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This page was generated on 2021-12-06 13:05:49 -0500 (Mon, 06 Dec 2021).

CHECK results for alsace on machv2

To the developers/maintainers of the alsace package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alsace.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 47/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alsace 1.30.0  (landing page)
Ron Wehrens
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/alsace
git_branch: RELEASE_3_14
git_last_commit: d0e09b2
git_last_commit_date: 2021-10-26 12:12:10 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: alsace
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alsace.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alsace_1.30.0.tar.gz
StartedAt: 2021-12-05 11:40:15 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 11:41:37 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 81.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: alsace.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alsace.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alsace_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/alsace.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alsace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alsace’ version ‘1.30.0’
* 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 ‘alsace’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'alsace' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/alsace.Rcheck/00install.out’ for details.
* 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
'library' or 'require' call to ‘lattice’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPeakTable : clusterPeaks: no visible global function definition for
  ‘stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.abline’
Undefined global functions or variables:
  panel.abline panel.stripplot stripplot
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
components   14.071  0.634  14.717
teaMerged     7.337  0.174   7.517
correctPeaks  6.488  0.197   6.697
fitpeaks      5.820  0.141   5.968
doALS         5.753  0.162   5.919
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/alsace.Rcheck/00check.log’
for details.



Installation output

alsace.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL alsace
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘alsace’ ...
** 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
Warning: Package 'alsace' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package can be loaded from final location
Warning: Package 'alsace' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package keeps a record of temporary installation path
* DONE (alsace)

Tests output


Example timings

alsace.Rcheck/alsace-Ex.timings

nameusersystemelapsed
components14.071 0.63414.717
correctPeaks6.4880.1976.697
correctRT3.2480.1043.355
doALS5.7530.1625.919
filterPeaks0.0560.0030.060
fitpeaks5.8200.1415.968
getAllPeaks0.0380.0030.042
getPeakTable3.2180.1043.323
opa1.6120.0341.647
preprocess0.1400.0050.146
showALSresult0.1250.0150.139
tea0.1350.0070.143
teaMerged7.3370.1747.517
windows0.1520.0190.171