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This page was generated on 2022-03-18 11:08:08 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for mygene on riesling1


To the developers/maintainers of the mygene package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mygene.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1265/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mygene 1.31.0  (landing page)
Adam Mark, Cyrus Afrasiabi, Chunlei Wu
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/mygene
git_branch: master
git_last_commit: 64d853b
git_last_commit_date: 2021-10-26 12:17:38 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mygene
Version: 1.31.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mygene.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mygene_1.31.0.tar.gz
StartedAt: 2022-03-17 19:42:16 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:45:33 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 197.1 seconds
RetCode: 0
Status:   OK  
CheckDir: mygene.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mygene.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mygene_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/mygene.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mygene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mygene' version '1.31.0'
* 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 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
  'D:/biocbuild/bbs-3.15-bioc/meat/mygene.Rcheck/00check.log'
for details.



Installation output

mygene.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mygene
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mygene' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mygene'
    finding HTML links ... done
    MyGene-class                            html  
    MyGene                                  html  
    getGene                                 html  
    getGenes                                html  
    makeTxDbFromMyGene                      html  
    metadata                                html  
    mygene-package                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-mygene/00new/mygene/help/mygene.html
    query                                   html  
    queryMany                               html  
** 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 (mygene)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'annotatr' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'preciseTAD' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'XCIR' is missing or broken
 done

Tests output


Example timings

mygene.Rcheck/mygene-Ex.timings

nameusersystemelapsed
MyGene-class0.020.000.01
MyGene000
getGene0.140.040.77
getGenes0.080.000.31
makeTxDbFromMyGene2.061.313.48
metadata0.030.000.27
query0.050.000.77
queryMany0.030.010.42