Back to Build/check report for BioC 3.12 experimental data
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

CHECK report for EatonEtAlChIPseq on malbec1

This page was generated on 2021-05-06 14:10:07 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the EatonEtAlChIPseq package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 108/398HostnameOS / ArchINSTALLBUILDCHECK
EatonEtAlChIPseq 0.28.0  (landing page)
Patrick Aboyoun
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/EatonEtAlChIPseq
Branch: RELEASE_3_12
Last Commit: 2fdb80c
Last Changed Date: 2020-10-27 09:51:54 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository

Summary

Package: EatonEtAlChIPseq
Version: 0.28.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:EatonEtAlChIPseq.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings EatonEtAlChIPseq_0.28.0.tar.gz
StartedAt: 2021-05-06 11:56:36 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 11:58:41 -0400 (Thu, 06 May 2021)
EllapsedTime: 125.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: EatonEtAlChIPseq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:EatonEtAlChIPseq.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings EatonEtAlChIPseq_0.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/EatonEtAlChIPseq.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EatonEtAlChIPseq/DESCRIPTION’ ... OK
* this is package ‘EatonEtAlChIPseq’ version ‘0.28.0’
* 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 ‘EatonEtAlChIPseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.6Mb
  sub-directories of 1Mb or more:
    extdata  20.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... 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 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 ... WARNING
Output for data("orcAlignsRep1", package = "EatonEtAlChIPseq"):
  Loading required package: BiocGenerics
  Loading required package: parallel
  
  Attaching package: ‘BiocGenerics’
  
  The following objects are masked from ‘package:parallel’:
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  Loading required package: BiocParallel
  Loading required package: Biostrings
  Loading required package: S4Vectors
  Loading required package: stats4
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: XVector
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Loading required package: Rsamtools
  Loading required package: GenomeInfoDb
  Loading required package: GenomicRanges
  Loading required package: GenomicAlignments
  Loading required package: SummarizedExperiment
  Loading required package: MatrixGenerics
  Loading required package: matrixStats
  
  Attaching package: ‘MatrixGenerics’
  
  The following objects are masked from ‘package:matrixStats’:
  
      colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
      colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
      colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
      colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
      colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
      colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
      colWeightedMeans, colWeightedMedians, colWeightedSds,
      colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
      rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
      rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
      rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
      rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
      rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
      rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
      rowWeightedSds, rowWeightedVars
  
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  
  Attaching package: ‘Biobase’
  
  The following object is masked from ‘package:MatrixGenerics’:
  
      rowMedians
  
  The following objects are masked from ‘package:matrixStats’:
  
      anyMissing, rowMedians
  
  Search path was changed
Output for data("orcAlignsRep2", package = "EatonEtAlChIPseq"):
  Loading required package: BiocGenerics
  Loading required package: parallel
  
  Attaching package: ‘BiocGenerics’
  
  The following objects are masked from ‘package:parallel’:
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  Loading required package: BiocParallel
  Loading required package: Biostrings
  Loading required package: S4Vectors
  Loading required package: stats4
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: XVector
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Loading required package: Rsamtools
  Loading required package: GenomeInfoDb
  Loading required package: GenomicRanges
  Loading required package: GenomicAlignments
  Loading required package: SummarizedExperiment
  Loading required package: MatrixGenerics
  Loading required package: matrixStats
  
  Attaching package: ‘MatrixGenerics’
  
  The following objects are masked from ‘package:matrixStats’:
  
      colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
      colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
      colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
      colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
      colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
      colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
      colWeightedMeans, colWeightedMedians, colWeightedSds,
      colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
      rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
      rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
      rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
      rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
      rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
      rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
      rowWeightedSds, rowWeightedVars
  
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  
  Attaching package: ‘Biobase’
  
  The following object is masked from ‘package:MatrixGenerics’:
  
      rowMedians
  
  The following objects are masked from ‘package:matrixStats’:
  
      anyMissing, rowMedians
  
  Search path was changed
Output for data("orcPeaksRep1", package = "EatonEtAlChIPseq"):
  Loading required package: GenomicRanges
  Loading required package: stats4
  Loading required package: BiocGenerics
  Loading required package: parallel
  
  Attaching package: ‘BiocGenerics’
  
  The following objects are masked from ‘package:parallel’:
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  Loading required package: S4Vectors
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Search path was changed
Output for data("orcPeaksRep2", package = "EatonEtAlChIPseq"):
  Loading required package: GenomicRanges
  Loading required package: stats4
  Loading required package: BiocGenerics
  Loading required package: parallel
  
  Attaching package: ‘BiocGenerics’
  
  The following objects are masked from ‘package:parallel’:
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  Loading required package: S4Vectors
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Search path was changed
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
orcAligns 7.476  0.128   7.615
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/EatonEtAlChIPseq.Rcheck/00check.log’
for details.



Installation output

EatonEtAlChIPseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL EatonEtAlChIPseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘EatonEtAlChIPseq’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EatonEtAlChIPseq)

Tests output


Example timings

EatonEtAlChIPseq.Rcheck/EatonEtAlChIPseq-Ex.timings

nameusersystemelapsed
orcAligns7.4760.1287.615
orcPeaks0.2440.0000.246