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CHECK report for Uniquorn on merida1

This page was generated on 2019-04-16 11:59:22 -0400 (Tue, 16 Apr 2019).

Package 1612/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Uniquorn 2.2.1
'Raik Otto'
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Uniquorn
Branch: RELEASE_3_8
Last Commit: 9a1b9e4
Last Changed Date: 2019-01-04 13:08:11 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Uniquorn
Version: 2.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Uniquorn.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Uniquorn_2.2.1.tar.gz
StartedAt: 2019-04-16 03:18:53 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:23:19 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 265.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Uniquorn.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Uniquorn.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Uniquorn_2.2.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Uniquorn.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.2.1’
* package encoding: UTF-8
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘Uniquorn’
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/Uniquorn.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
* 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 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 ... NOTE
add_p_q_values_statistics: no visible binding for '<<-' assignment to
  ‘sig_vec’
add_p_q_values_statistics: no visible binding for global variable
  ‘sig_vec’
create_bed_file: no visible binding for global variable ‘res_table’
create_bed_file: no visible binding for global variable ‘sim_list’
identify_vcf_file: no visible binding for global variable
  ‘vcf_fingerprint’
identify_vcf_file: no visible binding for global variable
  ‘output_file_xls’
init_and_load_identification: no visible global function definition for
  ‘tail’
parse_ccle_genotype_data: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
parse_ccle_genotype_data: no visible binding for global variable
  ‘Index’
parse_cosmic_genotype_data: no visible binding for global variable
  ‘position’
parse_cosmic_genotype_data: no visible binding for global variable
  ‘Index’
show_contained_ccls: no visible binding for '<<-' assignment to
  ‘ccls_all’
show_contained_ccls: no visible binding for global variable ‘ccls_all’
write_w0_and_split_w0_into_lower_weights: no visible binding for '<<-'
  assignment to ‘g_mat_exclude’
write_w0_and_split_w0_into_lower_weights: no visible binding for global
  variable ‘g_mat_exclude’
Undefined global functions or variables:
  Index Tumor_Sample_Barcode ccls_all g_mat_exclude output_file_xls
  position res_table sig_vec sim_list tail vcf_fingerprint
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/Uniquorn.Rcheck/00check.log’
for details.



Installation output

Uniquorn.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Uniquorn
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Uniquorn’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘Uniquorn’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘Uniquorn’
* DONE (Uniquorn)

Tests output

Uniquorn.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv(R_TESTS="")
> library("testthat")
> library("Uniquorn")
Warning message:
replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn' 
> 
> test_check("Uniquorn")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 21 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 19.167   0.893  20.203 

Example timings

Uniquorn.Rcheck/Uniquorn-Ex.timings

nameusersystemelapsed
add_custom_vcf_to_database4.0020.1964.233
identify_vcf_file1.2230.0531.287
initiate_canonical_databases0.0010.0010.001
read_library_names0.0000.0000.001
remove_ccls_from_database0.6960.0070.716
remove_library_from_database0.0030.0010.002
show_contained_ccls0.0090.0020.011
show_contained_variants_for_ccl0.0620.0010.063
show_contained_variants_in_library0.0360.0010.037
show_which_ccls_contain_variant0.0580.0020.061