Package: regsplice

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regsplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings regsplice_1.10.0.tar.gz

StartedAt: 2019-10-16 06:25:47 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:31:29 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 341.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: regsplice.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:regsplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings regsplice_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/regsplice.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 'regsplice/DESCRIPTION' ... OK
* this is package 'regsplice' version '1.10.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'regsplice' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpklJHMg/R.INSTALL1618210746ce/regsplice/man/RegspliceData.Rd:75: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/regsplice.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
* 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
LRTests        14.99   0.44   15.80
summaryTable   13.15   0.00   13.14
regsplice      12.69   0.03   12.72
fitRegMultiple 12.52   0.00   12.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
LRTests        16.59   0.05   16.64
fitRegMultiple 12.28   0.03   12.31
regsplice      11.46   0.01   11.47
summaryTable   11.47   0.00   11.47
* 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
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/regsplice.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/regsplice_1.10.0.tar.gz && rm -rf regsplice.buildbin-libdir && mkdir regsplice.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=regsplice.buildbin-libdir regsplice_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL regsplice_1.10.0.zip && rm regsplice_1.10.0.tar.gz regsplice_1.10.0.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 67947    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 67947  100 67947    0     0  1016k      0 --:--:-- --:--:-- --:--:-- 1124k

install for i386

* installing *source* package 'regsplice' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'regsplice'
    finding HTML links ... done
    LRTests                                 html  
    RegspliceData                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpklJHMg/R.INSTALL1618210746ce/regsplice/man/RegspliceData.Rd:75: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    RegspliceResults                        html  
    createDesignMatrix                      html  
    filterLowCounts                         html  
    filterZeros                             html  
    fitRegMultiple                          html  
    initializeResults                       html  
    finding level-2 HTML links ... done

    regsplice                               html  
    runNormalization                        html  
    runVoom                                 html  
    summaryTable                            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 'regsplice' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'regsplice' as regsplice_1.10.0.zip
* DONE (regsplice)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'regsplice' successfully unpacked and MD5 sums checked

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(regsplice)
> 
> test_check("regsplice")
== testthat results  ===========================================================
[ OK: 90 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  26.04    0.89   26.92 

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(regsplice)
> 
> test_check("regsplice")
== testthat results  ===========================================================
[ OK: 90 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  23.29    0.31   23.59