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CHECK report for mygene on malbec1

This page was generated on 2019-04-16 11:50:58 -0400 (Tue, 16 Apr 2019).

Package 1032/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mygene 1.18.0
Adam Mark, Cyrus Afrasiabi, Chunlei Wu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/mygene
Branch: RELEASE_3_8
Last Commit: 247454a
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mygene
Version: 1.18.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:mygene.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings mygene_1.18.0.tar.gz
StartedAt: 2019-04-16 01:42:06 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:45:47 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 220.7 seconds
RetCode: 0
Status:  OK 
CheckDir: mygene.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:mygene.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings mygene_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/mygene.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mygene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mygene’ 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 ‘mygene’ 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
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
.df2DF: no visible binding for global variable ‘as’
.unnest.df : <anonymous>: no visible global function definition for
  ‘is’
.unnest.df : <anonymous>: no visible global function definition for
  ‘setNames’
MyGene: no visible global function definition for ‘new’
index.tx.id: no visible global function definition for
  ‘installed.packages’
validMyGeneObject: no visible global function definition for ‘slot’
.request.get,MyGene: no visible global function definition for
  ‘capture.output’
.request.post,MyGene: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  as capture.output installed.packages is new setNames slot
Consider adding
  importFrom("methods", "as", "is", "new", "slot")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output", "installed.packages")
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 installed files from ‘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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/mygene.Rcheck/00check.log’
for details.



Installation output

mygene.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL mygene
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘mygene’ ...
** 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
* DONE (mygene)

Tests output


Example timings

mygene.Rcheck/mygene-Ex.timings

nameusersystemelapsed
MyGene-class0.0000.0000.001
MyGene0.0000.0000.001
getGene0.2120.0280.678
getGenes0.1040.0040.542
makeTxDbFromMyGene1.7760.1642.169
metadata0.0680.0000.251
query0.0840.0080.614
queryMany0.0920.0040.697