Package: SpectralTAD

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpectralTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SpectralTAD_1.2.0.tar.gz

StartedAt: 2020-04-15 06:49:31 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:53:38 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 247.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SpectralTAD.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpectralTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SpectralTAD_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SpectralTAD.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SpectralTAD/DESCRIPTION' ... OK
* this is package 'SpectralTAD' version '1.2.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SpectralTAD     11.63    1.1   13.15
SpectralTAD_Par  3.61    0.5   23.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SpectralTAD     15.05   0.61   16.32
SpectralTAD_Par  3.50   0.30   30.71
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/SpectralTAD.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SpectralTAD_1.2.0.tar.gz && rm -rf SpectralTAD.buildbin-libdir && mkdir SpectralTAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpectralTAD.buildbin-libdir SpectralTAD_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SpectralTAD_1.2.0.zip && rm SpectralTAD_1.2.0.tar.gz SpectralTAD_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 1262k  100 1262k    0     0  21.5M      0 --:--:-- --:--:-- --:--:-- 23.2M

install for i386

* installing *source* package 'SpectralTAD' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SpectralTAD'
    finding HTML links ... done
    SpectralTAD                             html  
    SpectralTAD_Par                         html  
    rao_chr20_25_rep                        html  
** 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

install for x64

* installing *source* package 'SpectralTAD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpectralTAD' as SpectralTAD_1.2.0.zip
* DONE (SpectralTAD)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SpectralTAD' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  12.89    1.32   14.40 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  15.82    0.67   16.48