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This page was generated on 2022-12-05 11:09:27 -0500 (Mon, 05 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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 Guitar on merida1


To the developers/maintainers of the Guitar package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Guitar.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 866/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Guitar 2.15.0  (landing page)
Jia Meng
Snapshot Date: 2022-12-04 14:00:12 -0500 (Sun, 04 Dec 2022)
git_url: https://git.bioconductor.org/packages/Guitar
git_branch: master
git_last_commit: 90c0b89
git_last_commit_date: 2022-11-01 11:12:15 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicFeatures' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'GenomicFeatures' which is not available

Summary

Package: Guitar
Version: 2.15.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Guitar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Guitar_2.15.0.tar.gz
StartedAt: 2022-12-05 02:04:30 -0500 (Mon, 05 Dec 2022)
EndedAt: 2022-12-05 02:18:26 -0500 (Mon, 05 Dec 2022)
EllapsedTime: 835.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Guitar.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Guitar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Guitar_2.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Guitar.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Guitar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Guitar’ version ‘2.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'GenomicFeatures', 'rtracklayer', 'AnnotationDbi', 'GenomicRanges',
  'magrittr', 'ggplot2', 'knitr', 'dplyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘Guitar’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.8Mb
  sub-directories of 1Mb or more:
    extdata  15.7Mb
* 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 in Depends field not imported from: ‘knitr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘GenomicRanges:::get_out_of_bound_index’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.extractComponent: no visible binding for global variable ‘gene_id’
.generate_guitar_coordinates: no visible global function definition for
  ‘makeGuitarCoordsFromTxDb’
.generate_guitar_coordinates: no visible binding for global variable
  ‘noBins’
Undefined global functions or variables:
  gene_id makeGuitarCoordsFromTxDb noBins
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
GuitarPlot                  57.776  0.503  76.812
GRangesListmapToTranscripts 31.098  0.398  41.328
samplePoints                30.805  0.115  42.029
normalize                   29.084  0.103  37.135
makeGuitarTxdb              27.467  0.092  36.512
* 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-3.17-bioc/meat/Guitar.Rcheck/00check.log’
for details.



Installation output

Guitar.Rcheck/00install.out

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

Tests output


Example timings

Guitar.Rcheck/Guitar-Ex.timings

nameusersystemelapsed
GRangesListmapToTranscripts31.098 0.39841.328
GuitarPlot57.776 0.50376.812
makeGuitarTxdb27.467 0.09236.512
normalize29.084 0.10337.135
samplePoints30.805 0.11542.029