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CHECK report for SpectralTAD on tokay2

This page was generated on 2019-10-16 12:43:29 -0400 (Wed, 16 Oct 2019).

Package 1563/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpectralTAD 1.0.0
Kellen Cresswell
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SpectralTAD
Branch: RELEASE_3_9
Last Commit: 64a1278
Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SpectralTAD
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpectralTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SpectralTAD_1.0.0.tar.gz
StartedAt: 2019-10-16 07:17:06 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:21:01 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 235.5 seconds
RetCode: 0
Status:  OK  
CheckDir: SpectralTAD.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpectralTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SpectralTAD_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SpectralTAD.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.0.0'
* 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 ... OK
* 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'
Undefined global functions or variables:
  Group ID Sil_Score group_place
* 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 or elapsed time > 5s
                user system elapsed
SpectralTAD     9.39   0.89   21.14
SpectralTAD_Par 3.04   0.50   23.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SpectralTAD     11.28   0.68   13.92
SpectralTAD_Par  3.68   0.49   23.64
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-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 https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SpectralTAD_1.0.0.tar.gz && rm -rf SpectralTAD.buildbin-libdir && mkdir SpectralTAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpectralTAD.buildbin-libdir SpectralTAD_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SpectralTAD_1.0.0.zip && rm SpectralTAD_1.0.0.tar.gz SpectralTAD_1.0.0.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
  0 1259k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1259k  100 1259k    0     0  7739k      0 --:--:-- --:--:-- --:--:-- 8020k

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_1.0.0.zip
* DONE (SpectralTAD)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SpectralTAD' successfully unpacked and MD5 sums checked

Tests output

SpectralTAD.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.34    0.90   15.23 

SpectralTAD.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.75    0.64   12.37 

Example timings

SpectralTAD.Rcheck/examples_i386/SpectralTAD-Ex.timings

nameusersystemelapsed
SpectralTAD 9.39 0.8921.14
SpectralTAD_Par 3.04 0.5023.56

SpectralTAD.Rcheck/examples_x64/SpectralTAD-Ex.timings

nameusersystemelapsed
SpectralTAD11.28 0.6813.92
SpectralTAD_Par 3.68 0.4923.64