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CHECK report for Uniquorn on tokay1

This page was generated on 2019-04-13 11:26:25 -0400 (Sat, 13 Apr 2019).

Package 1612/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Uniquorn 2.2.1
'Raik Otto'
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK 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: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Uniquorn.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Uniquorn_2.2.1.tar.gz
StartedAt: 2019-04-13 06:07:46 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:13:46 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 360.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Uniquorn.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Uniquorn.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings Uniquorn_2.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Uniquorn.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/Uniquorn.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.3Mb
  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
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
add_custom_vcf_to_database 3.64   0.36    5.56
** 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: 1 WARNING, 3 NOTEs
See
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/Uniquorn_2.2.1.tar.gz && rm -rf Uniquorn.buildbin-libdir && mkdir Uniquorn.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Uniquorn.buildbin-libdir Uniquorn_2.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL Uniquorn_2.2.1.zip && rm Uniquorn_2.2.1.tar.gz Uniquorn_2.2.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2330k  100 2330k    0     0  32.9M      0 --:--:-- --:--:-- --:--:-- 35.0M

install for i386

* 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
  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
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
In R CMD INSTALL

install for x64

* installing *source* package 'Uniquorn' ...
** testing if installed package can be loaded
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'Uniquorn'
* MD5 sums
packaged installation of 'Uniquorn' as Uniquorn_2.2.1.zip
* DONE (Uniquorn)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'Uniquorn' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Uniquorn.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
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 
  13.40    1.57   14.95 

Uniquorn.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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")
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 
  14.85    0.56   15.42 

Example timings

Uniquorn.Rcheck/examples_i386/Uniquorn-Ex.timings

nameusersystemelapsed
add_custom_vcf_to_database3.640.365.56
identify_vcf_file1.150.272.25
initiate_canonical_databases000
read_library_names000
remove_ccls_from_database0.860.020.88
remove_library_from_database0.000.010.01
show_contained_ccls000
show_contained_variants_for_ccl0.070.000.07
show_contained_variants_in_library0.030.000.03
show_which_ccls_contain_variant0.060.000.07

Uniquorn.Rcheck/examples_x64/Uniquorn-Ex.timings

nameusersystemelapsed
add_custom_vcf_to_database2.770.052.81
identify_vcf_file1.700.031.73
initiate_canonical_databases000
read_library_names000
remove_ccls_from_database0.690.030.72
remove_library_from_database000
show_contained_ccls0.010.000.02
show_contained_variants_for_ccl0.060.000.06
show_contained_variants_in_library0.020.020.03
show_which_ccls_contain_variant0.060.000.06