Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:08:07 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 SCATE on merida1


To the developers/maintainers of the SCATE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SCATE.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 1756/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SCATE 1.6.0  (landing page)
Wenpin Hou
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/SCATE
git_branch: RELEASE_3_15
git_last_commit: 49cdb67
git_last_commit_date: 2022-04-26 12:07:48 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: SCATE
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SCATE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SCATE_1.6.0.tar.gz
StartedAt: 2022-06-24 08:15:45 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 08:39:36 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 1431.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SCATE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SCATE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SCATE_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/SCATE.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.6.0’
* 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         171.119  5.953 288.835
SCATEpipeline 165.851  8.572 285.243
peakcall      141.676  4.364 221.485
cellcluster    28.255  1.980  41.681
* 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-3.15-bioc/meat/SCATE.Rcheck/00check.log’
for details.



Installation output

SCATE.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SCATE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘SCATE’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
snapshotDate(): 2022-04-26
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2022-04-26
** testing if installed package can be loaded from final location
snapshotDate(): 2022-04-26
** testing if installed package keeps a record of temporary installation path
* DONE (SCATE)

Tests output


Example timings

SCATE.Rcheck/SCATE-Ex.timings

nameusersystemelapsed
SCATE171.119 5.953288.835
SCATEpipeline165.851 8.572285.243
cellcluster28.255 1.98041.681
extractfeature0.0770.0010.107
peakcall141.676 4.364221.485
satacprocess0.1530.0010.257