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CHECK report for SpectralTAD on tokay1

This page was generated on 2021-05-06 12:33:44 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SpectralTAD package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1765/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpectralTAD 1.6.0  (landing page)
Kellen Cresswell
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SpectralTAD
Branch: RELEASE_3_12
Last Commit: 2643c90
Last Changed Date: 2020-10-27 11:43:10 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SpectralTAD
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpectralTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SpectralTAD_1.6.0.tar.gz
StartedAt: 2021-05-06 07:12:03 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:16:14 -0400 (Thu, 06 May 2021)
EllapsedTime: 250.9 seconds
RetCode: 0
Status:   OK   
CheckDir: SpectralTAD.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpectralTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SpectralTAD_1.6.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SpectralTAD.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.6.0'
* 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'
Undefined global functions or variables:
  Group ID Sil_Score end end1 group_place start1
Consider adding
  importFrom("stats", "end")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
SpectralTAD     13.18   0.91   14.44
SpectralTAD_Par  2.72   0.56   24.85
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
SpectralTAD     12.09   0.59   13.76
SpectralTAD_Par  2.72   0.50   29.06
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/SpectralTAD.Rcheck/00check.log'
for details.



Installation output

SpectralTAD.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/SpectralTAD_1.6.0.tar.gz && rm -rf SpectralTAD.buildbin-libdir && mkdir SpectralTAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpectralTAD.buildbin-libdir SpectralTAD_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL SpectralTAD_1.6.0.zip && rm SpectralTAD_1.6.0.tar.gz SpectralTAD_1.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1297k  100 1297k    0     0  10.9M      0 --:--:-- --:--:-- --:--:-- 11.0M

install for i386

* installing *source* package 'SpectralTAD' ...
** using staged installation
** R
** data
** inst
** 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_1.6.0.zip
* DONE (SpectralTAD)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'SpectralTAD' successfully unpacked and MD5 sums checked

Tests output

SpectralTAD.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  16.95    1.29   18.23 

SpectralTAD.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  20.40    0.75   21.37 

Example timings

SpectralTAD.Rcheck/examples_i386/SpectralTAD-Ex.timings

nameusersystemelapsed
SpectralTAD13.18 0.9114.44
SpectralTAD_Par 2.72 0.5624.85

SpectralTAD.Rcheck/examples_x64/SpectralTAD-Ex.timings

nameusersystemelapsed
SpectralTAD12.09 0.5913.76
SpectralTAD_Par 2.72 0.5029.06