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CHECK report for SCATE on merida1

This page was generated on 2021-05-06 12:36:40 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SCATE package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1628/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SCATE 1.0.0  (landing page)
Wenpin Hou
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SCATE
Branch: RELEASE_3_12
Last Commit: 00a484b
Last Changed Date: 2020-10-27 12:00:07 -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: SCATE
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SCATE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SCATE_1.0.0.tar.gz
StartedAt: 2021-05-06 05:51:34 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:04:46 -0400 (Thu, 06 May 2021)
EllapsedTime: 791.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SCATE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SCATE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SCATE_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/SCATE.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SCATE/DESCRIPTION’ ... OK
* this is package ‘SCATE’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'parallel', 'preprocessCore', 'splines', 'splines2', 'xgboost',
  'SCATEData', 'Rtsne', 'mclust'
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 ‘SCATE’ 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
* 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: ‘SCATEData’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SCATE : SCATEsingle: no visible global function definition for
  ‘IRanges’
cellcluster : <anonymous>: no visible global function definition for
  ‘IRanges’
extractfeature: no visible global function definition for ‘IRanges’
makedatabase: no visible global function definition for ‘IRanges’
makedatabase: no visible global function definition for ‘seqlevels’
peakcall: no visible global function definition for ‘IRanges’
Undefined global functions or variables:
  IRanges seqlevels
* 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
SCATE         190.790  4.648 195.956
SCATEpipeline 143.882  4.611 150.255
peakcall      111.079  2.998 114.186
cellcluster    25.571  1.400  27.006
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/SCATE.Rcheck/00check.log’
for details.



Installation output

SCATE.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SCATE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SCATE’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
snapshotDate(): 2020-10-27
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2020-10-27
** testing if installed package can be loaded from final location
snapshotDate(): 2020-10-27
** testing if installed package keeps a record of temporary installation path
* DONE (SCATE)

Tests output


Example timings

SCATE.Rcheck/SCATE-Ex.timings

nameusersystemelapsed
SCATE190.790 4.648195.956
SCATEpipeline143.882 4.611150.255
cellcluster25.571 1.40027.006
extractfeature0.0560.0000.056
peakcall111.079 2.998114.186
satacprocess0.1070.0030.110