lconway Summary
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Package: GenomicPlot |
Version: 0.99.7 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicPlot |
BuildTime: 1 minutes 7.66 seconds |
CheckCommand: BiocCheckGitClone('GenomicPlot') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3046/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot.install-out.txt GenomicPlot_0.99.7.tar.gz && BiocCheck('GenomicPlot_0.99.7.tar.gz', `new-package`=TRUE) |
CheckTime: 9 minutes 21.28 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh GenomicPlot_0.99.7.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 51.05 seconds |
PackageFileSize: 13087.14 KiB |
BuildID:: GenomicPlot_20230601211243 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GenomicPlot. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* 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_0.99.7.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('GenomicPlot')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.7
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* 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 ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/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 ‘0.99.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'GenomicRanges', 'GenomicFeatures', 'ggplot2', 'BiocGenerics',
'dplyr', 'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... OK
* checking installed package size ... NOTE
installed size is 22.1Mb
sub-directories of 1Mb or more:
extdata 17.0Mb
tests 4.6Mb
* 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 ... [17s/19s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/23s] OK
* checking whether the package can be unloaded cleanly ... [22s/27s] OK
* checking whether the namespace can be loaded with stated dependencies ... [16s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [22s/27s] OK
* checking loading without being on the library search path ... [19s/21s] 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 ... [63s/64s] 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 ‘pos’
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 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 ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 files in ‘vignettes’ ... OK
* checking examples ... [132s/129s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_peak_annotation 11.323 1.624 11.097
get_targeted_genes 10.993 1.069 11.254
get_txdb_features 6.231 0.491 6.427
plot_named_list 5.660 0.067 5.727
prepare_5parts_genomic_features 5.132 0.037 5.170
* 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 ... [7s/7s] OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot.Rcheck/00check.log’
for details.
===============================
BiocCheck('GenomicPlot_0.99.7.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.7
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp2nUIVd/filedc59447b4e9e/GenomicPlot
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//Rtmp2nUIVd/filedc598fad642
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
Error in `[.data.frame`(pkg_status, , "PackageStatus") :
undefined columns selected
Calls: BiocCheck ... getAllDeprecatedPkgs -> get_deprecated_status -> [ -> [.data.frame
Execution halted
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir GenomicPlot_0.99.7.tar.gz'
>>>>>>>
* installing *source* package ‘GenomicPlot’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicPlot)
nebbiolo2 Summary
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Package: GenomicPlot |
Version: 0.99.7 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicPlot |
BuildTime: 0 minutes 57.22 seconds |
CheckCommand: BiocCheckGitClone('GenomicPlot') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3046/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot.install-out.txt GenomicPlot_0.99.7.tar.gz && BiocCheck('GenomicPlot_0.99.7.tar.gz', `new-package`=TRUE) |
CheckTime: 7 minutes 51.27 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 13087.10 KiB |
BuildID:: GenomicPlot_20230601211243 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GenomicPlot. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* 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_0.99.7.tar.gz’
nebbiolo2 CHECK output
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===============================
BiocCheckGitClone('GenomicPlot')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.7
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* 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 ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicPlot’ version ‘0.99.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'GenomicRanges', 'GenomicFeatures', 'ggplot2', 'BiocGenerics',
'dplyr', 'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... OK
* checking installed package size ... NOTE
installed size is 22.1Mb
sub-directories of 1Mb or more:
extdata 17.0Mb
tests 4.7Mb
* 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 ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [14s/14s] 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 ... [57s/57s] 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 ‘pos’
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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [148s/145s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_peak_annotation 11.442 1.530 12.155
get_targeted_genes 9.299 1.355 10.171
get_txdb_features 7.098 0.797 7.814
plot_named_list 5.997 0.412 6.410
prepare_5parts_genomic_features 5.867 0.288 6.155
* 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/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot.Rcheck/00check.log’
for details.
===============================
BiocCheck('GenomicPlot_0.99.7.tar.gz')
===============================
─ BiocCheckVersion: 1.37.1
─ BiocVersion: 3.18
─ Package: GenomicPlot
─ PackageVersion: 0.99.7
─ sourceDir: /tmp/RtmpaJ4cJa/file2c4b665945e91/GenomicPlot
─ installDir: /tmp/RtmpaJ4cJa/file2c4b6621d25e2f
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3046/a439622e8bad71690e135e04e96dd5b548d0872e/GenomicPlot.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
Error in `[.data.frame`(pkg_status, , "PackageStatus") :
undefined columns selected
Calls: BiocCheck ... getAllDeprecatedPkgs -> get_deprecated_status -> [ -> [.data.frame
Execution halted
nebbiolo2 BUILD BIN output
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