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BioC 3.5: CHECK report for Uniquorn on toluca2

This page was generated on 2017-04-23 14:41:20 -0400 (Sun, 23 Apr 2017).

Package 1347/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Uniquorn 1.3.1
'Raik Otto'
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Uniquorn
Last Changed Rev: 124890 / Revision: 129046
Last Changed Date: 2016-12-07 07:56:53 -0500 (Wed, 07 Dec 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
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: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Uniquorn_1.3.1.tar.gz
StartedAt: 2017-04-23 11:02:08 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 11:04:30 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 142.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Uniquorn.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Uniquorn_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Uniquorn.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Uniquorn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Uniquorn’ version ‘1.3.1’
* 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 for sufficient/correct file permissions ... 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 ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
add_custom_vcf_to_database 21.453  0.464  22.133
identify_vcf_file          18.457  0.347  18.828
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Uniquorn.Rcheck/00check.log’
for details.


Uniquorn.Rcheck/00install.out:

* 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
* DONE (Uniquorn)

Uniquorn.Rcheck/Uniquorn-Ex.timings:

nameusersystemelapsed
add_custom_vcf_to_database21.453 0.46422.133
identify_vcf_file18.457 0.34718.828
initiate_canonical_databases0.2140.0120.228
remove_custom_vcf_from_database1.3380.0621.401
show_contained_cls0.0060.0000.006
show_contained_mutations0.2340.0160.250
show_contained_mutations_for_cl0.1950.0150.211
show_which_cls_contain_mutation0.1820.0150.197