Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:05:14 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

CHECK results for CNVgears on nebbiolo2


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.

raw results

Package 357/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNVgears 1.2.0  (landing page)
Simone Montalbano
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/CNVgears
git_branch: RELEASE_3_14
git_last_commit: 705feb3
git_last_commit_date: 2021-10-26 13:05:33 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: CNVgears
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CNVgears.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CNVgears_1.2.0.tar.gz
StartedAt: 2022-01-18 06:48:29 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 06:49:55 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 86.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CNVgears.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CNVgears.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CNVgears_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CNVgears.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVgears/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVgears’ version ‘1.2.0’
* 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 ‘CNVgears’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  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      9.617  0.348   9.961
read_vcf             8.430  0.332   8.763
cnmops_to_CNVresults 6.923  0.139   7.063
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/CNVgears.Rcheck/00check.log’
for details.



Installation output

CNVgears.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CNVgears
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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
** 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)

Tests output

CNVgears.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  2.103   0.068   2.156 

Example timings

CNVgears.Rcheck/CNVgears-Ex.timings

nameusersystemelapsed
CNVresults_to_GRanges2.4920.1402.632
chr_uniform0.0120.0010.012
cleaning_filter0.0010.0000.001
cnmops_to_CNVresults6.9230.1397.063
cnvrs_create1.1420.0131.154
genic_load0.0000.0000.001
genomic_locus000
immuno_regions0.0000.0000.001
inter_res_merge9.6170.3489.961
merge_calls3.1030.0792.664
read_NGS_intervals0.0110.0000.011
read_finalreport_raw0.1330.0000.110
read_finalreport_snps0.1960.0000.154
read_metadt0.0140.0000.011
read_results1.7520.0641.558
read_vcf8.4300.3328.763
summary.CNVresults0.0240.0000.023
telom_centrom0.0280.0000.015