Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the CNVgears package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVgears.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. |
Package 349/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNVgears 1.0.0 (landing page) Simone Montalbano
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: CNVgears |
Version: 1.0.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVgears.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVgears_1.0.0.tar.gz |
StartedAt: 2021-10-14 21:19:41 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:22:22 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 160.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNVgears.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVgears.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVgears_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVgears.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 'CNVgears/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CNVgears' version '1.0.0' * 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 whether package 'CNVgears' can be installed ... OK * checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: data 1.4Mb extdata 3.6Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * 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 CNVresults_to_GRanges: no visible global function definition for '.' CNVresults_to_GRanges: no visible binding for global variable 'sample_ID' CNVresults_to_GRanges: no visible binding for global variable 'GT' CNVresults_to_GRanges: no visible binding for global variable 'meth_ID' CNVresults_to_GRangesList: no visible binding for global variable 'GRL' DT_uniform_internal: no visible binding for global variable 'chr' DT_uniform_internal: no visible binding for global variable 'start' DT_uniform_internal: no visible binding for global variable 'end' DT_uniform_internal: no visible binding for global variable 'CN' DT_uniform_internal: no visible binding for global variable 'GT' DT_uniform_internal: no visible binding for global variable 'P_ID' DT_uniform_internal: no visible binding for global variable 'last_P' DT_uniform_internal: no visible binding for global variable 'first_P' DT_uniform_snps: no visible binding for global variable 'pos' DT_uniform_snps: no visible binding for global variable 'chr' DT_uniform_snps: no visible binding for global variable 'start' check_cnvrs: no visible binding for global variable 'start' check_cnvrs: no visible binding for global variable 'end' check_cnvrs: no visible binding for global variable 'cnvr' check_cnvrs: no visible binding for global variable 'r_ID' chr_st_en_etc: no visible binding for global variable 'V1' chr_st_en_etc: no visible global function definition for '.' chr_st_en_etc: no visible binding for global variable 'V2' chr_st_en_etc: no visible binding for global variable 'V3' chr_uniform: no visible binding for global variable 'chr' cleaning_filter: no visible binding for global variable 'sample_ID' cleaning_filter: no visible binding for global variable 'chr' cleaning_filter: no visible binding for global variable 'len' cleaning_filter: no visible binding for global variable 'NP' cleaning_filter : filter_region: no visible binding for global variable 'start' cleaning_filter : filter_region: no visible binding for global variable 'end' cleaning_filter : filter_region: no visible binding for global variable 'chr' cnmops_to_CNVresults: no visible global function definition for '.' cnmops_to_CNVresults: no visible binding for global variable 'chr' cnmops_to_CNVresults: no visible binding for global variable 'start' cnmops_to_CNVresults: no visible binding for global variable 'end' cnmops_to_CNVresults: no visible binding for global variable 'sample_ID' cnmops_to_CNVresults: no visible binding for global variable 'CN' cnvrs_create: no visible binding for global variable 'start' cnvrs_create: no visible binding for global variable 'end' cnvrs_create: no visible binding for global variable 'chr' cnvrs_create: no visible binding for global variable 'cnvr' cnvrs_create: no visible binding for global variable 'arm_ID' cnvrs_create: no visible binding for global variable 'ix' cnvrs_create: no visible binding for global variable 'r_ID' cnvrs_create: no visible binding for global variable 'freq' cnvrs_create: no visible binding for global variable 'N' cnvs_inheritance: no visible binding for global variable 'role' cnvs_inheritance: no visible binding for global variable 'sample_ID' cnvs_inheritance: no visible binding for global variable 'fam_ID' cnvs_inheritance: no visible binding for global variable 'chr' cnvs_inheritance: no visible binding for global variable 'GT' cnvs_inheritance: no visible binding for global variable 'seg_ID' cnvs_inheritance: no visible binding for global variable 'inheritance' cnvs_inheritance: no visible binding for global variable 'start' cnvs_inheritance: no visible binding for global variable 'end' cnvs_inheritance: no visible binding for global variable 'copyratio' cnvs_inheritance: no visible global function definition for 'wilcox.test' cnvs_inheritance: no visible global function definition for 'sd' cnvs_inheritance: no visible binding for global variable 'mmmethod' cnvs_inheritance: no visible binding for global variable 'm_pval' cnvs_inheritance: no visible binding for global variable 'p_pval' cnvs_inheritance: no visible global function definition for 'p.adjust' create_fill_CNVR: no visible binding for global variable 'ix' create_fill_CNVR: no visible binding for global variable 'r_ID' create_fill_CNVR: no visible binding for global variable 'start' create_fill_CNVR: no visible binding for global variable 'end' create_fill_CNVR: no visible binding for global variable 'cnvr' dupl_cnvrs: no visible binding for global variable 'chr' dupl_cnvrs: no visible binding for global variable 'r_ID' dupl_cnvrs: no visible binding for global variable 'start' dupl_cnvrs: no visible binding for global variable 'end' dupl_cnvrs: no visible binding for global variable 'cnvr' genic_load: no visible binding for global variable 'gene_biotype' genic_load: no visible binding for global variable 'chr' genic_load: no visible binding for global variable 'start' genic_load: no visible binding for global variable 'ix' genic_load: no visible binding for global variable 'end' genomic_locus: no visible binding for global variable 'chr' genomic_locus: no visible binding for global variable 'start' genomic_locus : match_band: no visible binding for global variable 'chr' genomic_locus : match_band: no visible binding for global variable 'start' genomic_locus : match_band: no visible binding for global variable 'end' genomic_locus: no visible binding for global variable 'end' genomic_locus: no visible binding for global variable 'locus_start' genomic_locus: no visible binding for global variable 'locus_end' genomic_locus: no visible binding for global variable 'locus' immuno_regions: no visible binding for global variable 'chr' immuno_regions: no visible binding for global variable 'start' immuno_regions: no visible binding for global variable 'gene_biotype' inter_res_merge: no visible binding for global variable 'meth_ID' inter_res_merge: no visible binding for global variable 'len' inter_res_merge: no visible binding for global variable 'end' inter_res_merge: no visible binding for global variable 'start' inter_res_merge: no visible binding for global variable 'GT' inter_res_merge: no visible global function definition for '.' inter_res_merge: no visible binding for global variable 'chr' inter_res_merge: no visible binding for global variable 'sample_ID' inter_res_merge: no visible binding for global variable 'CN' inter_res_merge: no visible binding for global variable 'arm_ID' inter_res_merge: no visible binding for global variable 'ix' inter_res_merge: no visible binding for global variable 'used' inter_res_merge: no visible binding for global variable 'outer_end' inter_res_merge: no visible binding for global variable 'outer_start' inter_res_merge: no visible binding for global variable 'seg_ID' load_RDS: no visible binding for global variable 'start' load_RDS: no visible binding for global variable 'end' lrr_trio_plot: no visible binding for global variable 'sample_ID' lrr_trio_plot: no visible binding for global variable 'fam_ID' lrr_trio_plot: no visible binding for global variable 'role' lrr_trio_plot: no visible binding for global variable 'start' merge_calls: no visible binding for global variable 'chr' merge_calls: no visible binding for global variable 'start' merge_cnvrs: no visible binding for global variable 'start' merge_cnvrs: no visible binding for global variable 'end' merge_cnvrs: no visible binding for global variable 'r_ID' merge_cnvrs: no visible binding for global variable 'cnvr' pl: no visible binding for global variable 'center' pl: no visible binding for global variable 'end' pl: no visible binding for global variable 'start' pl: no visible binding for global variable 'cr' pl: no visible binding for global variable 'copyratio' pl: no visible binding for global variable 'CN' read_NGS_intervals : DT_uniform_internal: no visible binding for global variable 'start' read_NGS_intervals : DT_uniform_internal: no visible binding for global variable 'end' read_NGS_intervals : DT_uniform_internal: no visible binding for global variable 'chr' read_NGS_raw: no visible binding for global variable 'chr' read_NGS_raw: no visible binding for global variable 'start' read_NGS_raw: no visible binding for global variable 'end' read_NGS_raw: no visible binding for global variable 'log2R' read_NGS_raw: no visible binding for global variable 'copyratio' read_NGS_raw: no visible binding for global variable 'P_ID' read_NGS_raw: no visible binding for global variable 'P_CN' read_finalreport_raw: no visible binding for global variable 'chr' read_finalreport_raw: no visible binding for global variable 'start' read_finalreport_raw: no visible binding for global variable 'log2R' read_finalreport_raw: no visible global function definition for '.' read_finalreport_raw: no visible binding for global variable 'end' read_finalreport_raw: no visible binding for global variable 'BAF' read_finalreport_raw: no visible binding for global variable 'P_ID' read_metadt: no visible binding for global variable 'role' read_metadt: no visible binding for global variable 'sex' read_results: no visible binding for global variable 'sample_ID' read_results: no visible binding for global variable 'seg_ID' read_results: no visible binding for global variable 'meth_ID' read_vcf: no visible binding for global variable '..end_vcf' remove_cnvs: no visible binding for global variable 'ix' remove_cnvs: no visible binding for global variable 'cnvr' select_cnvs: no visible binding for global variable 'sample_ID' select_cnvs: no visible binding for global variable 'GT' select_cnvs: no visible binding for global variable 'fam_ID' select_cnvs: no visible binding for global variable 'role' select_cnvs: no visible binding for global variable 'inheritance' start_end: no visible binding for global variable 'len' start_end: no visible binding for global variable 'end' start_end: no visible binding for global variable 'start' start_end: no visible binding for global variable 'outer_start' summary.CNVresults: no visible binding for global variable 'role' summary.CNVresults: no visible binding for global variable 'sample_ID' summary.CNVresults: no visible binding for global variable 'GT' summary.CNVresults: no visible binding for global variable 'len' summary.CNVresults: no visible binding for global variable 'NP' summary.CNVresults: no visible global function definition for 'pdf' summary.CNVresults: no visible global function definition for 'reorder' summary.CNVresults: no visible binding for global variable 'chr' summary.CNVresults: no visible binding for global variable 'CN' summary.CNVresults: no visible global function definition for 'dev.off' summary.CNVresults: no visible global function definition for '.' summary.CNVresults: no visible binding for global variable 'n_cnvs' summary.CNVresults: no visible global function definition for 'head' summary.CNVresults: no visible global function definition for 'tail' summary.CNVresults: no visible binding for global variable 'mean_len' trim_res: no visible binding for global variable 'sample_ID' trim_res: no visible binding for global variable 'chr' trim_res: no visible binding for global variable 'start' trim_res: no visible binding for global variable 'end' Undefined global functions or variables: . ..end_vcf BAF CN GRL GT N NP P_CN P_ID V1 V2 V3 arm_ID center chr cnvr copyratio cr dev.off end fam_ID first_P freq gene_biotype head inheritance ix last_P len locus locus_end locus_start log2R m_pval mean_len meth_ID mmmethod n_cnvs outer_end outer_start p.adjust p_pval pdf pos r_ID reorder role sample_ID sd seg_ID sex start tail used wilcox.test Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("stats", "end", "p.adjust", "reorder", "sd", "start", "wilcox.test") importFrom("utils", "head", "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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed inter_res_merge 10.92 0.55 11.47 cnmops_to_CNVresults 9.36 0.33 9.69 read_vcf 6.51 0.42 6.96 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed inter_res_merge 12.88 0.16 13.03 cnmops_to_CNVresults 9.97 0.18 10.14 read_vcf 6.87 0.10 6.97 * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVgears.Rcheck/00check.log' for details.
CNVgears.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CNVgears_1.0.0.tar.gz && rm -rf CNVgears.buildbin-libdir && mkdir CNVgears.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVgears.buildbin-libdir CNVgears_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CNVgears_1.0.0.zip && rm CNVgears_1.0.0.tar.gz CNVgears_1.0.0.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 79 2112k 79 1672k 0 0 2494k 0 --:--:-- --:--:-- --:--:-- 2493k 100 2112k 100 2112k 0 0 2812k 0 --:--:-- --:--:-- --:--:-- 2813k install for i386 * installing *source* package 'CNVgears' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CNVgears' finding HTML links ... done CNVgears html CNVresults_to_GRanges html chr_uniform html cleaning_filter html cnmops_to_CNVresults html cnvrs_create html cnvs_inheritance html cohort_examples html genic_load html genomic_locus html hg18_chr_arms html hg18_start_end_centromeres html hg19_chr_arms html hg19_start_end_centromeres html hg38_chr_arms html hg38_start_end_centromeres html immuno_regions html inter_res_merge html lrr_trio_plot html markers_examples html merge_calls html penn_22 html quanti_22 html read_NGS_intervals html read_NGS_raw html read_finalreport_raw html read_finalreport_snps html read_metadt html read_results html read_vcf html summary.CNVresults html telom_centrom 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 'CNVgears' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'CNVgears' as CNVgears_1.0.0.zip * DONE (CNVgears) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'CNVgears' successfully unpacked and MD5 sums checked
CNVgears.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. > library(testthat) > library(CNVgears) Loading required package: data.table > library(data.table) > > test_check("CNVgears") == Skipped tests =============================================================== * empty test (1) [ FAIL 0 | WARN 6 | SKIP 1 | PASS 11 ] > > proc.time() user system elapsed 2.51 0.12 2.62 |
CNVgears.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. > library(testthat) > library(CNVgears) Loading required package: data.table > library(data.table) > > test_check("CNVgears") == Skipped tests =============================================================== * empty test (1) [ FAIL 0 | WARN 6 | SKIP 1 | PASS 11 ] > > proc.time() user system elapsed 2.76 0.10 2.85 |
CNVgears.Rcheck/examples_i386/CNVgears-Ex.timings
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CNVgears.Rcheck/examples_x64/CNVgears-Ex.timings
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