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This page was generated on 2022-03-18 11:11:46 -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 gprege on merida1


To the developers/maintainers of the gprege package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gprege.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 816/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gprege 1.39.0  (landing page)
Alfredo Kalaitzis
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/gprege
git_branch: master
git_last_commit: 570c1d1
git_last_commit_date: 2021-10-26 12:02:36 -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: gprege
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gprege.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gprege_1.39.0.tar.gz
StartedAt: 2022-03-18 01:51:36 -0400 (Fri, 18 Mar 2022)
EndedAt: 2022-03-18 01:54:13 -0400 (Fri, 18 Mar 2022)
EllapsedTime: 157.7 seconds
RetCode: 0
Status:   OK  
CheckDir: gprege.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gprege.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gprege_1.39.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/gprege.Rcheck’
* using R Under development (unstable) (2022-03-02 r81842)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gprege/DESCRIPTION’ ... OK
* this is package ‘gprege’ version ‘1.39.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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 ‘gprege’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
* 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 in Depends field not imported from: ‘gptk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compareROC: no visible global function definition for ‘par’
compareROC: no visible global function definition for ‘lines’
compareROC: no visible global function definition for ‘legend’
demTp63Gp1: no visible global function definition for ‘data’
demTp63Gp1: no visible binding for global variable ‘FullDellaGattaData’
demTp63Gp1: no visible binding for global variable
  ‘FragmentDellaGattaData’
demTp63Gp1: no visible binding for global variable ‘DGdat_p63’
demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case1_GL’
demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case2_GL’
demTp63Gp1: no visible binding for global variable ‘DGdat_p63_case3_GL’
demTp63Gp1: no visible global function definition for ‘graphics.off’
exhaustivePlot: no visible global function definition for ‘sd’
exhaustivePlot: no visible global function definition for ‘gpCreate’
exhaustivePlot: no visible global function definition for
  ‘gpExpandParam’
exhaustivePlot: no visible global function definition for
  ‘gpLogLikelihood’
exhaustivePlot: no visible global function definition for
  ‘filled.contour’
exhaustivePlot: no visible binding for global variable ‘gray.colors’
exhaustivePlot: no visible global function definition for ‘axis’
exhaustivePlot: no visible global function definition for ‘points’
exhaustivePlot: no visible global function definition for ‘dev.set’
exhaustivePlot: no visible global function definition for ‘gpPlot’
gprege: no visible global function definition for ‘gpOptions’
gprege: no visible global function definition for ‘sd’
gprege: no visible global function definition for ‘pdf’
gprege: no visible global function definition for ‘close.screen’
gprege: no visible global function definition for ‘split.screen’
gprege: no visible global function definition for ‘gpCreate’
gprege: no visible global function definition for ‘gpExpandParam’
gprege: no visible global function definition for ‘gpOptimise’
gprege: no visible global function definition for ‘gpExtractParam’
gprege: no visible global function definition for ‘gpLogLikelihood’
gprege: no visible global function definition for ‘screen’
gprege: no visible global function definition for ‘erase.screen’
gprege: no visible global function definition for ‘gpPlot’
gprege: no visible global function definition for ‘gpPosteriorMeanVar’
gprege: no visible global function definition for ‘rnorm’
gprege: no visible global function definition for ‘points’
gprege: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  DGdat_p63 DGdat_p63_case1_GL DGdat_p63_case2_GL DGdat_p63_case3_GL
  FragmentDellaGattaData FullDellaGattaData axis close.screen data
  dev.off dev.set erase.screen filled.contour gpCreate gpExpandParam
  gpExtractParam gpLogLikelihood gpOptimise gpOptions gpPlot
  gpPosteriorMeanVar graphics.off gray.colors legend lines par pdf
  points rnorm screen sd split.screen
Consider adding
  importFrom("grDevices", "dev.off", "dev.set", "graphics.off",
             "gray.colors", "pdf")
  importFrom("graphics", "axis", "close.screen", "erase.screen",
             "filled.contour", "legend", "lines", "par", "points",
             "screen", "split.screen")
  importFrom("stats", "rnorm", "sd")
  importFrom("utils", "data")
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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
exhaustivePlot 18.061  0.195  18.287
demTp63Gp1     17.919  0.138  18.085
gprege         15.516  0.132  15.680
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/gprege.Rcheck/00check.log’
for details.



Installation output

gprege.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gprege
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘gprege’ ...
** using staged installation
** R
** data
** 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 (gprege)

Tests output


Example timings

gprege.Rcheck/gprege-Ex.timings

nameusersystemelapsed
compareROC0.0720.0090.082
demTp63Gp117.919 0.13818.085
exhaustivePlot18.061 0.19518.287
gprege-package000
gprege15.516 0.13215.680
rocStats0.5020.7591.262