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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ZygosityPredictor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ZygosityPredictor_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ZygosityPredictor.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ZygosityPredictor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ZygosityPredictor’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘ZygosityPredictor’ 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 ... OK
* 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 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
ZP_ov: no visible binding for global variable ‘status’
ZP_ov: no visible binding for global variable ‘eval_by’
ZP_ov: no visible binding for global variable ‘nconst’
ZP_ov: no visible binding for global variable ‘gene’
add_snps_to_matrices: no visible binding for global variable ‘mut_id’
add_snps_to_matrices: no visible binding for global variable
  ‘block_final’
add_snps_to_matrices: no visible binding for global variable ‘gt_final’
add_snps_to_matrices: no visible binding for global variable ‘.’
add_snps_to_matrices : <anonymous>: no visible binding for global
  variable ‘block_final’
add_snps_to_matrices : <anonymous>: no visible binding for global
  variable ‘mut_id’
aggregate_likelihoods: no visible binding for global variable ‘.’
aggregate_likelihoods : <anonymous>: no visible binding for global
  variable ‘mut_id’
aggregate_likelihoods : <anonymous>: no visible binding for global
  variable ‘gt’
aggregate_likelihoods : <anonymous>: no visible binding for global
  variable ‘lklhd’
aggregate_phasing : <anonymous>: no visible binding for global variable
  ‘mut_id’
aggregate_phasing : <anonymous>: no visible binding for global variable
  ‘p_same’
aggregate_phasing : <anonymous>: no visible binding for global variable
  ‘p_diff’
aggregate_phasing : <anonymous>: no visible binding for global variable
  ‘ep’
aggregate_phasing: no visible binding for global variable ‘comb’
aggregate_phasing: no visible binding for global variable ‘nconst’
aggregate_phasing: no visible binding for global variable ‘const’
aggregate_phasing: no visible binding for global variable ‘phasing’
aggregate_phasing: no visible binding for global variable ‘via’
aggregate_phasing: no visible binding for global variable ‘conf’
aggregate_phasing: no visible binding for global variable ‘unplausible’
aggregate_phasing: no visible binding for global variable ‘subclonal’
aggregate_phasing: no visible binding for global variable ‘wt_cp’
aggregate_phasing: no visible binding for global variable
  ‘min_poss_wt_cp’
aggregate_phasing: no visible binding for global variable
  ‘max_poss_wt_cp’
aggregate_phasing: no visible binding for global variable ‘score’
append_loglist: no visible binding for global variable ‘.’
bind_incdel_to_final_eval: no visible binding for global variable
  ‘status’
calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for
  global variable ‘mapq’
calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for
  global variable ‘.’
calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for
  global variable ‘qual’
calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for
  global variable ‘processed_bq’
calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for
  global variable ‘processed_mapq’
calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for
  global variable ‘aggregated_qual’
cigar_element: no visible binding for global variable ‘.’
classify_combination: no visible binding for global variable ‘baseq1’
classify_combination: no visible binding for global variable ‘baseq2’
classify_combination: no visible binding for global variable ‘mapq1’
classify_combination: no visible binding for global variable ‘mapq2’
classify_combination: no visible binding for global variable ‘pb1’
classify_combination: no visible binding for global variable ‘mq1’
classify_combination: no visible binding for global variable ‘pb2’
classify_combination: no visible binding for global variable ‘mq2’
classify_combination: no visible binding for global variable ‘ppos1’
classify_combination: no visible binding for global variable ‘ppos2’
classify_combination: no visible binding for global variable ‘p_result’
classify_combination: no visible binding for global variable ‘prob_sum’
classify_combination: no visible binding for global variable ‘origin’
eval_lost_in_tumor: no visible binding for global variable ‘gene’
eval_lost_in_tumor: no visible binding for global variable ‘pre_info’
eval_lost_in_tumor: no visible binding for global variable ‘wt_cp’
eval_one_mut: no visible binding for global variable ‘gene’
eval_one_mut: no visible binding for global variable ‘n_mut’
eval_one_mut: no visible binding for global variable ‘vn_status’
eval_one_mut: no visible binding for global variable ‘conf’
eval_one_mut: no visible binding for global variable ‘pre_info’
eval_one_mut: no visible binding for global variable ‘wt_cp’
eval_one_mut: no visible binding for global variable ‘eval_by’
eval_one_mut_affects_all: no visible binding for global variable
  ‘vn_status’
eval_one_mut_affects_all: no visible binding for global variable ‘.’
eval_one_mut_affects_all: no visible binding for global variable
  ‘mut_id’
eval_one_mut_affects_all: no visible binding for global variable ‘gene’
eval_one_mut_affects_all: no visible binding for global variable
  ‘n_mut’
eval_one_mut_affects_all: no visible binding for global variable ‘conf’
eval_one_mut_affects_all: no visible binding for global variable
  ‘eval_by’
eval_one_mut_affects_all: no visible binding for global variable
  ‘wt_cp’
eval_phasing_new: no visible binding for global variable ‘score’
eval_phasing_new: no visible binding for global variable ‘wt_cp’
eval_phasing_new: no visible binding for global variable ‘.’
eval_phasing_new: no visible binding for global variable ‘p_comb’
eval_phasing_new: no visible binding for global variable ‘comb’
eval_phasing_new: no visible binding for global variable ‘gene’
eval_phasing_new: no visible binding for global variable ‘phasing’
eval_rare_case: no visible binding for global variable ‘.’
find_unplaus_issues: no visible binding for global variable
  ‘unplausible’
find_unplaus_issues: no visible binding for global variable ‘comb’
find_unplaus_issues: no visible binding for global variable ‘.’
gene_ov: no visible binding for global variable ‘gene’
gene_ov: no visible binding for global variable ‘vn_status’
gene_ov: no visible binding for global variable ‘pre_info’
gene_ov: no visible binding for global variable ‘purity’
gene_ov: no visible binding for global variable ‘nconst’
gene_ov: no visible binding for global variable ‘conf’
gene_ov: no visible binding for global variable ‘xsq_diff’
gene_ov: no visible binding for global variable ‘xsq_same’
gene_ov: no visible binding for global variable ‘v_same’
gene_ov: no visible binding for global variable ‘v_diff’
gene_ov: no visible binding for global variable ‘phasing’
get_next_path: no visible binding for global variable ‘.’
get_xy_index: no visible binding for global variable ‘.’
loadVcf: no visible binding for global variable ‘.’
load_snps: no visible binding for global variable ‘.’
load_snps: no visible binding for global variable ‘QUAL’
load_snps: no visible binding for global variable ‘gt’
load_snps: no visible binding for global variable ‘mut_id’
make_mut_template: no visible global function definition for
  ‘expand_grid’
make_mut_template: no visible binding for global variable ‘.’
merge_sCNAs: no visible binding for global variable ‘all_imb’
merge_sCNAs: no visible binding for global variable ‘gt_cna’
merge_sCNAs: no visible binding for global variable ‘seg_id’
parse_cigar: no visible binding for global variable ‘.’
perform_copy_number_phasing : <anonymous>: no visible binding for
  global variable ‘seg_id’
perform_copy_number_phasing : <anonymous>: no visible binding for
  global variable ‘mut_id2’
perform_copy_number_phasing : <anonymous>: no visible binding for
  global variable ‘mut_id1’
perform_copy_number_phasing : <anonymous>: no visible binding for
  global variable ‘llr’
perform_indirect_phasing: no visible binding for global variable ‘af’
perform_indirect_phasing: no visible binding for global variable ‘tcn’
perform_indirect_phasing: no visible binding for global variable ‘chr’
perform_indirect_phasing: no visible binding for global variable ‘pos’
perform_indirect_phasing: no visible binding for global variable ‘ref’
perform_indirect_phasing: no visible binding for global variable ‘alt’
perform_indirect_phasing: no visible binding for global variable
  ‘mut_id’
perform_indirect_phasing: no visible binding for global variable ‘REF’
perform_indirect_phasing: no visible binding for global variable ‘ALT’
perform_indirect_phasing: no visible binding for global variable
  ‘gt_final’
phase: no visible binding for global variable ‘comb’
phase: no visible binding for global variable ‘ncomb’
phase_combination: no visible binding for global variable ‘purity’
phase_combination: no visible binding for global variable ‘printLog’
predict_zygosity: no visible binding for global variable ‘n_mut’
predict_zygosity: no visible binding for global variable ‘conf’
predict_zygosity: no visible binding for global variable ‘eval_by’
predict_zygosity: no visible binding for global variable ‘wt_cp_range’
predict_zygosity: no visible binding for global variable ‘phasing’
predict_zygosity: no visible binding for global variable ‘eval_time_s’
predict_zygosity_genewise: no visible binding for global variable
  ‘vn_status’
prepare_germline_variants: no visible binding for global variable
  ‘all_imb’
prepare_germline_variants: no visible binding for global variable
  ‘gt_cna’
prepare_germline_variants: no visible binding for global variable
  ‘seg_id’
prepare_germline_variants: no visible binding for global variable
  ‘vn_status’
prioritize_combination: no visible binding for global variable ‘.’
prioritize_combination : <anonymous>: no visible binding for global
  variable ‘.’
prioritize_combination: no visible binding for global variable ‘m’
prioritize_combination: no visible binding for global variable ‘n’
prioritize_combination: no visible binding for global variable ‘n1’
prioritize_combination: no visible binding for global variable ‘n2’
remove_duplicated_variants: no visible binding for global variable
  ‘chr’
remove_duplicated_variants: no visible binding for global variable
  ‘pos’
remove_duplicated_variants: no visible binding for global variable ‘n’
remove_duplicated_variants : <anonymous>: no visible binding for global
  variable ‘chr’
remove_duplicated_variants : <anonymous>: no visible binding for global
  variable ‘pos’
remove_duplicated_variants : <anonymous>: no visible binding for global
  variable ‘.’
remove_duplicated_variants : <anonymous>: no visible binding for global
  variable ‘mut_id’
vm: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . ALT QUAL REF af aggregated_qual all_imb alt baseq1 baseq2
  block_final chr comb conf const ep eval_by eval_time_s expand_grid
  gene gt gt_cna gt_final lklhd llr m mapq mapq1 mapq2 max_poss_wt_cp
  min_poss_wt_cp mq1 mq2 mut_id mut_id1 mut_id2 n n1 n2 n_mut ncomb
  nconst origin p_comb p_diff p_result p_same pb1 pb2 phasing pos ppos1
  ppos2 pre_info printLog prob_sum processed_bq processed_mapq purity
  qual ref score seg_id status subclonal tcn unplausible v_diff v_same
  via vn_status wt_cp wt_cp_range xsq_diff xsq_same
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ZygosityPredictor.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ZygosityPredictor
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘ZygosityPredictor’ ...
** using staged installation
** R
** data
** 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 (ZygosityPredictor)