Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:08:13 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 Oscope on machv2


To the developers/maintainers of the Oscope package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Oscope.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 1354/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Oscope 1.24.0  (landing page)
Ning Leng
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/Oscope
git_branch: RELEASE_3_14
git_last_commit: 9c26bea
git_last_commit_date: 2021-10-26 12:21:51 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Oscope
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Oscope.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Oscope_1.24.0.tar.gz
StartedAt: 2022-01-20 16:04:50 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 16:06:37 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 106.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Oscope.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Oscope.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Oscope_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/Oscope.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 ‘Oscope/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Oscope’ version ‘1.24.0’
* 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 ‘Oscope’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AbsCor: no visible global function definition for ‘cor’
CalcMV: no visible binding for global variable ‘median’
CalcMV: no visible global function definition for ‘lm’
CalcMV: no visible global function definition for ‘coef’
CalcMV: no visible global function definition for ‘lines’
CalcMV: no visible global function definition for ‘points’
CalcMV: no visible global function definition for ‘abline’
FlagCluster: no visible global function definition for ‘quantile’
ImpShift: no visible global function definition for ‘txtProgressBar’
ImpShift: no visible global function definition for ‘setTxtProgressBar’
NISFun: no visible global function definition for ‘str’
NormForSine : <anonymous>: no visible global function definition for
  ‘quantile’
PipeR : <anonymous>: no visible global function definition for
  ‘residuals’
PipeR : <anonymous>: no visible global function definition for ‘lm’
PipeShiftCDF : <anonymous>: no visible global function definition for
  ‘quantile’
PipeShiftCDF : <anonymous>: no visible global function definition for
  ‘ecdf’
SineOptim: no visible global function definition for ‘optim’
scanK: no visible global function definition for ‘quantile’
scanK: no visible global function definition for ‘dist’
scanK : <anonymous>: no visible global function definition for ‘median’
Undefined global functions or variables:
  abline coef cor dist ecdf lines lm median optim points quantile
  residuals setTxtProgressBar str txtProgressBar
Consider adding
  importFrom("graphics", "abline", "lines", "points")
  importFrom("stats", "coef", "cor", "dist", "ecdf", "lm", "median",
             "optim", "quantile", "residuals")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
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 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
PermuCut  11.953  0.029  12.019
OscopeENI  6.059  0.115   6.195
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/Oscope.Rcheck/00check.log’
for details.



Installation output

Oscope.Rcheck/00install.out

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


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

Tests output


Example timings

Oscope.Rcheck/Oscope-Ex.timings

nameusersystemelapsed
AbsCor0.0030.0000.003
CalcMV0.9450.0220.969
FlagCluster1.5880.0401.635
FormatSineOut0.0270.0020.028
ImpShift1.5290.0311.566
NISFun2.9550.0543.020
NormForSine0.0230.0010.024
Opt2Shift2.8210.0532.892
OscopeENI6.0590.1156.195
OscopeExampleData0.0100.0020.013
OscopeKM1.4200.0151.439
OscopeSine0.0320.0020.034
PermuCut11.953 0.02912.019
PipeR0.2040.0000.204
PipeShiftCDF0.0210.0000.022
SineFun0.0030.0000.004
SineOptim0.0020.0000.002
scanK1.1440.0141.158