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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings primirTSS_1.25.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/primirTSS.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘primirTSS/DESCRIPTION’ ... OK
* this is package ‘primirTSS’ version ‘1.25.0’
* 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 ‘primirTSS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::setequal’ by ‘dplyr::setequal’ when loading ‘primirTSS’
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/primirTSS.Rcheck/00install.out’ for details.
* 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 ... WARNING
'::' or ':::' import not declared from: 'magrittr'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
check_DHS_df: no visible binding for global variable ‘can_tss’
check_DHS_df: no visible binding for global variable ‘new_info’
check_DHS_s: no visible binding for global variable ‘dhs_p1’
check_DHS_s: no visible binding for global variable ‘dhs_p2’
eponine_score: no visible binding for global variable ‘previous’
eponine_score: no visible binding for global variable
  ‘histone_p1_flank’
eponine_score: no visible binding for global variable
  ‘histone_p2_flank’
eponine_score: no visible binding for global variable ‘tss_p1’
eponine_score: no visible binding for global variable ‘tss_p2’
find_nearest_peak: no visible binding for global variable ‘mir_name’
find_nearest_peak: no visible binding for global variable ‘start1’
find_nearest_peak: no visible binding for global variable ‘end1’
mir_tf: no visible binding for global variable ‘arrow’
mir_tf: no visible binding for global variable ‘seqname’
mir_tf: no visible binding for global variable ‘TF’
mir_tf: no visible binding for global variable ‘TF_class’
phast_score: no visible binding for global variable ‘loci’
phast_score: no visible binding for global variable ‘eponine_rank’
phast_score: no visible binding for global variable ‘phast_rank’
phast_score: no visible binding for global variable ‘e_p_rank’
phast_score_plot: no visible binding for global variable ‘loci’
plot_primiRNA_track: no visible binding for global variable
  ‘predicted_tss’
plot_primiRNA_track: no visible binding for global variable
  ‘symbol_name’
plot_primiRNA_track: no visible binding for global variable
  ‘stem_loop_p1’
plot_primiRNA_track: no visible binding for global variable
  ‘stem_loop_p2’
plot_primiRNA_track: no visible binding for global variable ‘gene_id’
plot_primiRNA_track: no visible binding for global variable ‘gene_p1’
plot_primiRNA_track: no visible binding for global variable ‘gene_p2’
plot_primiRNA_track: no visible binding for global variable ‘tss_p1’
plot_primiRNA_track: no visible binding for global variable ‘tss_p2’
require_fa: no visible binding for global variable ‘arrow’
tss_filter: no visible binding for global variable ‘gene_id’
tss_filter: no visible binding for global variable ‘new_info’
tss_filter: no visible binding for global variable ‘predicted_tss’
tss_filter: no visible binding for global variable ‘tss_type’
Undefined global functions or variables:
  TF TF_class arrow can_tss dhs_p1 dhs_p2 e_p_rank end1 eponine_rank
  gene_id gene_p1 gene_p2 histone_p1_flank histone_p2_flank loci
  mir_name new_info phast_rank predicted_tss previous seqname start1
  stem_loop_p1 stem_loop_p2 symbol_name tss_p1 tss_p2 tss_type
* 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 R/sysdata.rda ... 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/primirTSS.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL primirTSS
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘primirTSS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘BiocGenerics::setequal’ by ‘dplyr::setequal’ when loading ‘primirTSS’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘BiocGenerics::setequal’ by ‘dplyr::setequal’ when loading ‘primirTSS’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘BiocGenerics::setequal’ by ‘dplyr::setequal’ when loading ‘primirTSS’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’
** testing if installed package keeps a record of temporary installation path
* DONE (primirTSS)