This page was generated on 2024-04-18 11:32:16 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake"
| 4388 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
| r3Cseq 1.48.0 (landing page) Supat Thongjuea or
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
git_url: https://git.bioconductor.org/packages/r3Cseq |
git_branch: RELEASE_3_18 |
git_last_commit: d9ef32a |
git_last_commit_date: 2023-10-24 09:48:26 -0400 (Tue, 24 Oct 2023) |
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ![UNNEEDED, same version is already published UNNEEDED, same version is already published](../120px-Blue_Light_Icon.svg.png) | |
CHECK results for r3Cseq on kjohnson1
To the developers/maintainers of the r3Cseq package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
|
raw results
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:r3Cseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings r3Cseq_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/r3Cseq.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.48.0’
* 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 ‘r3Cseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘BSgenome.Hsapiens.UCSC.hg18.masked’
‘BSgenome.Hsapiens.UCSC.hg19.masked’
‘BSgenome.Mmusculus.UCSC.mm10.masked’
‘BSgenome.Mmusculus.UCSC.mm9.masked’
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign3CseqSigContact: no visible global function definition for
‘fitted’
assign3CseqSigContact: no visible binding for global variable
‘relative.position’
assign3CseqSigContact: no visible binding for global variable
‘chromosome’
excludeReadsNearViewpoint: no visible global function definition for
‘subjectHits’
generate3CseqReport: no visible global function definition for ‘pdf’
generate3CseqReport: no visible global function definition for
‘dev.off’
get3CseqRefGene: no visible binding for global variable ‘hg18refGene’
get3CseqRefGene: no visible binding for global variable ‘hg19refGene’
get3CseqRefGene: no visible binding for global variable ‘mm9refGene’
get3CseqRefGene: no visible binding for global variable ‘mm10refGene’
get3CseqRefGene: no visible binding for global variable ‘rn5refGene’
getContrInteractionsInRefseq: no visible global function definition for
‘queryHits’
getContrInteractionsInRefseq: no visible global function definition for
‘subjectHits’
getExpInteractionsInRefseq: no visible global function definition for
‘queryHits’
getExpInteractionsInRefseq: no visible global function definition for
‘subjectHits’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
getFragmentsPerWindow: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
getPowerLawFittedCoeficient: no visible binding for global variable
‘num’
getPowerLawFittedCoeficient: no visible binding for global variable
‘nr_reads’
getPowerLawFittedCoeficient: no visible global function definition for
‘coefficients’
getViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
getViewpoint: no visible global function definition for ‘DNAString’
getViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
getViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
getViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
getViewpoint: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
makeInteractionMatrixNearCisPerWindow: no visible global function
definition for ‘fitted’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotInteractionsNearViewpoint: no visible binding for global variable
‘chromosome’
plotInteractionsNearViewpoint: no visible global function definition
for ‘par’
plotInteractionsNearViewpoint: no visible global function definition
for ‘abline’
plotInteractionsNearViewpoint: no visible global function definition
for ‘text’
plotInteractionsNearViewpoint: no visible global function definition
for ‘lines’
plotInteractionsNearViewpoint: no visible global function definition
for ‘rect’
plotInteractionsNearViewpoint: no visible global function definition
for ‘legend’
plotInteractionsNearViewpoint: no visible global function definition
for ‘points’
plotInteractionsNearViewpoint: no visible binding for global variable
‘exp_RPMs’
plotInteractionsNearViewpoint: no visible binding for global variable
‘contr_RPMs’
plotInteractionsNearViewpoint: no visible binding for global variable
‘log2fold’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotInteractionsPerChromosome: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotInteractionsPerChromosome: no visible global function definition
for ‘fitted’
plotInteractionsPerChromosome: no visible global function definition
for ‘abline’
plotInteractionsPerChromosome: no visible global function definition
for ‘lines’
plotInteractionsPerChromosome: no visible global function definition
for ‘legend’
plotInteractionsPerChromosome: no visible global function definition
for ‘par’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotOverviewInteractions: no visible binding for global variable
‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotOverviewInteractions: no visible global function definition for
‘axis’
plotOverviewInteractions: no visible global function definition for
‘polygon’
plotOverviewInteractions: no visible global function definition for
‘text’
plotOverviewInteractions: no visible global function definition for
‘rect’
plotOverviewInteractions: no visible global function definition for
‘legend’
getBatchInteractions,r3CseqInBatch: no visible global function
definition for ‘na.omit’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
getEnzymeRestrictionSequences,repbaseEnzyme-character: no visible
binding for global variable ‘enzyme’
initialize,repbaseEnzyme: no visible binding for global variable
‘enzyme.db’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg18.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Hsapiens.UCSC.hg19.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm9.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Mmusculus.UCSC.mm10.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘BSgenome.Rnorvegicus.UCSC.rn5.masked’
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable ‘chromosome’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘par’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘abline’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘text’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘lines’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘rect’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘legend’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘points’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘colorRampPalette’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘image’
plotDomainogramNearViewpoint,r3Cseq: no visible global function
definition for ‘axis’
Undefined global functions or variables:
BSgenome.Hsapiens.UCSC.hg18.masked BSgenome.Hsapiens.UCSC.hg19.masked
BSgenome.Mmusculus.UCSC.mm10.masked
BSgenome.Mmusculus.UCSC.mm9.masked
BSgenome.Rnorvegicus.UCSC.rn5.masked DNAString abline axis chromosome
coefficients colorRampPalette contr_RPMs dev.off enzyme enzyme.db
exp_RPMs fitted hg18refGene hg19refGene image legend lines log2fold
mm10refGene mm9refGene na.omit nr_reads num par pdf points polygon
queryHits rect relative.position rn5refGene subjectHits text
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
importFrom("graphics", "abline", "axis", "image", "legend", "lines",
"par", "points", "polygon", "rect", "text")
importFrom("stats", "coefficients", "fitted", "na.omit")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/r3Cseq.Rcheck/00check.log’
for details.
Installation output
r3Cseq.Rcheck/00install.out
Tests output
Example timings
r3Cseq.Rcheck/r3Cseq-Ex.timings