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CHECK report for ASSET on machv2

This page was generated on 2020-10-17 11:58:04 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ASSET PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 94/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASSET 2.6.0
Samsiddhi Bhattacharjee
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ASSET
Branch: RELEASE_3_11
Last Commit: 9183346
Last Changed Date: 2020-04-27 14:36:01 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ASSET
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASSET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASSET_2.6.0.tar.gz
StartedAt: 2020-10-16 22:46:20 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 22:47:43 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 83.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ASSET.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ASSET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ASSET_2.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASSET.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 ‘ASSET/DESCRIPTION’ ... OK
* this is package ‘ASSET’ version ‘2.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ASSET’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
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 ... NOTE
Package in Depends field not imported from: ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dlm.pval: no visible global function definition for ‘pnorm’
getCI: no visible global function definition for ‘qnorm’
h.forest: no visible global function definition for ‘meta.colors’
h.forest: no visible global function definition for ‘title’
h.traits1: no visible global function definition for ‘qnorm’
h.traits2: no visible global function definition for ‘pchisq’
h.types0: no visible global function definition for ‘qnorm’
p.bon: no visible global function definition for ‘pnorm’
qxd.prod.coef: no visible global function definition for ‘pnorm’
qxd.prod.cor: no visible global function definition for ‘pnorm’
qxd.prod.int: no visible global function definition for ‘integrate’
qxd.prod.int : <anonymous>: no visible global function definition for
  ‘dnorm’
traits.forest: no visible global function definition for ‘pnorm’
traits.forest0: no visible global function definition for ‘pnorm’
traits.meta: no visible global function definition for ‘pnorm’
tube.pval: no visible global function definition for ‘pnorm’
tubeSim: no visible global function definition for ‘rnorm’
types.score: no visible global function definition for ‘model.matrix’
types.score: no visible global function definition for ‘as.formula’
types.score: no visible global function definition for ‘glm’
types.score: no visible global function definition for ‘binomial’
types.wald: no visible global function definition for ‘model.frame’
types.wald: no visible global function definition for ‘as.formula’
types.wald : <anonymous>: no visible global function definition for
  ‘glm’
types.wald : <anonymous>: no visible global function definition for
  ‘binomial’
types.wald : <anonymous>: no visible global function definition for
  ‘as.formula’
types.wald: no visible global function definition for ‘pnorm’
z.max: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial dnorm glm integrate meta.colors model.frame
  model.matrix pchisq pnorm qnorm rnorm title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "as.formula", "binomial", "dnorm", "glm",
             "integrate", "model.frame", "model.matrix", "pchisq",
             "pnorm", "qnorm", "rnorm")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'h.traits.Rd':
  ‘p.tube’

Missing link or links in documentation object 'h.types.Rd':
  ‘p.tube’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘p.tube’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
h.types 5.385  0.306   5.695
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ASSET.Rcheck/00check.log’
for details.



Installation output

ASSET.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ASSET
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ASSET’ ...
** using staged installation
** R
** data
** 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 (ASSET)

Tests output

ASSET.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.

> BiocGenerics:::testPackage("ASSET")


RUNIT TEST PROTOCOL -- Fri Oct 16 22:47:35 2020 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ASSET RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead. 
2: Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead. 
3: Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead. 
4: Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead. 
> 
> proc.time()
   user  system elapsed 
  6.225   0.376   6.623 

Example timings

ASSET.Rcheck/ASSET-Ex.timings

nameusersystemelapsed
ex_trait0.0250.0070.033
ex_types0.0140.0020.017
h.forestPlot0.6690.0260.695
h.summary0.4600.0040.463
h.traits0.5420.0110.554
h.types5.3850.3065.695
p.dlm0.0400.0010.041
z.max0.0210.0010.022