##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CNVgears.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CNVgears_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CNVgears.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘CNVgears/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVgears’ version ‘1.12.0’
* 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 ... OK
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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      9.023  0.236   9.255
read_vcf             8.407  0.288   8.701
cnmops_to_CNVresults 6.791  0.184   6.975
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘CNVgears.Rmd’ using rmarkdown
Error: processing vignette 'CNVgears.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘CNVgears.Rmd’

SUMMARY: processing the following file failed:
  ‘CNVgears.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/CNVgears.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CNVgears
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
Warning in fun(libname, pkgname) :
  Package 'CNVgears' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'CNVgears' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (CNVgears)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
Warning message:
In fun(libname, pkgname) :
  Package 'CNVgears' is deprecated and will be removed from Bioconductor
  version 3.20
> library(data.table)
> 
> test_check("CNVgears")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 11 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-inter_results_compare_merge.R:79:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  1.899   0.088   1.977