Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:53 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 Sushi on machv2


To the developers/maintainers of the Sushi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Sushi.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 1908/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sushi 1.32.0  (landing page)
Douglas H Phanstiel
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Sushi
git_branch: RELEASE_3_14
git_last_commit: 55042b9
git_last_commit_date: 2021-10-26 12:13:10 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Sushi
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Sushi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Sushi_1.32.0.tar.gz
StartedAt: 2022-04-12 19:11:19 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:14:27 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 187.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Sushi.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Sushi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Sushi_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/Sushi.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Sushi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sushi’ version ‘1.32.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Sushi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... WARNING
Undocumented arguments in documentation object 'plotBedpe'
  ‘border’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
  Warning: large data file saved inefficiently:
                      size ASCII compress
  Sushi_5C.bedpe.rda 321Kb  TRUE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                  old_size new_size compress
  Sushi_5C.bedpe.rda                 321Kb     62Kb       xz
  Sushi_ChIAPET_pol2.bedpe.rda       846Kb    450Kb       xz
  Sushi_ChIPExo_CTCF.bedgraph.rda     29Kb     13Kb       xz
  Sushi_ChIPSeq_CTCF.bedgraph.rda    160Kb     37Kb       xz
  Sushi_ChIPSeq_pol2.bedgraph.rda     28Kb     11Kb       xz
  Sushi_DNaseI.bedgraph.rda           23Kb     12Kb       xz
  Sushi_GWAS.bed.rda                 515Kb    241Kb       xz
  Sushi_HiC.matrix.rda                40Kb     31Kb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/Sushi.Rcheck/00check.log’
for details.



Installation output

Sushi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Sushi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘Sushi’ ...
** using staged installation
** R
** data
** 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 (Sushi)

Tests output


Example timings

Sushi.Rcheck/Sushi-Ex.timings

nameusersystemelapsed
SushiColors0.0240.0020.026
addlegend0.6270.0220.649
labelgenome1.4840.0551.540
labelplot0.0470.0050.053
maptocolors0.0030.0010.004
maptolwd0.0020.0010.003
opaque0.0020.0010.003
plotBed0.5110.0090.520
plotBedgraph0.0240.0050.029
plotBedpe0.3480.0120.362
plotGenes0.0380.0030.041
plotHic0.5840.0150.600
plotManhattan0.4570.0590.518
zoombox0.8120.0250.840
zoomsregion0.0660.0090.075