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CHECK report for myvariant on machv2

This page was generated on 2020-10-17 11:59:02 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE myvariant PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1166/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
myvariant 1.18.0
Adam Mark, Chunlei Wu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/myvariant
Branch: RELEASE_3_11
Last Commit: 4202a6c
Last Changed Date: 2020-04-27 14:50:46 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: myvariant
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:myvariant.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings myvariant_1.18.0.tar.gz
StartedAt: 2020-10-17 03:24:58 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:31:49 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 411.1 seconds
RetCode: 0
Status:  OK 
CheckDir: myvariant.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:myvariant.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings myvariant_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/myvariant.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 ‘myvariant/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘myvariant’ version ‘1.18.0’
* 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 ‘myvariant’ 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.
* 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 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.convertColumn4csv: no visible binding for global variable ‘is’
.df2DF: no visible binding for global variable ‘as’
.getIndels: no visible binding for global variable ‘REF’
.getIndels: no visible binding for global variable ‘ALT’
.unnest.df : <anonymous>: no visible global function definition for
  ‘is’
.unnest.df : <anonymous>: no visible global function definition for
  ‘setNames’
MyVariant: no visible global function definition for ‘new’
formatHgvs: no visible global function definition for
  ‘seqlevelsStyle<-’
validMyVariantObject: no visible global function definition for ‘slot’
.request.get,MyVariant: no visible global function definition for
  ‘capture.output’
.request.post,MyVariant: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  ALT REF as capture.output is new seqlevelsStyle<- setNames slot
Consider adding
  importFrom("methods", "as", "is", "new", "slot")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/myvariant.Rcheck/00check.log’
for details.



Installation output

myvariant.Rcheck/00install.out

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

Tests output


Example timings

myvariant.Rcheck/myvariant-Ex.timings

nameusersystemelapsed
MyVariant-class0.0010.0010.001
MyVariant0.0030.0010.004
formatHgvs1.0280.0551.086
formatSingleHgvs0.0010.0000.001
getVariant0.1700.0390.468
getVariants0.0800.0090.218
metadata0.0260.0090.126
queryVariant0.1690.0360.401
queryVariants000