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This page was generated on 2021-10-15 15:06:53 -0400 (Fri, 15 Oct 2021).

CHECK results for SingleMoleculeFootprinting on machv2

To the developers/maintainers of the SingleMoleculeFootprinting package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleMoleculeFootprinting.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1779/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleMoleculeFootprinting 1.0.0  (landing page)
Guido Barzaghi
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/SingleMoleculeFootprinting
git_branch: RELEASE_3_13
git_last_commit: 398e2fb
git_last_commit_date: 2021-05-19 13:04:02 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: SingleMoleculeFootprinting
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SingleMoleculeFootprinting_1.0.0.tar.gz
StartedAt: 2021-10-15 00:05:28 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:12:01 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 392.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SingleMoleculeFootprinting.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SingleMoleculeFootprinting.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SingleMoleculeFootprinting_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SingleMoleculeFootprinting.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleMoleculeFootprinting/DESCRIPTION’ ... OK
* this is package ‘SingleMoleculeFootprinting’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SingleMoleculeFootprinting’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotAvgSMF: no visible global function definition for ‘points’
PlotAvgSMF: no visible global function definition for ‘abline’
PlotAvgSMF: no visible global function definition for ‘rect’
PlotAvgSMF: no visible global function definition for ‘text’
PlotSingleMoleculeStack: no visible global function definition for
  ‘points’
SampleCorrelation: no visible global function definition for ‘pairs’
SampleCorrelation: no visible binding for global variable ‘panel.cor’
SampleCorrelation: no visible binding for global variable ‘panel.hist’
SampleCorrelation: no visible binding for global variable ‘panel.jet’
SingleTFStateQuantificationPlot: no visible global function definition
  for ‘points’
SingleTFStateQuantificationPlot: no visible global function definition
  for ‘text’
TFPairStateQuantificationPlot: no visible global function definition
  for ‘points’
TFPairStateQuantificationPlot: no visible global function definition
  for ‘text’
Undefined global functions or variables:
  abline pairs panel.cor panel.hist panel.jet points rect text
Consider adding
  importFrom("graphics", "abline", "pairs", "points", "rect", "text")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/SingleMoleculeFootprinting.Rcheck/00check.log’
for details.



Installation output

SingleMoleculeFootprinting.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SingleMoleculeFootprinting
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘SingleMoleculeFootprinting’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (SingleMoleculeFootprinting)

Tests output

SingleMoleculeFootprinting.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SingleMoleculeFootprinting)
> 
> test_check("SingleMoleculeFootprinting")
Loading required package: BSgenome
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
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
all necessary alignment files found
Detected experiment type: DE
all necessary alignment files found
snapshotDate(): 2021-05-18
see ?SingleMoleculeFootprintingData and browseVignettes('SingleMoleculeFootprintingData') for documentation
loading from cache
counting alignments...done
counting alignments...done
Setting QuasR project
all necessary alignment files found
Calling methylation at all Cytosines
1.05% of reads found with conversion rate above 0.2
Subsetting Cytosines by permissive genomic context (NGCNN, NNCGN)
Collapsing strands
0 reads found mapping to the + strand, collapsing to -
0 reads found mapping to the + strand, collapsing to -
Filtering Cs for coverage
Detected experiment type: DE
Subsetting Cytosines by strict genomic context (GCH, HCG) based on the detected experiment type: DE
Merging matrixes
Collecting summarized methylation for bins
Single TF mode
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
 38.130   2.053  41.396 

Example timings

SingleMoleculeFootprinting.Rcheck/SingleMoleculeFootprinting-Ex.timings

nameusersystemelapsed
BaitCapture0.3540.0240.378
BinMethylation0.2600.0130.274
CallContextMethylation0.2630.0150.278
ConversionRate0.2440.0150.259
DetectExperimentType0.0010.0000.001
FilterByConversionRate0.2970.0160.313
FilterContextCytosines0.3060.0180.324
GetQuasRprj0.1920.0130.205
GetSingleMolMethMat0.1990.0140.213
PlotAvgSMF0.2700.0180.289
PlotSM0.2630.0140.278
PlotSingleSiteSMF0.2750.0140.290
SortReads0.2560.0130.270
SortReadsBySingleTF0.2540.0120.265
SortReadsByTFCluster0.2230.0120.235
StateQuantificationPlot0.2470.0110.259