Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:56:06 -0400 (Wed, 17 Oct 2018).
Package 1527/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Uniquorn 2.0.0 'Raik Otto'
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: Uniquorn |
Version: 2.0.0 |
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_2.0.0.tar.gz |
StartedAt: 2018-10-17 00:34:50 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 00:39:03 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 252.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Uniquorn.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/Uniquorn.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘2.0.0’ * 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 ... WARNING Found the following significant warnings: Note: possible error in 'create_bed_file(match_t, ': unused argument (manual_identifier_bed_file) See ‘/Users/biocbuild/bbs-3.7-bioc/meat/Uniquorn.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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: possible error in create_bed_file(match_t, vcf_fingerprint, res_table, output_file, ref_gen, manual_identifier_bed_file): unused argument (manual_identifier_bed_file) identify_vcf_file: no visible binding for global variable ‘vcf_fingerprint’ identify_vcf_file: no visible binding for global variable ‘res_table’ 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 ‘.SD’ 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 ‘.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 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 installed files from ‘inst/doc’ ... 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-3.7-bioc/meat/Uniquorn.Rcheck/00check.log’ for details.
Uniquorn.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Uniquorn ### ############################################################################## ############################################################################## * 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 Note: possible error in 'create_bed_file(match_t, ': unused argument (manual_identifier_bed_file) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Uniquorn)
Uniquorn.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 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") > > test_check("Uniquorn") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 21 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 18.396 0.926 19.470
Uniquorn.Rcheck/Uniquorn-Ex.timings
name | user | system | elapsed | |
add_custom_vcf_to_database | 3.919 | 0.229 | 4.173 | |
identify_vcf_file | 1.892 | 0.060 | 1.975 | |
initiate_canonical_databases | 0.003 | 0.001 | 0.004 | |
read_library_names | 0.003 | 0.000 | 0.003 | |
remove_ccls_from_database | 0.024 | 0.000 | 0.024 | |
show_contained_ccls | 0.013 | 0.002 | 0.014 | |
show_contained_variants_for_ccl | 0.088 | 0.004 | 0.091 | |
show_contained_variants_in_library | 0.055 | 0.002 | 0.057 | |
show_which_ccls_contain_variant | 0.077 | 0.004 | 0.080 | |