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CHECK report for TCseq on tokay1

This page was generated on 2019-04-13 11:27:26 -0400 (Sat, 13 Apr 2019).

Package 1549/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCseq 1.6.1
Mengjun Wu
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/TCseq
Branch: RELEASE_3_8
Last Commit: bd2c43e
Last Changed Date: 2019-01-04 13:52:21 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TCseq
Version: 1.6.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TCseq_1.6.1.tar.gz
StartedAt: 2019-04-13 05:53:21 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:58:34 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 312.6 seconds
RetCode: 0
Status:  OK  
CheckDir: TCseq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TCseq_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TCseq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.6.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* 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
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.8-bioc/meat/TCseq.Rcheck/00check.log'
for details.



Installation output

TCseq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/TCseq_1.6.1.tar.gz && rm -rf TCseq.buildbin-libdir && mkdir TCseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCseq.buildbin-libdir TCseq_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL TCseq_1.6.1.zip && rm TCseq_1.6.1.tar.gz TCseq_1.6.1.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  600k  100  600k    0     0  12.1M      0 --:--:-- --:--:-- --:--:-- 13.3M

install for i386

* installing *source* package 'TCseq' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare 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_1.6.1.zip
* DONE (TCseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'TCseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

TCseq.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(TCseq)
> 
> test_check("TCseq")
== testthat results  ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.43    0.50    6.93 

TCseq.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(TCseq)
> 
> test_check("TCseq")
== testthat results  ===========================================================
OK: 8 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.39    0.42    7.81 

Example timings

TCseq.Rcheck/examples_i386/TCseq-Ex.timings

nameusersystemelapsed
DBanalysis1.190.081.27
DBresult2.970.033.00
TCA000
TCA.accessors0.050.020.06
counts0.040.000.05
countsTable000
experiment000
experiment_BAMfile000
genomicIntervals000
peakreference0.020.000.02
tca_ATAC000
timeclust0.010.000.01
timeclustplot1.750.001.75
timecourseTable1.280.031.32

TCseq.Rcheck/examples_x64/TCseq-Ex.timings

nameusersystemelapsed
DBanalysis2.350.002.34
DBresult3.120.003.13
TCA0.020.000.01
TCA.accessors0.030.010.05
counts0.060.000.06
countsTable000
experiment000
experiment_BAMfile000
genomicIntervals0.000.020.02
peakreference000
tca_ATAC000
timeclust0.020.000.02
timeclustplot1.670.001.67
timecourseTable1.890.051.94