Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:09 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for r3Cseq on tokay2


To the developers/maintainers of the r3Cseq package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1516/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
r3Cseq 1.40.0  (landing page)
Supat Thongjuea or
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/r3Cseq
git_branch: RELEASE_3_14
git_last_commit: 4ade9b7
git_last_commit_date: 2021-10-26 12:00:54 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: r3Cseq
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:r3Cseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings r3Cseq_1.40.0.tar.gz
StartedAt: 2022-04-13 01:11:46 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:17:10 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 324.7 seconds
RetCode: 0
Status:   OK  
CheckDir: r3Cseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:r3Cseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings r3Cseq_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/r3Cseq.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'r3Cseq/DESCRIPTION' ... OK
* this is package 'r3Cseq' version '1.40.0'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/r3Cseq.Rcheck/00check.log'
for details.

Installation output

r3Cseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/r3Cseq_1.40.0.tar.gz && rm -rf r3Cseq.buildbin-libdir && mkdir r3Cseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=r3Cseq.buildbin-libdir r3Cseq_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL r3Cseq_1.40.0.zip && rm r3Cseq_1.40.0.tar.gz r3Cseq_1.40.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  9 3405k    9  307k    0     0   683k      0  0:00:04 --:--:--  0:00:04  682k
 52 3405k   52 1782k    0     0  1229k      0  0:00:02  0:00:01  0:00:01 1229k
100 3405k  100 3405k    0     0  1581k      0  0:00:02  0:00:02 --:--:-- 1582k

install for i386

* 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
  converting help for package 'r3Cseq'
    finding HTML links ... done
    Myb_prom_FB                             html  
    Myb_prom_FL                             html  
    calculateBatchRPM                       html  
    calculateRPM                            html  
    contrCoverage                           html  
    contrInteractionRegions                 html  
    contrRPM                                html  
    contrRawData                            html  
    contrReadCount                          html  
    enzymeDb                                html  
    expCoverage                             html  
    expInteractionRegions                   html  
    expRPM                                  html  
    expRawData                              html  
    expReadCount                            html  
    export3Cseq2bedGraph                    html  
    export3CseqRawReads2bedGraph            html  
    exportBatchInteractions2text            html  
    exportInteractions2text                 html  
    generate3CseqReport                     html  
    getBatchInteractions                    html  
    finding level-2 HTML links ... done

    getBatchRawReads                        html  
    getBatchReadCountPerRestrictionFragment
                                            html  
    getBatchReadCountPerWindow              html  
    getContrInteractionsInRefseq            html  
    getCoverage                             html  
    getExpInteractionsInRefseq              html  
    getInteractions                         html  
    getRawReads                             html  
    getReadCountPerRestrictionFragment      html  
    getReadCountPerWindow                   html  
    getViewpoint                            html  
    hg18refGene                             html  
    hg19refGene                             html  
    mm10refGene                             html  
    mm9refGene                              html  
    plot3Cecdf                              html  
    plotDomainogramNearViewpoint            html  
    plotInteractionsNearViewpoint           html  
    plotInteractionsPerChromosome           html  
    plotOverviewInteractions                html  
    r3Cseq-class                            html  
    r3CseqCommon-class                      html  
    r3CseqInBatch-class                     html  
    rn5refGene                              html  
** 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

install for x64

* installing *source* package 'r3Cseq' ...
** testing if installed package can be loaded
No methods found in package 'Biostrings' for request: 'DNAString' when loading 'r3Cseq'
* MD5 sums
packaged installation of 'r3Cseq' as r3Cseq_1.40.0.zip
* DONE (r3Cseq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'r3Cseq' successfully unpacked and MD5 sums checked

Tests output

Example timings

r3Cseq.Rcheck/examples_i386/r3Cseq-Ex.timings

nameusersystemelapsed
calculateBatchRPM000
calculateRPM000
contrInteractionRegions000
contrRPM000
contrRawData000
contrReadCount000
expInteractionRegions000
expRPM000
expRawData000
expReadCount000
export3Cseq2bedGraph000
export3CseqRawReads2bedGraph000
exportBatchInteractions2text000
exportInteractions2text000
generate3CseqReport000
getBatchInteractions000
getBatchRawReads000
getBatchReadCountPerRestrictionFragment000
getBatchReadCountPerWindow000
getContrInteractionsInRefseq000
getExpInteractionsInRefseq000
getInteractions000
getRawReads000
getReadCountPerRestrictionFragment000
getReadCountPerWindow000
getViewpoint000
plotDomainogramNearViewpoint000
plotInteractionsNearViewpoint000
plotInteractionsPerChromosome000
plotOverviewInteractions000
r3Cseq-class000
r3CseqCommon-class000
r3CseqInBatch-class0.000.010.01

r3Cseq.Rcheck/examples_x64/r3Cseq-Ex.timings

nameusersystemelapsed
calculateBatchRPM000
calculateRPM000
contrInteractionRegions000
contrRPM000
contrRawData000
contrReadCount000
expInteractionRegions000
expRPM000
expRawData000
expReadCount000
export3Cseq2bedGraph000
export3CseqRawReads2bedGraph000
exportBatchInteractions2text000
exportInteractions2text000
generate3CseqReport000
getBatchInteractions000
getBatchRawReads000
getBatchReadCountPerRestrictionFragment000
getBatchReadCountPerWindow000
getContrInteractionsInRefseq000
getExpInteractionsInRefseq000
getInteractions000
getRawReads000
getReadCountPerRestrictionFragment000
getReadCountPerWindow000
getViewpoint000
plotDomainogramNearViewpoint000
plotInteractionsNearViewpoint000
plotInteractionsPerChromosome000
plotOverviewInteractions000
r3Cseq-class000
r3CseqCommon-class000
r3CseqInBatch-class000