BioC 3.4: CHECK report for Uniquorn on malbec1

Package: Uniquorn

Version: 1.2.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Uniquorn_1.2.0.tar.gz

StartedAt: 2017-04-15 01:46:32 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:48:23 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 110.6 seconds

RetCode: 0

Status:  OK

CheckDir: Uniquorn.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Uniquorn_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Uniquorn.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 16.480  0.052  17.270
identify_vcf_file          15.756  0.004  16.463
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/Uniquorn.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
add_custom_vcf_to_database	16.480	0.052	17.270
identify_vcf_file	15.756	0.004	16.463
initiate_canonical_databases	0.108	0.000	0.108
remove_custom_vcf_from_database	1.008	0.008	1.014
show_contained_cls	0.004	0.000	0.004
show_contained_mutations	0.140	0.008	0.149
show_contained_mutations_for_cl	0.168	0.000	0.167
show_which_cls_contain_mutation	0.196	0.000	0.196