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This page was generated on 2022-01-18 11:07:27 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 riesling1


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? 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 840/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Guitar 2.11.0  (landing page)
Jia Meng
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/Guitar
git_branch: master
git_last_commit: ca81e9c
git_last_commit_date: 2021-10-26 12:22:48 -0500 (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  NO, package depends on 'GenomicFeatures' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Guitar
Version: 2.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Guitar.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Guitar_2.11.0.tar.gz
StartedAt: 2022-01-17 19:08:48 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 19:13:51 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 303.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Guitar.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:Guitar.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Guitar_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Guitar.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 'Guitar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Guitar' version '2.11.0'
* 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 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
GuitarPlot                  32.68   1.37   34.05
GRangesListmapToTranscripts 13.21   0.18   13.39
samplePoints                10.64   0.01   10.65
normalize                    9.45   0.00    9.45
makeGuitarTxdb               9.30   0.05    9.35
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/Guitar.Rcheck/00check.log'
for details.



Installation output

Guitar.Rcheck/00install.out

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Guitar' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Guitar'
    finding HTML links ... done
    GRangesListmapToTranscripts             html  
    GuitarPlot                              html  
    makeGuitarTxdb                          html  
    normalize                               html  
    samplePoints                            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 (Guitar)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RJMCMCNucleosomes' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'wavClusteR' is missing or broken
 done

Tests output


Example timings

Guitar.Rcheck/Guitar-Ex.timings

nameusersystemelapsed
GRangesListmapToTranscripts13.21 0.1813.39
GuitarPlot32.68 1.3734.05
makeGuitarTxdb9.300.059.35
normalize9.450.009.45
samplePoints10.64 0.0110.65