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BioC 3.4: CHECK report for chipenrich on tokay1

This page was generated on 2017-04-15 16:18:10 -0400 (Sat, 15 Apr 2017).

Package 192/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 1.12.1
Raymond G. Cavalcante
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/chipenrich
Last Changed Rev: 127283 / Revision: 128728
Last Changed Date: 2017-03-09 18:15:22 -0500 (Thu, 09 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chipenrich
Version: 1.12.1
Command: rm -rf chipenrich.buildbin-libdir chipenrich.Rcheck && mkdir chipenrich.buildbin-libdir chipenrich.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipenrich.buildbin-libdir chipenrich_1.12.1.tar.gz >chipenrich.Rcheck\00install.out 2>&1 && cp chipenrich.Rcheck\00install.out chipenrich-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=chipenrich.buildbin-libdir --install="check:chipenrich-install.out" --force-multiarch --no-vignettes --timings chipenrich_1.12.1.tar.gz
StartedAt: 2017-04-14 21:27:04 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:32:06 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 302.5 seconds
RetCode: 0
Status:  OK  
CheckDir: chipenrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chipenrich.buildbin-libdir chipenrich.Rcheck && mkdir chipenrich.buildbin-libdir chipenrich.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipenrich.buildbin-libdir chipenrich_1.12.1.tar.gz >chipenrich.Rcheck\00install.out 2>&1 && cp chipenrich.Rcheck\00install.out chipenrich-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=chipenrich.buildbin-libdir --install="check:chipenrich-install.out" --force-multiarch --no-vignettes --timings chipenrich_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/chipenrich.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chipenrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chipenrich' version '1.12.1'
* 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 'chipenrich' 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plot_spline_length 19.64   0.08   19.83
chipenrich         13.80   0.17   15.22
plot_gene_coverage  6.16   0.01    6.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plot_spline_length 19.28   0.12   19.41
chipenrich         13.24   0.03   17.57
plot_gene_coverage  7.36   0.02    7.37
* 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: OK

chipenrich.Rcheck/00install.out:


install for i386

* installing *source* package 'chipenrich' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'chipenrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chipenrich' as chipenrich_1.12.1.zip
* DONE (chipenrich)

chipenrich.Rcheck/examples_i386/chipenrich-Ex.timings:

nameusersystemelapsed
assign_peak_segments0.630.033.90
assign_peaks0.690.020.71
calc_peak_gene_overlap0.760.020.78
chipenrich13.80 0.1715.22
load_peaks0.090.000.17
num_peaks_per_gene0.740.000.73
plot_dist_to_tss0.540.000.55
plot_gene_coverage6.160.016.17
plot_spline_length19.64 0.0819.83
read_bed0.060.000.06
read_bedgff0.030.000.03
supported_genesets000
supported_genomes0.020.000.02
supported_locusdefs000
supported_methods000
supported_read_lengths000

chipenrich.Rcheck/examples_x64/chipenrich-Ex.timings:

nameusersystemelapsed
assign_peak_segments0.300.000.29
assign_peaks0.750.010.77
calc_peak_gene_overlap0.790.000.80
chipenrich13.24 0.0317.57
load_peaks0.030.000.03
num_peaks_per_gene0.540.000.55
plot_dist_to_tss0.320.000.31
plot_gene_coverage7.360.027.37
plot_spline_length19.28 0.1219.41
read_bed0.080.000.08
read_bedgff0.040.000.05
supported_genesets000
supported_genomes000
supported_locusdefs0.020.000.01
supported_methods000
supported_read_lengths000