Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:13 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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 |
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 355/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CNVgears 1.3.0 (landing page) Simone Montalbano
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: CNVgears |
Version: 1.3.0 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVgears.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CNVgears_1.3.0.tar.gz |
StartedAt: 2022-03-17 18:45:45 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 18:47:16 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 91.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CNVgears.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CNVgears.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CNVgears_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CNVgears.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * 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 '1.3.0' * 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 * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed inter_res_merge 8.80 0.48 9.28 cnmops_to_CNVresults 6.70 0.33 7.03 read_vcf 5.13 0.25 5.37 * 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: 2 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/CNVgears.Rcheck/00check.log' for details.
CNVgears.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CNVgears ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * 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 * DONE (CNVgears) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'RGraph2js' is missing or broken done
CNVgears.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 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") [ FAIL 0 | WARN 6 | SKIP 1 | PASS 11 ] == Skipped tests =============================================================== * empty test (1) [ FAIL 0 | WARN 6 | SKIP 1 | PASS 11 ] > > proc.time() user system elapsed 1.71 0.25 1.95
CNVgears.Rcheck/CNVgears-Ex.timings
name | user | system | elapsed | |
CNVresults_to_GRanges | 1.74 | 0.22 | 1.95 | |
chr_uniform | 0.01 | 0.00 | 0.02 | |
cleaning_filter | 0 | 0 | 0 | |
cnmops_to_CNVresults | 6.70 | 0.33 | 7.03 | |
cnvrs_create | 0.64 | 0.02 | 0.66 | |
genic_load | 0 | 0 | 0 | |
genomic_locus | 0 | 0 | 0 | |
immuno_regions | 0 | 0 | 0 | |
inter_res_merge | 8.80 | 0.48 | 9.28 | |
merge_calls | 2.31 | 0.35 | 2.63 | |
read_NGS_intervals | 0.02 | 0.00 | 0.01 | |
read_finalreport_raw | 0.08 | 0.01 | 0.10 | |
read_finalreport_snps | 0.18 | 0.02 | 0.20 | |
read_metadt | 0.02 | 0.00 | 0.01 | |
read_results | 1.39 | 0.03 | 1.41 | |
read_vcf | 5.13 | 0.25 | 5.37 | |
summary.CNVresults | 0.01 | 0.02 | 0.03 | |
telom_centrom | 0.02 | 0.00 | 0.02 | |