Package: TCseq

Version: 1.2.0

Command: rm -rf TCseq.buildbin-libdir TCseq.Rcheck && mkdir TCseq.buildbin-libdir TCseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCseq.buildbin-libdir TCseq_1.2.0.tar.gz >TCseq.Rcheck\00install.out 2>&1 && cp TCseq.Rcheck\00install.out TCseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TCseq.buildbin-libdir --install="check:TCseq-install.out" --force-multiarch --no-vignettes --timings TCseq_1.2.0.tar.gz

StartedAt: 2018-04-12 03:33:40 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:38:19 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 278.9 seconds

RetCode: 0

Status:  OK

CheckDir: TCseq.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf TCseq.buildbin-libdir TCseq.Rcheck && mkdir TCseq.buildbin-libdir TCseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCseq.buildbin-libdir TCseq_1.2.0.tar.gz >TCseq.Rcheck\00install.out 2>&1 && cp TCseq.Rcheck\00install.out TCseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TCseq.buildbin-libdir --install="check:TCseq-install.out" --force-multiarch --no-vignettes --timings TCseq_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TCseq.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCseq' version '1.2.0'
* 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 'TCseq' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
DBresult: no visible global function definition for 'as'
DBresult.cluster: no visible global function definition for 'as'
TCA: no visible global function definition for 'is'
TCA: no visible global function definition for 'as'
TCAFromSummarizedExperiment: no visible global function definition for
  'is'
TCAFromSummarizedExperiment: no visible global function definition for
  'as'
countReads: no visible global function definition for
  'createAnnotationFile'
countReads: no visible global function definition for 'featureCounts'
timeclustplot: no visible binding for global variable 'group'
timecourseTable: no visible global function definition for 'as'
Undefined global functions or variables:
  as createAnnotationFile featureCounts group is
Consider adding
  importFrom("methods", "as", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
DBresult 5.11   0.03    5.31
* 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-3.6-bioc/meat/TCseq.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'TCseq' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'TCseq'
    finding HTML links ... done
    DBanalysis                              html  
    finding level-2 HTML links ... done

    DBresult                                html  
    TCA                                     html  
    TCA.accessors                           html  
    clust-class                             html  
    clust.accessors                         html  
    countReads                              html  
    counts                                  html  
    countsTable                             html  
    experiment                              html  
    experiment_BAMfile                      html  
    genomicIntervals                        html  
    peakreference                           html  
    tca_ATAC                                html  
    timeclust                               html  
    timeclustplot                           html  
    timecourseTable                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TCseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCseq' as TCseq_1.2.0.zip
* DONE (TCseq)
In R CMD INSTALL
In R CMD INSTALL

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(TCseq)
> 
> test_check("TCseq")
== testthat results  ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.09    0.21    6.31 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(TCseq)
> 
> test_check("TCseq")
== testthat results  ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.84    0.21   10.04