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BioC 3.5: CHECK report for Uniquorn on tokay2

This page was generated on 2017-10-18 14:25:43 -0400 (Wed, 18 Oct 2017).

Package 1351/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Uniquorn 1.4.2
'Raik Otto'
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/Uniquorn
Branch: RELEASE_3_5
Last Commit: d905b05
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: 2017-10-18 03:33:16 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:38:14 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 297.9 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 3.4.2 Patched (2017-10-07 r73498)
* 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 17.98   1.60   19.58
identify_vcf_file          17.99   1.53   19.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
add_custom_vcf_to_database 21.50   1.83   23.33
identify_vcf_file          19.12   1.49   20.62
* 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_database17.98 1.6019.58
identify_vcf_file17.99 1.5319.52
initiate_canonical_databases0.120.000.12
remove_custom_vcf_from_database1.270.031.30
show_contained_cls000
show_contained_mutations0.150.000.15
show_contained_mutations_for_cl0.160.000.16
show_which_cls_contain_mutation0.20.00.2

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

nameusersystemelapsed
add_custom_vcf_to_database21.50 1.8323.33
identify_vcf_file19.12 1.4920.62
initiate_canonical_databases0.280.010.29
remove_custom_vcf_from_database1.140.001.14
show_contained_cls0.020.000.02
show_contained_mutations0.060.030.09
show_contained_mutations_for_cl0.160.030.19
show_which_cls_contain_mutation0.090.020.11