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CHECK report for Guitar on tokay1

This page was generated on 2021-05-05 12:12:04 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the Guitar package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 805/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Guitar 2.6.0  (landing page)
Jia Meng
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/Guitar
Branch: RELEASE_3_12
Last Commit: fe492f5
Last Changed Date: 2020-10-27 11:08:17 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Guitar
Version: 2.6.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Guitar.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Guitar_2.6.0.tar.gz
StartedAt: 2021-05-05 03:31:12 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 03:43:32 -0400 (Wed, 05 May 2021)
EllapsedTime: 739.4 seconds
RetCode: 0
Status:   OK   
CheckDir: Guitar.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Guitar.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Guitar_2.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Guitar.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '2.6.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
GuitarPlot                  36.60   0.14   36.97
normalize                   17.84   0.01   17.86
GRangesListmapToTranscripts 16.97   0.50   28.97
samplePoints                17.08   0.07   17.14
makeGuitarTxdb              14.07   0.05   14.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
GuitarPlot                  47.69   0.09   47.79
samplePoints                23.97   0.00   24.95
normalize                   21.98   0.01   22.00
makeGuitarTxdb              21.36   0.00   21.36
GRangesListmapToTranscripts 21.13   0.10   21.22
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/Guitar.Rcheck/00check.log'
for details.



Installation output

Guitar.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Guitar_2.6.0.tar.gz && rm -rf Guitar.buildbin-libdir && mkdir Guitar.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Guitar.buildbin-libdir Guitar_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Guitar_2.6.0.zip && rm Guitar_2.6.0.tar.gz Guitar_2.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 3626k    0  8515    0     0   156k      0  0:00:23 --:--:--  0:00:23  156k
100 3626k  100 3626k    0     0  36.4M      0 --:--:-- --:--:-- --:--:-- 36.5M

install for i386

* 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

install for x64

* installing *source* package 'Guitar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Guitar' as Guitar_2.6.0.zip
* DONE (Guitar)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Guitar' successfully unpacked and MD5 sums checked

Tests output


Example timings

Guitar.Rcheck/examples_i386/Guitar-Ex.timings

nameusersystemelapsed
GRangesListmapToTranscripts16.97 0.5028.97
GuitarPlot36.60 0.1436.97
makeGuitarTxdb14.07 0.0514.11
normalize17.84 0.0117.86
samplePoints17.08 0.0717.14

Guitar.Rcheck/examples_x64/Guitar-Ex.timings

nameusersystemelapsed
GRangesListmapToTranscripts21.13 0.1021.22
GuitarPlot47.69 0.0947.79
makeGuitarTxdb21.36 0.0021.36
normalize21.98 0.0122.00
samplePoints23.97 0.0024.95