Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:26 -0400 (Fri, 15 Oct 2021).

CHECK results for Uniquorn on tokay2

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? here 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 1989/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Uniquorn 2.12.0  (landing page)
'Raik Otto'
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Uniquorn
git_branch: RELEASE_3_13
git_last_commit: 689be91
git_last_commit_date: 2021-05-19 12:18:31 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Uniquorn
Version: 2.12.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Uniquorn.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Uniquorn_2.12.0.tar.gz
StartedAt: 2021-10-15 07:05:53 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 07:11:53 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 359.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Uniquorn.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Uniquorn.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Uniquorn_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Uniquorn.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '2.12.0'
* 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 whether package 'Uniquorn' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   6.5Mb
* 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
* 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
* 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 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/Uniquorn.Rcheck/00check.log'
for details.



Installation output

Uniquorn.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Uniquorn_2.12.0.tar.gz && rm -rf Uniquorn.buildbin-libdir && mkdir Uniquorn.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Uniquorn.buildbin-libdir Uniquorn_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Uniquorn_2.12.0.zip && rm Uniquorn_2.12.0.tar.gz Uniquorn_2.12.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  6 2291k    6  152k    0     0   708k      0  0:00:03 --:--:--  0:00:03  707k
100 2291k  100 2291k    0     0  3214k      0 --:--:-- --:--:-- --:--:-- 3214k

install for i386

* installing *source* package 'Uniquorn' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Uniquorn'
    finding HTML links ... done
    add_custom_vcf_to_database              html  
    add_missing_cls                         html  
    add_p_q_values_statistics               html  
    add_penalty_statistics                  html  
    create_bed_file                         html  
    identify_vcf_file                       html  
    init_and_load_identification            html  
    initiate_canonical_databases            html  
    match_query_ccl_to_database             html  
    parse_ccle_genotype_data                html  
    parse_cosmic_genotype_data              html  
    parse_vcf_file                          html  
    parse_vcf_query_into_db                 html  
    read_library_names                      html  
    read_mutation_grange_objects            html  
    remove_ccls_from_database               html  
    remove_library_from_database            html  
    show_contained_ccls                     html  
    show_contained_variants_for_ccl         html  
    show_contained_variants_in_library      html  
    show_which_ccls_contain_variant         html  
** 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

install for x64

* installing *source* package 'Uniquorn' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Uniquorn' as Uniquorn_2.12.0.zip
* DONE (Uniquorn)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Uniquorn' successfully unpacked and MD5 sums checked

Tests output

Uniquorn.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  14.73    1.56   16.26 

Uniquorn.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  16.35    0.73   17.07 

Example timings

Uniquorn.Rcheck/examples_i386/Uniquorn-Ex.timings

nameusersystemelapsed
add_custom_vcf_to_database3.070.984.19
identify_vcf_file0.860.161.30
initiate_canonical_databases000
read_library_names000
remove_ccls_from_database0.950.030.99
remove_library_from_database000
show_contained_ccls000
show_contained_variants_for_ccl0.080.010.09
show_contained_variants_in_library0.030.020.05
show_which_ccls_contain_variant0.080.000.08

Uniquorn.Rcheck/examples_x64/Uniquorn-Ex.timings

nameusersystemelapsed
add_custom_vcf_to_database2.690.102.79
identify_vcf_file0.620.010.64
initiate_canonical_databases000
read_library_names000
remove_ccls_from_database0.760.030.80
remove_library_from_database000
show_contained_ccls000
show_contained_variants_for_ccl0.100.000.09
show_contained_variants_in_library0.040.000.05
show_which_ccls_contain_variant0.080.000.08