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BioC 3.6: CHECK report for chipenrich on tokay1

This page was generated on 2017-08-16 13:31:53 -0400 (Wed, 16 Aug 2017).

Package 208/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.1.1
Raymond G. Cavalcante
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chipenrich
Last Changed Rev: 129611 / Revision: 131943
Last Changed Date: 2017-05-15 09:43:03 -0400 (Mon, 15 May 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chipenrich
Version: 2.1.1
Command: rm -rf chipenrich.buildbin-libdir chipenrich.Rcheck && mkdir chipenrich.buildbin-libdir chipenrich.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipenrich.buildbin-libdir chipenrich_2.1.1.tar.gz >chipenrich.Rcheck\00install.out 2>&1 && cp chipenrich.Rcheck\00install.out chipenrich-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chipenrich.buildbin-libdir --install="check:chipenrich-install.out" --force-multiarch --no-vignettes --timings chipenrich_2.1.1.tar.gz
StartedAt: 2017-08-15 22:19:53 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:30:41 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 648.7 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-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chipenrich.buildbin-libdir chipenrich_2.1.1.tar.gz >chipenrich.Rcheck\00install.out 2>&1 && cp chipenrich.Rcheck\00install.out chipenrich-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=chipenrich.buildbin-libdir --install="check:chipenrich-install.out" --force-multiarch --no-vignettes --timings chipenrich_2.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/chipenrich.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.1.1'
* 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
broadenrich 9.36   0.16    9.61
polyenrich  7.49   0.06    7.54
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
broadenrich 7.93   0.04   13.13
polyenrich  6.74   0.00    6.73
* 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_2.1.1.zip
* DONE (chipenrich)

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

nameusersystemelapsed
assign_peak_segments0.450.000.56
assign_peaks1.190.011.22
broadenrich9.360.169.61
calc_peak_gene_overlap0.420.000.42
chipenrich2.710.113.36
load_peaks0.030.000.03
num_peaks_per_gene0.420.010.44
plot_chipenrich_spline3.220.053.29
plot_dist_to_tss0.280.000.28
plot_gene_coverage1.670.021.69
plot_polyenrich_spline3.810.093.91
polyenrich7.490.067.54
read_bed0.160.000.16
supported_genesets000
supported_genomes0.010.000.02
supported_locusdefs000
supported_methods000
supported_read_lengths0.020.000.01

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

nameusersystemelapsed
assign_peak_segments0.50.00.5
assign_peaks1.380.041.42
broadenrich 7.93 0.0413.13
calc_peak_gene_overlap0.40.00.4
chipenrich2.720.002.72
load_peaks0.050.000.05
num_peaks_per_gene0.400.010.42
plot_chipenrich_spline2.780.022.86
plot_dist_to_tss0.270.000.27
plot_gene_coverage0.910.010.92
plot_polyenrich_spline3.620.073.69
polyenrich6.740.006.73
read_bed0.180.000.19
supported_genesets000
supported_genomes000
supported_locusdefs0.020.000.01
supported_methods000
supported_read_lengths000