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This page was generated on 2022-04-13 12:08:04 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 GEOmetadb on machv2


To the developers/maintainers of the GEOmetadb package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GEOmetadb.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 766/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOmetadb 1.56.0  (landing page)
Jack Zhu
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GEOmetadb
git_branch: RELEASE_3_14
git_last_commit: 68547ef
git_last_commit_date: 2021-10-26 11:52:10 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GEOmetadb
Version: 1.56.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GEOmetadb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GEOmetadb_1.56.0.tar.gz
StartedAt: 2022-04-12 13:45:39 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 13:46:59 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 79.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GEOmetadb.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GEOmetadb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GEOmetadb_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GEOmetadb.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GEOmetadb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOmetadb’ version ‘1.56.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GEOmetadb’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getSQLiteFile: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getSQLiteFile':
getSQLiteFile
  Code: function(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz",
                 type = "full")
  Docs: function(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz",
                 type = "normal")
  Mismatches in argument default values:
    Name: 'type' Code: "full" Docs: "normal"

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
GEOmetadb-package 0.815  0.652   5.607
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/GEOmetadb.Rcheck/00check.log’
for details.



Installation output

GEOmetadb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GEOmetadb
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘GEOmetadb’ ...
** 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 (GEOmetadb)

Tests output


Example timings

GEOmetadb.Rcheck/GEOmetadb-Ex.timings

nameusersystemelapsed
GEOmetadb-package0.8150.6525.607
columnDescriptions0.0060.0010.007
geoConvert0.0350.0050.041
getBiocPlatformMap0.0130.0040.018
getSQLiteFile0.0010.0000.001