===============================
R CMD BUILD
===============================
* checking for file ‘FEVV/DESCRIPTION’ ... OK
* preparing ‘FEVV’:
* 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
* building ‘FEVV_0.99.5.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/.Rbuildignore’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/DESCRIPTION’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/NAMESPACE’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/BackendData_ChromatinStates.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/BackendData_GenomicFeatures.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/FEVV.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/SNPs.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/eQTL.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/README.md’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/BackendData_ChromatinStates.rda’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/BackendData_GenomicFeatures.rda’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/SNPs.rda’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/eQTL.rda’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/RESULTsChromatinState.txt’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/RESULTsGenomicFeatures.txt’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/extdata/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/extdata/Genotyping1000_samples_metatadata.txt’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/BackendData_ChromatinStates.Rd’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/BackendData_GenomicFeatures.Rd’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/SNPs.Rd’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/eQTL.Rd’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/eSNPsEnrichmentAnalysis.Rd’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/querySNPsEnrichmentAnalysis.Rd’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/vignettes/’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/vignettes/vignette.Rmd’
===============================
BiocCheckGitClone('FEVV')
===============================
This is BiocCheckGitClone version 1.29.8. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/.Rhistory
Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/.Rhistory
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2137/d45042984cd6ca7b54d7ea7100327190d419d49a/FEVV.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FEVV/DESCRIPTION’ ... OK
* this is package ‘FEVV’ version ‘0.99.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'SNPlocs.Hsapiens.dbSNP144.GRCh38', 'BSgenome.Hsapiens.UCSC.hg38',
'motifbreakR', 'snpStats', 'data.table', 'GenomicRanges', 'biomaRt',
'VariantAnnotation'
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 ... NOTE
Found the following hidden files and directories:
Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/.Rbuildignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/.Rbuildignore
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/DESCRIPTION
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/NAMESPACE
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/BackendData_ChromatinStates.R
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/BackendData_GenomicFeatures.R
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/FEVV.R
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/SNPs.R
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/R/eQTL.R
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/README.md
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/BackendData_ChromatinStates.rda
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/BackendData_GenomicFeatures.rda
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/SNPs.rda
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data/eQTL.rda
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/RESULTsChromatinState.txt
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/RESULTsGenomicFeatures.txt
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/extdata/Genotyping1000_samples_metatadata.txt
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/BackendData_ChromatinStates.Rd
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/BackendData_GenomicFeatures.Rd
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/SNPs.Rd
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/eQTL.Rd
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/eSNPsEnrichmentAnalysis.Rd
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man/querySNPsEnrichmentAnalysis.Rd
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/vignettes/vignette.Rmd
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/data
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/inst/extdata
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/man
FEVV/Desktop/Analysis_monocyte/KEY-FILES/Article_figures/FIGURES_TABLES-ciseQTLs/FEVV_package/FEVV/vignettes
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FEVV’ can be installed ... [36s/36s] WARNING
Found the following significant warnings:
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'FEVV'
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2137/d45042984cd6ca7b54d7ea7100327190d419d49a/FEVV.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicRanges’
A package should be listed in only one of these fields.
WARNING
Dependence on R version ‘3.6.3’ not with patchlevel 0
* 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 ... 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
'S4Vectors' 'ieugwasr'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [35s/35s] NOTE
eSNPsEnrichmentAnalysis: no visible global function definition for
'IRanges'
eSNPsEnrichmentAnalysis: no visible global function definition for
'Rle'
eSNPsEnrichmentAnalysis: no visible global function definition for
'subjectHits'
eSNPsEnrichmentAnalysis: no visible global function definition for
'fisher.test'
eSNPsEnrichmentAnalysis: no visible global function definition for
'write.table'
querySNPsEnrichmentAnalysis : GetVariantsInWindow: no visible global
function definition for 'is'
querySNPsEnrichmentAnalysis : GetVariantsInWindow: no visible global
function definition for 'as'
querySNPsEnrichmentAnalysis : GetVariantsInWindow: no visible global
function definition for 'TabixFile'
querySNPsEnrichmentAnalysis : GetVariantsInWindow: no visible global
function definition for 'import.bed'
querySNPsEnrichmentAnalysis : SetPopulation: no visible global function
definition for 'colData'
querySNPsEnrichmentAnalysis : SetPopulation: no visible global function
definition for 'DataFrame'
querySNPsEnrichmentAnalysis : SetPopulation: no visible global function
definition for 'colData<-'
querySNPsEnrichmentAnalysis : SetPopulation: no visible global function
definition for 'metadata'
querySNPsEnrichmentAnalysis : SetPopulation: no visible global function
definition for 'metadata<-'
querySNPsEnrichmentAnalysis : CalcLD: no visible global function
definition for 'is'
querySNPsEnrichmentAnalysis : CalcLD: no visible global function
definition for 'colData'
querySNPsEnrichmentAnalysis : CalcLD: no visible global function
definition for 'rowRanges'
querySNPsEnrichmentAnalysis : CalcLD: no visible global function
definition for 'rowRanges<-'
querySNPsEnrichmentAnalysis : CalcLD: no visible global function
definition for 'metadata'
querySNPsEnrichmentAnalysis : CalcLD: no visible global function
definition for 'metadata<-'
querySNPsEnrichmentAnalysis : GetBioFeatures: no visible global
function definition for 'head'
querySNPsEnrichmentAnalysis : GetBioFeatures: no visible global
function definition for 'Seqinfo'
querySNPsEnrichmentAnalysis : GetBioFeatures : <anonymous>: no visible
global function definition for 'cols_only'
querySNPsEnrichmentAnalysis : GetBioFeatures : <anonymous>: no visible
global function definition for 'col_character'
querySNPsEnrichmentAnalysis : GetBioFeatures : <anonymous>: no visible
global function definition for 'col_integer'
querySNPsEnrichmentAnalysis : GetBioFeatures : <anonymous>: no visible
global function definition for 'col_number'
querySNPsEnrichmentAnalysis : GetBioFeatures : <anonymous>: no visible
global function definition for 'read_tsv'
querySNPsEnrichmentAnalysis : GetBioFeatures : <anonymous>: no visible
global function definition for 'IRanges'
querySNPsEnrichmentAnalysis : GetSegmentations : <anonymous>: no
visible global function definition for 'import.bed'
querySNPsEnrichmentAnalysis : SplitVcfLd: no visible global function
definition for 'is'
querySNPsEnrichmentAnalysis : SplitVcfLd: no visible global function
definition for 'rowRanges'
querySNPsEnrichmentAnalysis : SplitVcfLd: no visible global function
definition for 'metadata'
querySNPsEnrichmentAnalysis : SplitVcfLd: no visible global function
definition for 'metadata<-'
querySNPsEnrichmentAnalysis : CalculateEnrichment: no visible global
function definition for 'metadata'
querySNPsEnrichmentAnalysis : CalculateEnrichment: no visible global
function definition for 'is'
querySNPsEnrichmentAnalysis : CalculateEnrichment: no visible global
function definition for 'rowRanges'
querySNPsEnrichmentAnalysis : CalculateEnrichment: no visible global
function definition for 'rowRanges<-'
querySNPsEnrichmentAnalysis : CalculateEnrichment: no visible global
function definition for 'keepSeqlevels'
querySNPsEnrichmentAnalysis : CalculateEnrichment: no visible global
function definition for 'subsetByOverlaps'
querySNPsEnrichmentAnalysis : CalculateEnrichment: no visible global
function definition for 'seqlevelsInUse'
querySNPsEnrichmentAnalysis : SetOverlaps: no visible global function
definition for 'from'
querySNPsEnrichmentAnalysis : SetOverlaps: no visible global function
definition for 'to'
querySNPsEnrichmentAnalysis : SetOverlaps: no visible global function
definition for 'is'
querySNPsEnrichmentAnalysis : SetOverlaps: no visible global function
definition for 'DataFrame'
querySNPsEnrichmentAnalysis : SetOverlaps: no visible global function
definition for 'rowRanges'
querySNPsEnrichmentAnalysis : SetOverlaps: no visible global function
definition for 'rowRanges<-'
querySNPsEnrichmentAnalysis : SetOverlaps: no visible global function
definition for 'metadata'
querySNPsEnrichmentAnalysis : SetOverlaps: no visible global function
definition for 'metadata<-'
querySNPsEnrichmentAnalysis : ShowOverlaps: no visible global function
definition for 'is'
querySNPsEnrichmentAnalysis : ShowOverlaps: no visible global function
definition for 'metadata'
querySNPsEnrichmentAnalysis : ShowOverlaps: no visible global function
definition for 'rowRanges'
querySNPsEnrichmentAnalysis : ShowOverlaps: no visible global function
definition for 'DataFrame'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'is'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'str_length'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'alpha'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'brewer.pal'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'colorRampPalette'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'ggplot'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'aes_string'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'theme_minimal'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'n_distinct'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'geom_crossbar'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'aes'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible binding for
global variable 'log.odds.lower'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible binding for
global variable 'log.odds.upper'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible binding for
global variable 'color'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible binding for
global variable 'lower'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible binding for
global variable 'upper'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'geom_pointrange'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'scale_x_discrete'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'scale_y_continuous'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'geom_hline'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'annotate'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'theme'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'element_blank'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'element_text'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'rel'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'as.formula'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'facet_grid'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'facet_wrap'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'scale_color_brewer'
querySNPsEnrichmentAnalysis : PlotEnrichment: no visible global
function definition for 'scale_color_identity'
querySNPsEnrichmentAnalysis : GetVariantsInWindowVCF: no visible global
function definition for 'keepSeqlevels'
querySNPsEnrichmentAnalysis : GetVariantsInWindowVCF: no visible global
function definition for 'seqlevelsInUse'
querySNPsEnrichmentAnalysis : GetVariantsInWindowVCF: no visible global
function definition for 'seqlevelsStyle<-'
querySNPsEnrichmentAnalysis : GetVariantsInWindowVCF: no visible global
function definition for 'metadata'
querySNPsEnrichmentAnalysis : GetVariantsInWindowVCF: no visible global
function definition for 'metadata<-'
querySNPsEnrichmentAnalysis : make.overlap.matrix: no visible global
function definition for 'is'
querySNPsEnrichmentAnalysis : enrich.segments: no visible global
function definition for 'is'
querySNPsEnrichmentAnalysis : enrich.segments: no visible binding for
global variable 'pblapply'
querySNPsEnrichmentAnalysis : enrich.segments : <anonymous>: no visible
global function definition for 'is'
querySNPsEnrichmentAnalysis : enrich.segments : <anonymous>: no visible
global function definition for 'rowRanges'
querySNPsEnrichmentAnalysis : enrich.segments : <anonymous>: no visible
global function definition for 'rowRanges<-'
querySNPsEnrichmentAnalysis : enrich.segments : <anonymous>: no visible
global function definition for 'metadata'
querySNPsEnrichmentAnalysis : enrich.features: no visible global
function definition for 'rbeta'
querySNPsEnrichmentAnalysis : enrich.features: no visible global
function definition for 'quantile'
querySNPsEnrichmentAnalysis : enrich.features: no visible global
function definition for 'fisher.test'
querySNPsEnrichmentAnalysis : clump_data: no visible global function
definition for 'random_string'
querySNPsEnrichmentAnalysis: no visible global function definition for
'IRanges'
querySNPsEnrichmentAnalysis: no visible global function definition for
'Rle'
querySNPsEnrichmentAnalysis: no visible global function definition for
'subjectHits'
querySNPsEnrichmentAnalysis: no visible global function definition for
'fisher.test'
querySNPsEnrichmentAnalysis: no visible global function definition for
'write.table'
Undefined global functions or variables:
DataFrame IRanges Rle Seqinfo TabixFile aes aes_string alpha annotate
as as.formula brewer.pal colData colData<- col_character col_integer
col_number color colorRampPalette cols_only element_blank
element_text facet_grid facet_wrap fisher.test from geom_crossbar
geom_hline geom_pointrange ggplot head import.bed is keepSeqlevels
log.odds.lower log.odds.upper lower metadata metadata<- n_distinct
pblapply quantile random_string rbeta read_tsv rel rowRanges
rowRanges<- scale_color_brewer scale_color_identity scale_x_discrete
scale_y_continuous seqlevelsInUse seqlevelsStyle<- str_length
subjectHits subsetByOverlaps theme theme_minimal to upper write.table
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("methods", "as", "is")
importFrom("stats", "as.formula", "fisher.test", "quantile", "rbeta")
importFrom("utils", "head", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'eSNPsEnrichmentAnalysis.Rd':
\examples lines wider than 100 characters:
eSNPsEnrichmentAnalysis(eQTL, TranscriptName = 'ENSG00000168310', windowSize=1000000, FDRthreshold = 0.001, BackendData_GenomicFeatures ... [TRUNCATED]
Rd file 'querySNPsEnrichmentAnalysis.Rd':
\examples lines wider than 100 characters:
querySNPsEnrichmentAnalysis(SNP = 'rs13149699', mafThreshold = 0.039, windowSize = 1000000, BackendData_GenomicFeatures, BackendData_Ch ... [TRUNCATED]
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 ... WARNING
Codoc mismatches from documentation object 'querySNPsEnrichmentAnalysis':
querySNPsEnrichmentAnalysis
Code: function(SNP, mafThreshold, windowSize,
BackendData_GenomicFeatures,
BackendData_ChromatinStates, vcfMetaData, vcfPATH)
Docs: function(SNP, mafThreshold, windowSize,
BackendData_GenomicFeatures,
BackendData_ChromatinStates, vcfsubset, vcfMetaData,
vcfPATH = NULL)
Argument names in docs not in code:
vcfsubset
Mismatches in argument names:
Position: 6 Code: vcfMetaData Docs: vcfsubset
Position: 7 Code: vcfPATH Docs: vcfMetaData
Mismatches in argument default values:
Name: 'vcfPATH' Code: Docs: NULL
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'querySNPsEnrichmentAnalysis'
‘vcfPATH’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
BackendData_ChromatinStates.rda 20Kb 7Kb xz
BackendData_GenomicFeatures.rda 23Kb 15Kb xz
SNPs.rda 112Kb 74Kb xz
eQTL.rda 400Kb 316Kb xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] ERROR
Running examples in ‘FEVV-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: querySNPsEnrichmentAnalysis
> ### Title: Single query SNP enrichment
> ### Aliases: querySNPsEnrichmentAnalysis
>
> ### ** Examples
>
> data(BackendData_GenomicFeatures)
> data(BackendData_ChromatinStates)
> Destiny_Folder <- system.file(package = "FEVV")
> querySNPsEnrichmentAnalysis(SNP = 'rs13149699', mafThreshold = 0.039, windowSize = 1000000, BackendData_GenomicFeatures, BackendData_ChromatinStates, vcf = vcfsubset, vcfMetaData = system.file("extdata", "Genotyping1000_samples_metatadata.txt", package="FEVV"), vcfPATH = NULL )
Error in querySNPsEnrichmentAnalysis(SNP = "rs13149699", mafThreshold = 0.039, :
unused argument (vcf = vcfsubset)
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 ... OK
* DONE
Status: 1 ERROR, 6 WARNINGs, 6 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2137/d45042984cd6ca7b54d7ea7100327190d419d49a/FEVV.Rcheck/00check.log’
for details.
===============================
BiocCheck('FEVV_0.99.5.tar.gz')
===============================
This is BiocCheck version 1.29.8. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: replacing previous import ‘S4Vectors::as.data.frame’ by ‘motifStack::as.data.frame’ when loading ‘motifbreakR’
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'FEVV'
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 103 object(s) are initialized.
Maybe they are part of a data set loaded with data(), or perhaps
part of an object referenced in with() or within().
function (object)
eSNPsEnrichmentAnalysis (IRanges)
eSNPsEnrichmentAnalysis (Rle)
eSNPsEnrichmentAnalysis (subjectHits)
eSNPsEnrichmentAnalysis (fisher.test)
eSNPsEnrichmentAnalysis (write.table)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (as)
querySNPsEnrichmentAnalysis (TabixFile)
querySNPsEnrichmentAnalysis (import.bed)
querySNPsEnrichmentAnalysis (colData)
querySNPsEnrichmentAnalysis (DataFrame)
querySNPsEnrichmentAnalysis (colData<-)
querySNPsEnrichmentAnalysis (metadata)
querySNPsEnrichmentAnalysis (metadata<-)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (colData)
querySNPsEnrichmentAnalysis (rowRanges)
querySNPsEnrichmentAnalysis (rowRanges<-)
querySNPsEnrichmentAnalysis (metadata)
querySNPsEnrichmentAnalysis (metadata<-)
querySNPsEnrichmentAnalysis (head)
querySNPsEnrichmentAnalysis (Seqinfo)
querySNPsEnrichmentAnalysis (cols_only)
querySNPsEnrichmentAnalysis (col_character)
querySNPsEnrichmentAnalysis (col_integer)
querySNPsEnrichmentAnalysis (col_number)
querySNPsEnrichmentAnalysis (read_tsv)
querySNPsEnrichmentAnalysis (IRanges)
querySNPsEnrichmentAnalysis (import.bed)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (rowRanges)
querySNPsEnrichmentAnalysis (metadata)
querySNPsEnrichmentAnalysis (metadata<-)
querySNPsEnrichmentAnalysis (metadata)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (rowRanges)
querySNPsEnrichmentAnalysis (rowRanges<-)
querySNPsEnrichmentAnalysis (keepSeqlevels)
querySNPsEnrichmentAnalysis (subsetByOverlaps)
querySNPsEnrichmentAnalysis (seqlevelsInUse)
querySNPsEnrichmentAnalysis (from)
querySNPsEnrichmentAnalysis (to)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (DataFrame)
querySNPsEnrichmentAnalysis (rowRanges)
querySNPsEnrichmentAnalysis (rowRanges<-)
querySNPsEnrichmentAnalysis (metadata)
querySNPsEnrichmentAnalysis (metadata<-)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (metadata)
querySNPsEnrichmentAnalysis (rowRanges)
querySNPsEnrichmentAnalysis (DataFrame)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (str_length)
querySNPsEnrichmentAnalysis (alpha)
querySNPsEnrichmentAnalysis (brewer.pal)
querySNPsEnrichmentAnalysis (colorRampPalette)
querySNPsEnrichmentAnalysis (ggplot)
querySNPsEnrichmentAnalysis (aes_string)
querySNPsEnrichmentAnalysis (theme_minimal)
querySNPsEnrichmentAnalysis (n_distinct)
querySNPsEnrichmentAnalysis (geom_crossbar)
querySNPsEnrichmentAnalysis (aes)
querySNPsEnrichmentAnalysis (log.odds.lower)
querySNPsEnrichmentAnalysis (log.odds.upper)
querySNPsEnrichmentAnalysis (color)
querySNPsEnrichmentAnalysis (lower)
querySNPsEnrichmentAnalysis (upper)
querySNPsEnrichmentAnalysis (geom_pointrange)
querySNPsEnrichmentAnalysis (scale_x_discrete)
querySNPsEnrichmentAnalysis (scale_y_continuous)
querySNPsEnrichmentAnalysis (geom_hline)
querySNPsEnrichmentAnalysis (annotate)
querySNPsEnrichmentAnalysis (theme)
querySNPsEnrichmentAnalysis (element_blank)
querySNPsEnrichmentAnalysis (element_text)
querySNPsEnrichmentAnalysis (rel)
querySNPsEnrichmentAnalysis (as.formula)
querySNPsEnrichmentAnalysis (facet_grid)
querySNPsEnrichmentAnalysis (facet_wrap)
querySNPsEnrichmentAnalysis (scale_color_brewer)
querySNPsEnrichmentAnalysis (scale_color_identity)
querySNPsEnrichmentAnalysis (keepSeqlevels)
querySNPsEnrichmentAnalysis (seqlevelsInUse)
querySNPsEnrichmentAnalysis (seqlevelsStyle<-)
querySNPsEnrichmentAnalysis (metadata)
querySNPsEnrichmentAnalysis (metadata<-)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (pblapply)
querySNPsEnrichmentAnalysis (is)
querySNPsEnrichmentAnalysis (rowRanges)
querySNPsEnrichmentAnalysis (rowRanges<-)
querySNPsEnrichmentAnalysis (metadata)
querySNPsEnrichmentAnalysis (rbeta)
querySNPsEnrichmentAnalysis (quantile)
querySNPsEnrichmentAnalysis (fisher.test)
querySNPsEnrichmentAnalysis (random_string)
querySNPsEnrichmentAnalysis (IRanges)
querySNPsEnrichmentAnalysis (Rle)
querySNPsEnrichmentAnalysis (subjectHits)
querySNPsEnrichmentAnalysis (fisher.test)
querySNPsEnrichmentAnalysis (write.table)
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 3.6.3 to 4.1.
* Checking package size...
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
Sequencing, Microarray, SingleCell, Coverage, GeneticVariability,
ChIPSeq, MotifAnnotation, VariantAnnotation, DataImport
See http://bioconductor.org/developers/how-to/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 DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of FEVV...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
FEVV.R (line 352, column 19)
FEVV.R (line 415, column 17)
FEVV.R (line 418, column 18)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
FEVV.R (line 61, column 76)
FEVV.R (line 104, column 12)
FEVV.R (line 136, column 14)
FEVV.R (line 374, column 47)
FEVV.R (line 380, column 47)
FEVV.R (line 506, column 82)
FEVV.R (line 508, column 60)
FEVV.R (line 519, column 82)
FEVV.R (line 521, column 60)
FEVV.R (line 629, column 30)
FEVV.R (line 855, column 76)
FEVV.R (line 861, column 54)
FEVV.R (line 869, column 76)
FEVV.R (line 875, column 54)
FEVV.R (line 1058, column 112)
FEVV.R (line 1138, column 12)
FEVV.R (line 1171, column 14)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
/tmp/RtmpKXSMtF/file16ceffa6d96e/FEVV/R/FEVV.R (line 355,
column 14)
/tmp/RtmpKXSMtF/file16ceffa6d96e/FEVV/R/FEVV.R (line 356,
column 14)
/tmp/RtmpKXSMtF/file16ceffa6d96e/FEVV/R/FEVV.R (line 358,
column 14)
/tmp/RtmpKXSMtF/file16ceffa6d96e/FEVV/R/FEVV.R (line 359,
column 14)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
/tmp/RtmpKXSMtF/file16ceffa6d96e/FEVV/R/FEVV.R (line 781,
column 30)
/tmp/RtmpKXSMtF/file16ceffa6d96e/FEVV/R/FEVV.R (line 802,
column 12)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.......
* NOTE: Recommended function length <= 50 lines.
There are 9 functions > 50 lines.
The longest 5 functions are:
querySNPsEnrichmentAnalysis() (R/FEVV.R, line 219): 993 lines
eSNPsEnrichmentAnalysis() (R/FEVV.R, line 38): 137 lines
PlotEnrichment() (R/FEVV.R, line 651): 127 lines
CalculateEnrichment() (R/FEVV.R, line 468): 106 lines
enrich.segments() (R/FEVV.R, line 824): 89 lines
* Checking man page documentation...
* 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
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 212 lines (14%) are > 80 characters
long.
First 6 lines:
R/BackendData_ChromatinStates.R:3 #'Integrative Fifteen-core chromatin ...
R/BackendData_ChromatinStates.R:6 #'1. Ernst, J. & Kellis, M. ChromHMM:...
R/BackendData_GenomicFeatures.R:3 #'biomaRt repository cover 409,304 re...
R/BackendData_GenomicFeatures.R:6 #'1. Smedley, D. et al. The BioMart c...
R/eQTL.R:3 #'eQTL profile including the following headers: seqnames, SN...
R/eQTL.R:6 #'1. Isar Nassiri, James Gilchrist, Evelyn Lau, Sara Daniell...
* NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain
tabs.
First 1 lines:
R/FEVV.R:207 #'meta data of 1000 Genomes project (phase3) including 'sa...
* NOTE: Consider multiples of 4 spaces for line indents, 591
lines(39%) are not.
First 6 lines:
R/FEVV.R:41 zScore <- function (cntA, totA, cntB, totB) {
R/FEVV.R:49 }
R/FEVV.R:51 #--------------------------- inputs
R/FEVV.R:52 states_bed <- BackendData_ChromatinStates
R/FEVV.R:54 chromatin_states <- GRanges(sample = states_bed[[4]],
R/FEVV.R:55 seqnames = gsub('chr','',state...
See http://bioconductor.org/developers/how-to/coding-style/
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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 15
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.