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CHECK report for GeneticsDesign on merida1

This page was generated on 2021-05-06 12:35:05 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GeneticsDesign package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 703/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneticsDesign 1.58.0  (landing page)
The R Genetics Project
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GeneticsDesign
Branch: RELEASE_3_12
Last Commit: 923bc00
Last Changed Date: 2020-10-27 10:30:27 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GeneticsDesign
Version: 1.58.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneticsDesign.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneticsDesign_1.58.0.tar.gz
StartedAt: 2021-05-06 02:04:02 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:04:34 -0400 (Thu, 06 May 2021)
EllapsedTime: 31.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GeneticsDesign.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneticsDesign.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneticsDesign_1.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneticsDesign/DESCRIPTION’ ... OK
* this is package ‘GeneticsDesign’ version ‘1.58.0’
* 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 ‘GeneticsDesign’ can be installed ... WARNING
Found the following significant warnings:
  Warning: newline within quoted string at GPC.Rd:38
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:40: unexpected section header '\value'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:49: unexpected UNKNOWN '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:51: unexpected UNKNOWN '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:53: unexpected UNKNOWN '\item'
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
  Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:53: All text must be in a section
  Warning: Package 'GeneticsDesign' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign.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 ... NOTE
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
  partial argument match of 'nr' to 'nrow'
power.casectrl.plot: warning in matrix(NA, nc = J, nr = length(p)):
  partial argument match of 'nc' to 'ncol'
pw: warning in matrix(c(1, pi, pi, 1), nr = 2): partial argument match
  of 'nr' to 'nrow'
pw: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2, sd2^2), nr = 2):
  partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(1, pi, pi, 1), nr = 2):
  partial argument match of 'nr' to 'nrow'
simu.genotype.conti: warning in matrix(c(sd1^2, sd1 * sd2, sd1 * sd2,
  sd2^2), nr = 2): partial argument match of 'nr' to 'nrow'
* checking Rd files ... WARNING
prepare_Rd: newline within quoted string at GPC.Rd:38
prepare_Rd: man/GPC.Rd:40: unexpected section header '\value'
prepare_Rd: man/GPC.Rd:49: unexpected UNKNOWN '\item'
prepare_Rd: man/GPC.Rd:51: unexpected UNKNOWN '\item'
prepare_Rd: man/GPC.Rd:53: unexpected UNKNOWN '\item'
prepare_Rd: GPC.Rd:49: All text must be in a section
prepare_Rd: GPC.Rd:51: All text must be in a section
prepare_Rd: GPC.Rd:53: All text must be in a section
prepare_Rd: power.genotype.conti.Rd:36-38: Dropping empty section \details
* 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
* 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Paragraph ended before \Rd@code was complete.
<to be read again> 
                   \par 
l.224 
      
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE

Status: 1 ERROR, 3 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign.Rcheck/00check.log’
for details.

Installation output

GeneticsDesign.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GeneticsDesign’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
Warning: newline within quoted string at GPC.Rd:38
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:40: unexpected section header '\value'
Warning: newline within quoted string at GPC.Rd:38
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:49: unexpected UNKNOWN '\item'
Warning: newline within quoted string at GPC.Rd:38
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:51: unexpected UNKNOWN '\item'
Warning: newline within quoted string at GPC.Rd:38
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:53: unexpected UNKNOWN '\item'
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:49: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:51: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:53: All text must be in a section
Warning: /Users/biocbuild/bbs-3.12-bioc/meat/GeneticsDesign/man/GPC.Rd:53: All text must be in a section
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'GeneticsDesign' is deprecated and will be removed from
  Bioconductor version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'GeneticsDesign' is deprecated and will be removed from
  Bioconductor version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (GeneticsDesign)

Tests output

Example timings

GeneticsDesign.Rcheck/GeneticsDesign-Ex.timings

nameusersystemelapsed
GPC0.0080.0030.011
GeneticPower.Quantitative.Numeric0.0020.0000.003
gregorius0.0010.0010.002
power.genotype.conti0.1480.0030.151