Multiple platform build/check report for BioC 3.11 - CHECK report for SpectralTAD on celaya2

Package: SpectralTAD

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SpectralTAD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SpectralTAD_1.3.0.tar.gz

StartedAt: 2020-01-16 09:08:30 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 09:12:00 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 210.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: SpectralTAD.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SpectralTAD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SpectralTAD_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SpectralTAD.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpectralTAD/DESCRIPTION’ ... OK
* this is package ‘SpectralTAD’ version ‘1.3.0’
* package encoding: UTF-8
* 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:
  .travis.yml
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 ‘SpectralTAD’ 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
.windowedSpec: no visible binding for global variable ‘Group’
.windowedSpec: no visible binding for global variable ‘group_place’
.windowedSpec: no visible binding for global variable ‘ID’
.windowedSpec: no visible binding for global variable ‘Sil_Score’
SpectralTAD: no visible binding for global variable ‘end’
SpectralTAD: no visible binding for global variable ‘start1’
SpectralTAD: no visible binding for global variable ‘end1’
SpectralTAD: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  Group ID Sil_Score end end1 group_place start1 write.table
Consider adding
  importFrom("stats", "end")
  importFrom("utils", "write.table")
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 ... WARNING
Codoc mismatches from documentation object 'SpectralTAD':
SpectralTAD
  Code: function(cont_mat, chr, levels = 1, qual_filter = FALSE,
                 z_clust = FALSE, eigenvalues = 2, min_size = 5,
                 window_size = 25, resolution = "auto", gap_threshold =
                 1, grange = FALSE, out_format = "none", out_path =
                 chr)
  Docs: function(cont_mat, chr, levels = 1, qual_filter = FALSE,
                 z_clust = TRUE, eigenvalues = 2, min_size = 5,
                 resolution = "auto", gap_threshold = 1, grange =
                 FALSE)
  Argument names in code not in docs:
    window_size out_format out_path
  Mismatches in argument names:
    Position: 8 Code: window_size Docs: resolution
    Position: 9 Code: resolution Docs: gap_threshold
    Position: 10 Code: gap_threshold Docs: grange
  Mismatches in argument default values:
    Name: 'z_clust' Code: FALSE Docs: TRUE

Codoc mismatches from documentation object 'SpectralTAD_Par':
SpectralTAD_Par
  Code: function(cont_list, chr, levels = 1, qual_filter = FALSE,
                 z_clust = FALSE, eigenvalues = 2, min_size = 5,
                 resolution = "auto", grange = FALSE, gap_threshold =
                 1, cores = "auto", labels = NULL)
  Docs: function(cont_list, chr, levels = 1, qual_filter = FALSE,
                 z_clust = TRUE, eigenvalues = 2, min_size = 5,
                 resolution = "auto", grange = FALSE, gap_threshold =
                 1, cores = "auto", labels = NULL)
  Mismatches in argument default values:
    Name: 'z_clust' Code: FALSE Docs: TRUE

* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
SpectralTAD     17.332  1.701  19.054
SpectralTAD_Par  9.139  3.574  12.917
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/SpectralTAD.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SpectralTAD
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SpectralTAD’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpectralTAD)


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> library(testthat)
> library(SpectralTAD)
> 
> test_check("SpectralTAD")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 23.961   2.337  26.245

name	user	system	elapsed
SpectralTAD	17.332	1.701	19.054
SpectralTAD_Par	9.139	3.574	12.917

CHECK report for SpectralTAD on celaya2

Summary

Command output

Installation output

Tests output

Example timings