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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 1348/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mygene 1.36.0  (landing page)
Adam Mark, Cyrus Afrasiabi, Chunlei Wu
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/mygene
git_branch: RELEASE_3_17
git_last_commit: dc5c25c
git_last_commit_date: 2023-04-25 10:36:27 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for mygene on kjohnson2


To the developers/maintainers of the mygene package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: mygene
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mygene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mygene_1.36.0.tar.gz
StartedAt: 2023-10-18 10:40:41 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 10:47:39 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 417.3 seconds
RetCode: 0
Status:   OK  
CheckDir: mygene.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mygene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mygene_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mygene.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mygene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mygene’ version ‘1.36.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
makeTxDbFromMyGene 3.297  1.787   8.941
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mygene.Rcheck/00check.log’
for details.



Installation output

mygene.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mygene
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘mygene’ ...
** 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 (mygene)

Tests output


Example timings

mygene.Rcheck/mygene-Ex.timings

nameusersystemelapsed
MyGene-class0.0010.0010.002
MyGene0.0020.0000.006
getGene0.1070.0621.377
getGenes0.0850.0131.078
makeTxDbFromMyGene3.2971.7878.941
metadata0.0340.0220.732
query0.0380.0071.662
queryMany0.0430.0081.105