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CHECK report for Guitar on tokay1

This page was generated on 2019-04-13 11:25:56 -0400 (Sat, 13 Apr 2019).

Package 700/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Guitar 1.20.1
Jia Meng
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/Guitar
Branch: RELEASE_3_8
Last Commit: a8093ea
Last Changed Date: 2019-01-04 13:35:27 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Guitar
Version: 1.20.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Guitar.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Guitar_1.20.1.tar.gz
StartedAt: 2019-04-13 02:57:10 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:03:47 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 397.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Guitar.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Guitar.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Guitar_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Guitar.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.20.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Depends: includes the non-default packages:
  'Rsamtools' 'GenomicFeatures' 'rtracklayer' 'GenomicAlignments'
  'GenomicRanges' 'ggplot2' 'grid' 'IRanges'
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 ... 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.makeFigure_fill: no visible global function definition for 'pdf'
.makeFigure_fill: no visible global function definition for 'dev.off'
.makeFigure_nofill: no visible global function definition for 'pdf'
.makeFigure_nofill: no visible global function definition for 'dev.off'
BED12toGRangesList: no visible global function definition for
  'read.table'
BED12toGRangesList: no visible global function definition for 'head'
narrowPeaktoGRanges: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  dev.off head pdf read.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "head", "read.table")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
combinedGuitarPlot 14.88   0.28   15.15
GuitarPlot         11.62   0.42   12.05
Guitar-package     11.57   0.13   14.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
combinedGuitarPlot 16.50   0.01   16.52
GuitarPlot         14.05   0.00   14.05
Guitar-package     12.80   0.07   12.86
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-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 https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Guitar_1.20.1.tar.gz && rm -rf Guitar.buildbin-libdir && mkdir Guitar.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Guitar.buildbin-libdir Guitar_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Guitar_1.20.1.zip && rm Guitar_1.20.1.tar.gz Guitar_1.20.1.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
 13 2310k   13  320k    0     0  7962k      0 --:--:-- --:--:-- --:--:-- 8648k
100 2310k  100 2310k    0     0  27.1M      0 --:--:-- --:--:-- --:--:-- 28.2M

install for i386

* installing *source* package 'Guitar' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Guitar'
    finding HTML links ... done
    BED12toGRangesList                      html  
    Guitar-package                          html  
    GuitarPlot                              html  
    combinedGuitarPlot                      html  
    getNeighborhood                         html  
    makeGuitarCoordsFromGRangesList         html  
    makeGuitarCoordsFromTxDb                html  
    narrowPeaktoGRanges                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Guitar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Guitar' as Guitar_1.20.1.zip
* DONE (Guitar)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Guitar' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

Guitar.Rcheck/examples_i386/Guitar-Ex.timings

nameusersystemelapsed
BED12toGRangesList1.280.161.47
Guitar-package11.57 0.1314.20
GuitarPlot11.62 0.4212.05
combinedGuitarPlot14.88 0.2815.15
getNeighborhood0.170.000.17
makeGuitarCoordsFromGRangesList0.620.000.63
makeGuitarCoordsFromTxDb4.740.004.73
narrowPeaktoGRanges0.030.000.03

Guitar.Rcheck/examples_x64/Guitar-Ex.timings

nameusersystemelapsed
BED12toGRangesList1.940.112.05
Guitar-package12.80 0.0712.86
GuitarPlot14.05 0.0014.05
combinedGuitarPlot16.50 0.0116.52
getNeighborhood0.20.00.2
makeGuitarCoordsFromGRangesList0.580.000.58
makeGuitarCoordsFromTxDb4.060.004.06
narrowPeaktoGRanges0.030.000.03