Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* preparing ‘GenomicPlot’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘GenomicPlot_0.99.5.tar.gz’

===============================

 BiocCheckGitClone('GenomicPlot')

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─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.5
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3046/GenomicPlot_20230530125942/GenomicPlot
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      GenomicPlot_gh.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3046/GenomicPlot_20230530125942/GenomicPlot.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicPlot’ version ‘0.99.5’
* 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 ‘GenomicPlot’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::residuals’ by ‘stats::residuals’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘GenomicRanges::start’ by ‘stats::start’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘GenomicRanges::end’ by ‘stats::end’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::weights’ by ‘stats::weights’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::IQR’ by ‘stats::IQR’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::xtabs’ by ‘stats::xtabs’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::density’ by ‘stats::density’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::mad’ by ‘stats::mad’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘GenomicRanges::update’ by ‘stats::update’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘BiocGenerics::relist’ by ‘utils::relist’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘dplyr::setdiff’ by ‘GenomicRanges::setdiff’ when loading ‘GenomicPlot’
  Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘GenomicPlot’
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/3046/GenomicPlot_20230530125942/GenomicPlot.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 36.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
    tests    28.6Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking use of S3 registration ... 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 ... [37s/38s] NOTE
draw_boxplot_by_factor: no visible binding for global variable ‘x2’
draw_boxplot_wo_outlier: no visible binding for global variable ‘x2’
draw_locus_profile: no visible binding for global variable ‘lower’
draw_locus_profile: no visible binding for global variable ‘upper’
draw_mean_se_barplot: no visible binding for global variable
  ‘sd_Intensity’
draw_mean_se_barplot: no visible binding for global variable
  ‘N_Intensity’
draw_mean_se_barplot: no visible binding for global variable
  ‘mean_Intensity’
draw_mean_se_barplot: no visible binding for global variable ‘se’
draw_mean_se_barplot: no visible binding for global variable
  ‘lower_limit’
draw_mean_se_barplot: no visible binding for global variable
  ‘upper_limit’
draw_mean_se_barplot: no visible binding for global variable ‘x2’
draw_quantile_plot: no visible binding for global variable ‘Fraction’
draw_quantile_plot: no visible binding for global variable ‘x2’
draw_rank_plot: no visible binding for global variable ‘cumCount’
draw_rank_plot: no visible binding for global variable ‘Rank’
draw_rank_plot: no visible binding for global variable ‘Fraction’
draw_region_landmark: no visible binding for global variable ‘x’
draw_region_landmark: no visible binding for global variable ‘y’
draw_region_landmark: no visible binding for global variable ‘value’
draw_region_landmark: no visible binding for global variable ‘fid’
draw_region_profile: no visible binding for global variable ‘lower’
draw_region_profile: no visible binding for global variable ‘upper’
draw_stacked_profile: no visible binding for global variable ‘Location’
draw_stacked_profile: no visible binding for global variable ‘lower’
draw_stacked_profile: no visible binding for global variable ‘upper’
draw_stacked_profile: no visible binding for global variable ‘Interval’
extract_longest_tx: no visible binding for global variable ‘gene_id’
extract_longest_tx: no visible binding for global variable ‘cds_len’
extract_longest_tx: no visible binding for global variable ‘utr5_len’
extract_longest_tx: no visible binding for global variable ‘utr3_len’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘chr’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘name’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘chrPeak’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘startPeak’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘endPeak’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘idPeak’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘scorePeak’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘strandPeak’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘chrfeature’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘startfeature’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘endfeature’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘widthfeature’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘strandfeature’
get_targeted_genes : <anonymous>: no visible binding for global
  variable ‘tx_name’
get_targeted_genes: no visible binding for global variable ‘chrPeak’
get_targeted_genes: no visible binding for global variable ‘startPeak’
get_targeted_genes: no visible binding for global variable ‘endPeak’
get_targeted_genes: no visible binding for global variable ‘strandPeak’
get_targeted_genes: no visible binding for global variable
  ‘feature_name’
get_targeted_genes: no visible binding for global variable ‘tx_name’
get_targeted_genes: no visible binding for global variable ‘5'UTR’
get_targeted_genes: no visible binding for global variable ‘CDS’
get_targeted_genes: no visible binding for global variable ‘3'UTR’
get_targeted_genes: no visible binding for global variable ‘Intron’
get_targeted_genes: no visible binding for global variable ‘Exon’
get_txdb_features : <anonymous>: no visible global function definition
  for ‘runValue’
plot_3parts_metagene: no visible binding for global variable
  ‘Intensity’
plot_3parts_metagene: no visible binding for global variable ‘se’
plot_3parts_metagene: no visible binding for global variable ‘Query’
plot_5parts_metagene: no visible binding for global variable
  ‘Intensity’
plot_5parts_metagene: no visible binding for global variable ‘se’
plot_5parts_metagene: no visible binding for global variable ‘Query’
plot_bam_correlation: no visible binding for global variable ‘Sample’
plot_bam_correlation: no visible binding for global variable ‘Count’
plot_bam_correlation: no visible binding for global variable ‘cumCount’
plot_bam_correlation: no visible binding for global variable ‘Rank’
plot_bam_correlation: no visible binding for global variable ‘Fraction’
plot_bam_correlation: no visible binding for global variable ‘X’
plot_bam_correlation: no visible binding for global variable ‘Y’
plot_bam_correlation: no visible binding for global variable
  ‘correlation’
plot_locus: no visible binding for global variable ‘se’
plot_locus_with_random: no visible binding for global variable ‘se’
plot_overlap_bed: no visible binding for global variable ‘X’
plot_overlap_bed: no visible binding for global variable ‘Y’
plot_peak_annotation: no visible global function definition for
  ‘runValue’
plot_peak_annotation: no visible binding for global variable ‘.’
plot_peak_annotation: no visible binding for global variable ‘len’
plot_peak_annotation: no visible binding for global variable
  ‘norm_count’
plot_peak_annotation: no visible binding for global variable
  ‘norm_percent’
plot_peak_annotation: no visible binding for global variable ‘feature’
plot_peak_annotation: no visible binding for global variable ‘csum’
plot_peak_annotation: no visible binding for global variable
  ‘norm_csum’
plot_peak_annotation: no visible binding for global variable ‘norm_pos’
plot_peak_annotation: no visible binding for global variable ‘chr’
plot_peak_annotation: no visible binding for global variable ‘name’
plot_peak_annotation: no visible binding for global variable
  ‘transcript_id’
plot_peak_annotation: no visible binding for global variable ‘gene_id’
plot_peak_annotation: no visible binding for global variable
  ‘gene_name’
plot_peak_annotation: no visible binding for global variable
  ‘queryIndex’
plot_peak_annotation: no visible binding for global variable ‘Promoter’
plot_peak_annotation: no visible binding for global variable
  ‘Transcript’
plot_region: no visible binding for global variable ‘se’
plot_start_end: no visible binding for global variable ‘Intensity’
plot_start_end: no visible binding for global variable ‘se’
plot_start_end: no visible binding for global variable ‘Query’
plot_start_end: no visible binding for global variable ‘Feature’
plot_start_end_with_random: no visible binding for global variable
  ‘Intensity’
plot_start_end_with_random: no visible binding for global variable ‘se’
plot_start_end_with_random: no visible binding for global variable
  ‘Query’
rank_rows: no visible global function definition for ‘rowMax’
Undefined global functions or variables:
  . 3'UTR 5'UTR CDS Count Exon Feature Fraction Intensity Interval
  Intron Location N_Intensity Promoter Query Rank Sample Transcript X Y
  cds_len chr chrPeak chrfeature correlation csum cumCount endPeak
  endfeature feature feature_name fid gene_id gene_name idPeak len
  lower lower_limit mean_Intensity name norm_count norm_csum
  norm_percent norm_pos queryIndex rowMax runValue scorePeak
  sd_Intensity se startPeak startfeature strandPeak strandfeature
  transcript_id tx_name upper upper_limit utr3_len utr5_len value
  widthfeature x x2 y
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'plot_start_end.Rd':
  \examples lines wider than 100 characters:
       insert = 100, verbose = TRUE, ext = c(-500, 100, -100, 500), hl = c(-50, 50, -50, 50), stranded = TRUE,

These lines will be truncated in the PDF manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [53s/53s] ERROR
Running examples in ‘GenomicPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_targeted_genes
> ### Title: Get the number of peaks overlapping each feature of all
> ###   protein-coding genes
> ### Aliases: get_targeted_genes
> 
> ### ** Examples
> 
> gtffile <- system.file("extdata", "gencode.v19.annotation_chr19.gtf", package = "GenomicPlot")
> gff <- RCAS::importGtf(saveObjectAsRds = TRUE, filePath = gtffile)
Reading existing granges.rds object from /Users/pkgbuild/packagebuilder/workers/jobs/3046/R-libs/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds
Keeping standard chromosomes only
File /Users/pkgbuild/packagebuilder/workers/jobs/3046/R-libs/GenomicPlot/extdata/gencode.v19.annotation_chr19.gtf.granges.rds already exists.
                  Use overwriteObjectAsRds = TRUE to overwrite the file
> txdb <- makeTxDbFromGRanges(gff)
Warning in .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
> f <- get_txdb_features(txdb, dsTSS = 100, fiveP = 0, threeP = 1000)
Error in start_parallel(nc = nc) : object 'my.cluster' not found
Calls: get_txdb_features -> start_parallel
Execution halted
* 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 ... [4s/5s] OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3046/GenomicPlot_20230530125942/GenomicPlot.Rcheck/00check.log’
for details.





===============================

 BiocCheck('GenomicPlot_0.99.5.tar.gz')

===============================

─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.5
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpPuOpty/fileadf75b3a07b/GenomicPlot
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpPuOpty/fileadf76807f0ca
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3046/GenomicPlot_20230530125942/GenomicPlot.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* Checking package size...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of GenomicPlot...
* Checking coding practice...
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 25 functions greater than 50 lines.
* Checking man page documentation...
Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::residuals’ by ‘stats::residuals’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::start’ by ‘stats::start’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::end’ by ‘stats::end’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::weights’ by ‘stats::weights’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::IQR’ by ‘stats::IQR’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::xtabs’ by ‘stats::xtabs’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::density’ by ‘stats::density’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::mad’ by ‘stats::mad’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::update’ by ‘stats::update’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::relist’ by ‘utils::relist’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::setdiff’ by ‘GenomicRanges::setdiff’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘GenomicPlot’
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 4% of man pages use at least one of these tags.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 1412 lines (13%) are > 80
      characters long.
    * NOTE: Consider multiples of 4 spaces for line indents; 3169 lines
      (29%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 10 NOTES

See the GenomicPlot.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir GenomicPlot_0.99.5.tar.gz'
>>>>>>> 

* installing *source* package ‘GenomicPlot’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::residuals’ by ‘stats::residuals’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::start’ by ‘stats::start’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::end’ by ‘stats::end’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::weights’ by ‘stats::weights’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::IQR’ by ‘stats::IQR’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::xtabs’ by ‘stats::xtabs’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::density’ by ‘stats::density’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::mad’ by ‘stats::mad’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::update’ by ‘stats::update’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::relist’ by ‘utils::relist’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::setdiff’ by ‘GenomicRanges::setdiff’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘GenomicPlot’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::residuals’ by ‘stats::residuals’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::start’ by ‘stats::start’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::end’ by ‘stats::end’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::weights’ by ‘stats::weights’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::IQR’ by ‘stats::IQR’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::xtabs’ by ‘stats::xtabs’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::density’ by ‘stats::density’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::mad’ by ‘stats::mad’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::update’ by ‘stats::update’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::relist’ by ‘utils::relist’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::setdiff’ by ‘GenomicRanges::setdiff’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘GenomicPlot’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘GenomicRanges::intersect’ by ‘dplyr::intersect’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::boxplot’ by ‘graphics::boxplot’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::residuals’ by ‘stats::residuals’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::start’ by ‘stats::start’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::lag’ by ‘stats::lag’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::end’ by ‘stats::end’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::weights’ by ‘stats::weights’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::filter’ by ‘stats::filter’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::IQR’ by ‘stats::IQR’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::var’ by ‘stats::var’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::xtabs’ by ‘stats::xtabs’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::sd’ by ‘stats::sd’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::density’ by ‘stats::density’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::mad’ by ‘stats::mad’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘GenomicRanges::update’ by ‘stats::update’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘BiocGenerics::relist’ by ‘utils::relist’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘dplyr::setdiff’ by ‘GenomicRanges::setdiff’ when loading ‘GenomicPlot’
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘GenomicPlot’
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicPlot)