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This page was generated on 2022-05-20 12:06:04 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Uniquorn on nebbiolo1


To the developers/maintainers of the Uniquorn package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Uniquorn.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2086/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Uniquorn 2.16.0  (landing page)
'Raik Otto'
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/Uniquorn
git_branch: RELEASE_3_15
git_last_commit: c389295
git_last_commit_date: 2022-04-26 11:29:51 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Uniquorn
Version: 2.16.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Uniquorn.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Uniquorn_2.16.0.tar.gz
StartedAt: 2022-05-19 22:00:56 -0400 (Thu, 19 May 2022)
EndedAt: 2022-05-19 22:05:21 -0400 (Thu, 19 May 2022)
EllapsedTime: 265.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Uniquorn.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Uniquorn.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Uniquorn_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Uniquorn.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.16.0’
* 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 ... 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 dependencies in R code ... WARNING
Missing or unexported object: ‘GenomicRanges::GenomicRangesList’
* 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 global function definition for
  ‘fread’
parse_ccle_genotype_data: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
parse_ccle_genotype_data: no visible global function definition for
  ‘data.table’
parse_ccle_genotype_data: no visible binding for global variable ‘.SD’
parse_ccle_genotype_data: no visible binding for global variable
  ‘Index’
parse_cosmic_genotype_data: no visible global function definition for
  ‘fread’
parse_cosmic_genotype_data: no visible binding for global variable
  ‘position’
parse_cosmic_genotype_data: no visible global function definition for
  ‘data.table’
parse_cosmic_genotype_data: no visible binding for global variable
  ‘.SD’
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:
  .SD Index Tumor_Sample_Barcode ccls_all data.table fread
  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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/Uniquorn.Rcheck/00check.log’
for details.



Installation output

Uniquorn.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Uniquorn
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘Uniquorn’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Uniquorn)

Tests output

Uniquorn.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
> 
> test_check("Uniquorn")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
 16.262   0.857  17.105 

Example timings

Uniquorn.Rcheck/Uniquorn-Ex.timings

nameusersystemelapsed
add_custom_vcf_to_database1.6080.0921.702
identify_vcf_file0.5590.0480.610
initiate_canonical_databases0.0010.0000.001
read_library_names0.0010.0000.001
remove_ccls_from_database0.7830.0040.788
remove_library_from_database0.0020.0000.002
show_contained_ccls0.0060.0040.010
show_contained_variants_for_ccl0.0700.0040.074
show_contained_variants_in_library0.0320.0040.036
show_which_ccls_contain_variant0.0560.0040.059