Supat Thongjuea
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/r3Cseq |
| git_branch: devel |
| git_last_commit: d021c8c |
| git_last_commit_date: 2024-10-29 09:39:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:16 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 | ||||
| Package 1635/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| r3Cseq 1.53.0 (landing page) Supat Thongjuea
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the r3Cseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/r3Cseq.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
| Package: r3Cseq |
| Version: 1.53.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:r3Cseq.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings r3Cseq_1.53.0.tar.gz |
| StartedAt: 2024-11-28 03:48:30 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 03:53:22 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 292.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: r3Cseq.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:r3Cseq.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings r3Cseq_1.53.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/r3Cseq.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'r3Cseq/DESCRIPTION' ... OK
* this is package 'r3Cseq' version '1.53.0'
* 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 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
getBatchInteractions.Rd: vsmooth.spline
getInteractions.Rd: vsmooth.spline
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/r3Cseq.Rcheck/00check.log'
for details.
r3Cseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL r3Cseq ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'r3Cseq' ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading No methods found in package 'Biostrings' for request: 'DNAString' when loading 'r3Cseq' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package 'Biostrings' for request: 'DNAString' when loading 'r3Cseq' ** testing if installed package can be loaded from final location No methods found in package 'Biostrings' for request: 'DNAString' when loading 'r3Cseq' ** testing if installed package keeps a record of temporary installation path * DONE (r3Cseq)
r3Cseq.Rcheck/r3Cseq-Ex.timings
| name | user | system | elapsed | |
| calculateBatchRPM | 0 | 0 | 0 | |
| calculateRPM | 0 | 0 | 0 | |
| contrInteractionRegions | 0 | 0 | 0 | |
| contrRPM | 0 | 0 | 0 | |
| contrRawData | 0 | 0 | 0 | |
| contrReadCount | 0 | 0 | 0 | |
| expInteractionRegions | 0 | 0 | 0 | |
| expRPM | 0 | 0 | 0 | |
| expRawData | 0 | 0 | 0 | |
| expReadCount | 0 | 0 | 0 | |
| export3Cseq2bedGraph | 0 | 0 | 0 | |
| export3CseqRawReads2bedGraph | 0 | 0 | 0 | |
| exportBatchInteractions2text | 0 | 0 | 0 | |
| exportInteractions2text | 0 | 0 | 0 | |
| generate3CseqReport | 0 | 0 | 0 | |
| getBatchInteractions | 0 | 0 | 0 | |
| getBatchRawReads | 0 | 0 | 0 | |
| getBatchReadCountPerRestrictionFragment | 0 | 0 | 0 | |
| getBatchReadCountPerWindow | 0 | 0 | 0 | |
| getContrInteractionsInRefseq | 0 | 0 | 0 | |
| getExpInteractionsInRefseq | 0 | 0 | 0 | |
| getInteractions | 0 | 0 | 0 | |
| getRawReads | 0 | 0 | 0 | |
| getReadCountPerRestrictionFragment | 0 | 0 | 0 | |
| getReadCountPerWindow | 0 | 0 | 0 | |
| getViewpoint | 0 | 0 | 0 | |
| plotDomainogramNearViewpoint | 0 | 0 | 0 | |
| plotInteractionsNearViewpoint | 0 | 0 | 0 | |
| plotInteractionsPerChromosome | 0 | 0 | 0 | |
| plotOverviewInteractions | 0 | 0 | 0 | |
| r3Cseq-class | 0 | 0 | 0 | |
| r3CseqCommon-class | 0 | 0 | 0 | |
| r3CseqInBatch-class | 0 | 0 | 0 | |