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BioC 3.5: CHECK report for Uniquorn on tokay2

This page was generated on 2017-08-16 13:25:28 -0400 (Wed, 16 Aug 2017).

Package 1352/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Uniquorn 1.4.2
'Raik Otto'
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Uniquorn
Last Changed Rev: 130561 / Revision: 131943
Last Changed Date: 2017-06-20 08:14:31 -0400 (Tue, 20 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Uniquorn
Version: 1.4.2
Command: rm -rf Uniquorn.buildbin-libdir Uniquorn.Rcheck && mkdir Uniquorn.buildbin-libdir Uniquorn.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Uniquorn.buildbin-libdir Uniquorn_1.4.2.tar.gz >Uniquorn.Rcheck\00install.out 2>&1 && cp Uniquorn.Rcheck\00install.out Uniquorn-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Uniquorn.buildbin-libdir --install="check:Uniquorn-install.out" --force-multiarch --no-vignettes --timings Uniquorn_1.4.2.tar.gz
StartedAt: 2017-08-16 03:27:11 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:31:59 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 288.2 seconds
RetCode: 0
Status:  OK  
CheckDir: Uniquorn.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Uniquorn.buildbin-libdir Uniquorn.Rcheck && mkdir Uniquorn.buildbin-libdir Uniquorn.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Uniquorn.buildbin-libdir Uniquorn_1.4.2.tar.gz >Uniquorn.Rcheck\00install.out 2>&1 && cp Uniquorn.Rcheck\00install.out Uniquorn-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Uniquorn.buildbin-libdir --install="check:Uniquorn-install.out" --force-multiarch --no-vignettes --timings Uniquorn_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Uniquorn.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 'Uniquorn/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Uniquorn' version '1.4.2'
* 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 'Uniquorn' 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
add_custom_vcf_to_database 21.61   1.64   23.25
identify_vcf_file          17.45   1.62   19.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
add_custom_vcf_to_database 20.08   1.66   21.73
identify_vcf_file          16.26   1.28   17.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
  Running 'testthat.R'
  Running 'uniquorn-Tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
  Running 'testthat.R'
  Running 'uniquorn-Tests.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

Uniquorn.Rcheck/00install.out:


install for i386

* installing *source* package 'Uniquorn' ...
** 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 'Uniquorn' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Uniquorn' as Uniquorn_1.4.2.zip
* DONE (Uniquorn)

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

nameusersystemelapsed
add_custom_vcf_to_database21.61 1.6423.25
identify_vcf_file17.45 1.6219.07
initiate_canonical_databases0.120.000.13
remove_custom_vcf_from_database1.070.051.10
show_contained_cls0.010.000.02
show_contained_mutations0.110.010.13
show_contained_mutations_for_cl0.240.000.23
show_which_cls_contain_mutation0.120.000.12

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

nameusersystemelapsed
add_custom_vcf_to_database20.08 1.6621.73
identify_vcf_file16.26 1.2817.55
initiate_canonical_databases0.090.000.10
remove_custom_vcf_from_database1.110.011.12
show_contained_cls0.020.000.02
show_contained_mutations0.060.020.08
show_contained_mutations_for_cl0.090.010.11
show_which_cls_contain_mutation0.110.000.10