend’
pskellam: no visible global function definition for ‘pchisq’
pskellam.sp: no visible global function definition for ‘pnorm’
pskellam.sp: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  abline colorRampPalette dnorm legend par pchisq pnorm points qnorm
  subsetByOverlaps
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "legend", "par", "points")
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
CexoR-package 16.024  0.543  16.588
plotcexor     14.659  0.486  15.161
cexor         13.845  0.476  14.375
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/CexoR.Rcheck/00check.log’
for details.



Installation output

CexoR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CexoR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CexoR’ ...
** 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 (CexoR)

Tests output

CexoR.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> require("CexoR") || stop("unable to load CexoR")
Loading required package: CexoR
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
[1] TRUE
> BiocGenerics:::testPackage("CexoR")


RUNIT TEST PROTOCOL -- Wed Oct 14 01:26:19 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CexoR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 29.071   0.987  30.061 

Example timings

CexoR.Rcheck/CexoR-Ex.timings

nameusersystemelapsed
CexoR-package16.024 0.54316.588
cexor13.845 0.47614.375
plotcexor14.659 0.48615.161