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CHECK report for M3D on machv2

This page was generated on 2020-10-17 11:58:49 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE M3D PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 965/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3D 1.22.0
Tom Mayo
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/M3D
Branch: RELEASE_3_11
Last Commit: 09ed714
Last Changed Date: 2020-04-27 14:42:10 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: M3D
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3D_1.22.0.tar.gz
StartedAt: 2020-10-17 02:33:29 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:39:24 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 355.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: M3D.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3D_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/M3D.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3D/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘M3D’ version ‘1.22.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘M3D’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'M3D' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/M3D.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
M3D_Wrapper: no visible global function definition for ‘txtProgressBar’
M3D_Wrapper: no visible global function definition for
  ‘setTxtProgressBar’
M3D_Wrapper_lite: no visible global function definition for
  ‘txtProgressBar’
M3D_Wrapper_lite: no visible global function definition for
  ‘setTxtProgressBar’
plotCoverageSampleProfiles: no visible global function definition for
  ‘lines’
plotCoverageSampleProfiles: no visible global function definition for
  ‘points’
plotCoverageSampleProfiles: no visible global function definition for
  ‘title’
plotMethProfile: no visible global function definition for ‘lines’
plotMethProfile: no visible global function definition for ‘points’
plotMethProfile: no visible global function definition for ‘title’
plotMethSampleProfiles: no visible global function definition for
  ‘lines’
plotMethSampleProfiles: no visible global function definition for
  ‘points’
plotMethSampleProfiles: no visible global function definition for
  ‘title’
pvals: no visible global function definition for ‘p.adjust’
pvals_lite: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  lines p.adjust points setTxtProgressBar title txtProgressBar
Consider adding
  importFrom("graphics", "lines", "points", "title")
  importFrom("stats", "p.adjust")
  importFrom("utils", "setTxtProgressBar", "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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/M3D.Rcheck/00check.log’
for details.



Installation output

M3D.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL M3D
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘M3D’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp_fns.cpp -o cpp_fns.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o M3D.so RcppExports.o cpp_fns.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-M3D/00new/M3D/libs
** 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 'M3D' is deprecated and will be removed from Bioconductor
  version 3.12
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'M3D' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (M3D)

Tests output

M3D.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(M3D)
Warning message:
Package 'M3D' is deprecated and will be removed from Bioconductor
  version 3.12 
> 
> test_check("M3D")

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══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 19.349   0.848  20.194 

Example timings

M3D.Rcheck/M3D-Ex.timings

nameusersystemelapsed
M3D_Wrapper0.4030.0140.417
M3D_Wrapper_lite0.2260.0060.232
determineGroupComps1.1100.0201.131
findComps0.4130.0200.435
median_freq000
plotCoverageSampleProfiles0.3130.0040.318
plotMethProfile0.3430.0070.351
plotMethSampleProfiles0.3180.0090.326
pvals0.6000.0520.652
pvals_lite0.5590.0210.581
readBedFiles000
readBedRaw000