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CHECK report for scruff on celaya2

This page was generated on 2019-10-16 13:02:55 -0400 (Wed, 16 Oct 2019).

Package 1479/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scruff 1.2.5
Zhe Wang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/scruff
Branch: RELEASE_3_9
Last Commit: e0ef246
Last Changed Date: 2019-10-03 20:02:15 -0400 (Thu, 03 Oct 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: scruff
Version: 1.2.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scruff.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scruff_1.2.5.tar.gz
StartedAt: 2019-10-16 06:39:58 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:51:25 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 687.4 seconds
RetCode: 0
Status:  OK 
CheckDir: scruff.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scruff.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scruff_1.2.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scruff.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scruff/DESCRIPTION’ ... OK
* this is package ‘scruff’ version ‘1.2.5’
* 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 ‘scruff’ 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
Unexported object imported by a ':::' call: 'ShortRead:::.set_omp_threads'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
.countUmiUnit: no visible global function definition for '.'
.countUmiUnit: no visible binding for global variable 'gene_id'
.countUmiUnit: no visible binding for global variable 'umi'
.countUmiUnit: no visible binding for global variable 'inferred_umi'
.countUmiUnit: no visible global function definition for 'median'
.demultiplexUnit: no visible binding for global variable 'experiment'
.demultiplexUnit: no visible binding for global variable 'lane'
.demultiplexUnit: no visible binding for global variable 'filename'
.demultiplexUnit: no visible binding for global variable 'project'
.demultiplexUnit: no visible binding for global variable 'cell_index'
.demultiplexUnit: no visible binding for global variable 'reads'
.demultiplexUnit: no visible binding for global variable
  'percent_assigned'
.demultiplexUnit: no visible binding for global variable 'read1_path'
.demultiplexUnit: no visible binding for global variable 'read2_path'
.demultiplexUnit: no visible binding for global variable 'min.phred1'
.demultiplexUnit: no visible binding for global variable 'length1'
.demultiplexUnit: no visible binding for global variable 'bc_correct'
.demultiplexUnit: no visible binding for global variable 'barcode'
.demultiplexUnit: no visible binding for global variable 'read2'
.demultiplexUnit: no visible binding for global variable 'qtring2'
.demultiplexUnit: no visible binding for global variable 'rname2'
.demultiplexUnit: no visible binding for global variable 'umi'
.demultiplexUnit: no visible binding for global variable 'fastq_path'
.demultiplexUnit: no visible binding for global variable 'read1'
.demultiplexUnit: no visible binding for global variable 'qtring1'
.demultiplexUnit: no visible binding for global variable 'rname1'
.getGeneAnnotation: no visible binding for global variable 'type'
.getGeneAnnotation: no visible binding for global variable 'gene_id'
.getGeneAnnotation: no visible binding for global variable 'gene_name'
.getGeneAnnotation: no visible binding for global variable
  'gene_biotype'
.plotAvgReadsPerCorrectedUMI: no visible binding for global variable
  'avg_reads_per_corrected_umi'
.plotAvgReadsPerCorrectedUMI: no visible binding for global variable
  'experiment'
.plotAvgReadsPerCorrectedUMI: no visible binding for global variable
  'number_of_cells'
.plotAvgReadsPerCorrectedUMI: no visible binding for global variable
  '.x'
.plotAvgReadsPerUMI: no visible binding for global variable
  'experiment'
.plotAvgReadsPerUMI: no visible binding for global variable
  'avg_reads_per_umi'
.plotAvgReadsPerUMI: no visible binding for global variable
  'number_of_cells'
.plotAvgReadsPerUMI: no visible binding for global variable '.x'
.plotCounts: no visible binding for global variable 'experiment'
.plotCounts: no visible binding for global variable 'total_counts'
.plotCounts: no visible binding for global variable 'number_of_cells'
.plotCounts: no visible binding for global variable '.x'
.plotFracProteinCodingGenes: no visible binding for global variable
  'experiment'
.plotFracProteinCodingGenes: no visible binding for global variable
  'protein_coding_genes'
.plotFracProteinCodingGenes: no visible binding for global variable
  'number_of_cells'
.plotFracProteinCodingTranscripts: no visible binding for global
  variable 'experiment'
.plotFracProteinCodingTranscripts: no visible binding for global
  variable 'protein_coding_counts'
.plotFracProteinCodingTranscripts: no visible binding for global
  variable 'total_counts'
.plotFracProteinCodingTranscripts: no visible binding for global
  variable 'number_of_cells'
.plotGeneToGenomeFraction: no visible binding for global variable
  'experiment'
.plotGeneToGenomeFraction: no visible binding for global variable
  'reads_mapped_to_genes'
.plotGeneToGenomeFraction: no visible binding for global variable
  'reads_mapped_to_genome'
.plotGeneToGenomeFraction: no visible binding for global variable
  'number_of_cells'
.plotGeneToTotalFraction: no visible binding for global variable
  'experiment'
.plotGeneToTotalFraction: no visible binding for global variable
  'reads_mapped_to_genes'
.plotGeneToTotalFraction: no visible binding for global variable
  'reads'
.plotGeneToTotalFraction: no visible binding for global variable
  'number_of_cells'
.plotGenes: no visible binding for global variable 'experiment'
.plotGenes: no visible binding for global variable 'number_of_cells'
.plotGenes: no visible binding for global variable '.x'
.plotGenesPerMillionReads: no visible binding for global variable
  'experiment'
.plotGenesPerMillionReads: no visible binding for global variable
  'reads'
.plotGenesPerMillionReads: no visible binding for global variable
  'number_of_cells'
.plotGenesPerMillionReads: no visible binding for global variable '.x'
.plotGenomeReadsFraction: no visible binding for global variable
  'experiment'
.plotGenomeReadsFraction: no visible binding for global variable
  'reads_mapped_to_genome'
.plotGenomeReadsFraction: no visible binding for global variable
  'reads'
.plotGenomeReadsFraction: no visible binding for global variable
  'number_of_cells'
.plotMedReadsPerCorrectedUMI: no visible binding for global variable
  'median_reads_per_corrected_umi'
.plotMedReadsPerCorrectedUMI: no visible binding for global variable
  'experiment'
.plotMedReadsPerCorrectedUMI: no visible binding for global variable
  'number_of_cells'
.plotMedReadsPerCorrectedUMI: no visible binding for global variable
  '.x'
.plotMedReadsPerUMI: no visible binding for global variable
  'experiment'
.plotMedReadsPerUMI: no visible binding for global variable
  'median_reads_per_umi'
.plotMedReadsPerUMI: no visible binding for global variable
  'number_of_cells'
.plotMedReadsPerUMI: no visible binding for global variable '.x'
.plotMtCounts: no visible binding for global variable 'experiment'
.plotMtCounts: no visible binding for global variable 'mt_counts'
.plotMtCounts: no visible binding for global variable 'number_of_cells'
.plotMtCounts: no visible binding for global variable '.x'
.plotMtCountsFraction: no visible binding for global variable
  'experiment'
.plotMtCountsFraction: no visible binding for global variable
  'mt_counts'
.plotMtCountsFraction: no visible binding for global variable
  'total_counts'
.plotMtCountsFraction: no visible binding for global variable
  'number_of_cells'
.plotReadsMappedToGenes: no visible binding for global variable
  'experiment'
.plotReadsMappedToGenes: no visible binding for global variable
  'reads_mapped_to_genes'
.plotReadsMappedToGenes: no visible binding for global variable
  'number_of_cells'
.plotReadsMappedToGenes: no visible binding for global variable '.x'
.plotReadsMappedToGenome: no visible binding for global variable
  'experiment'
.plotReadsMappedToGenome: no visible binding for global variable
  'reads_mapped_to_genome'
.plotReadsMappedToGenome: no visible binding for global variable
  'number_of_cells'
.plotReadsMappedToGenome: no visible binding for global variable '.x'
.plotTotalReads: no visible binding for global variable 'experiment'
.plotTotalReads: no visible binding for global variable 'reads'
.plotTotalReads: no visible binding for global variable
  'number_of_cells'
.plotTotalReads: no visible binding for global variable '.x'
.tenxBamqcUnit: no visible binding for global variable 'CB'
.tenxBamqcUnit: no visible global function definition for '.'
.tenxBamqcUnit: no visible binding for global variable 'readname'
.tenxBamqcUnit: no visible binding for global variable 'NH'
.tenxBamqcUnit: no visible binding for global variable 'GX'
.tenxBamqcUnit: no visible binding for global variable 'MM'
.tenxBamqcUnit: no visible binding for global variable 'cell_barcode'
.tenxBamqcUnit: no visible binding for global variable
  'reads_mapped_to_genome'
.tenxBamqcUnit: no visible binding for global variable
  'reads_mapped_to_genes'
.tenxCheckCellBarcodes: no visible binding for global variable
  'cbtop10000'
.tenxCheckCellBarcodes: no visible binding for global variable
  'v2chemistry'
.tenxCheckCellBarcodes: no visible global function definition for
  'complete.cases'
.tenxCheckCellBarcodes: no visible binding for global variable
  'v1chemistry'
.tenxCheckCellBarcodes: no visible binding for global variable
  'v3chemistry'
alignRsubread: no visible global function definition for
  'capture.output'
countUMI: no visible binding for global variable 'geneid'
countUMI: no visible binding for global variable 'gene_id'
countUMI: no visible binding for global variable 'gene_biotype'
demultiplex: no visible binding for global variable 'cell_index'
demultiplex: no visible binding for global variable 'filename'
gview : .getLevel: no visible binding for global variable 'level'
gview : .getTxdt: no visible binding for global variable
  'transcript_id'
gview : .getTxdt: no visible binding for global variable
  'transcript_name'
gview : .getTxdt: no visible binding for global variable 'gene_id'
gview : .getTxdt: no visible binding for global variable 'gene_name'
gview : .transRect: no visible binding for global variable
  'transcript_id'
gview : .transRect: no visible binding for global variable 'level'
gview : .transRect: no visible binding for global variable 'type'
gview : .transRect: no visible binding for global variable
  'exon_number'
gview : .transRect: no visible binding for global variable 'gene_id'
gview : .transRect: no visible binding for global variable 'gene_name'
gview : .transArrow: no visible binding for global variable 'level'
gview : .transArrow: no visible binding for global variable
  'transcript_id'
gview : .transArrow: no visible binding for global variable
  'transcript_name'
gview : .transArrow: no visible binding for global variable 'gene_id'
gview : .transArrow: no visible binding for global variable 'gene_name'
gview : .transText: no visible binding for global variable 'level'
gview : .transText: no visible binding for global variable
  'transcript_name'
gview: no visible binding for global variable 'type'
gview: no visible binding for global variable 'x1'
gview: no visible binding for global variable 'x2'
gview: no visible binding for global variable 'y1'
gview: no visible binding for global variable 'y2'
gview: no visible binding for global variable 'x'
gview: no visible binding for global variable 'y'
gview: no visible binding for global variable 'transcript_name'
tenxBamqc: no visible binding for global variable 'cbtop10000'
tenxBamqc: no visible binding for global variable
  'reads_mapped_to_genome'
tenxBamqc: no visible binding for global variable
  'reads_mapped_to_genes'
tenxBamqc: no visible binding for global variable 'cb'
tenxBamqc: no visible binding for global variable 'cell_barcode'
tenxBamqc: no visible binding for global variable 'number_of_cells'
Undefined global functions or variables:
  . .x CB GX MM NH avg_reads_per_corrected_umi avg_reads_per_umi
  barcode bc_correct capture.output cb cbtop10000 cell_barcode
  cell_index complete.cases exon_number experiment fastq_path filename
  gene_biotype gene_id gene_name geneid inferred_umi lane length1 level
  median median_reads_per_corrected_umi median_reads_per_umi min.phred1
  mt_counts number_of_cells percent_assigned project
  protein_coding_counts protein_coding_genes qtring1 qtring2 read1
  read1_path read2 read2_path readname reads reads_mapped_to_genes
  reads_mapped_to_genome rname1 rname2 total_counts transcript_id
  transcript_name type umi v1chemistry v2chemistry v3chemistry x x1 x2
  y y1 y2
Consider adding
  importFrom("stats", "complete.cases", "median")
  importFrom("utils", "capture.output")
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
Examples with CPU or elapsed time > 5s
              user system elapsed
tenxBamqc   22.920  6.267  24.462
demultiplex 15.319  7.511  12.550
rview       14.959  0.235  15.206
gview        9.939  2.711   4.585
qcplots      9.510  0.071   9.600
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/scruff.Rcheck/00check.log’
for details.



Installation output

scruff.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scruff’ ...
** using staged installation
** R
** data
** 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 (scruff)

Tests output

scruff.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(scruff)
> 
> test_check("scruff")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 22.999   1.856  24.807 

Example timings

scruff.Rcheck/scruff-Ex.timings

nameusersystemelapsed
alignRsubread0.0010.0010.001
countUMI0.0340.0040.038
demultiplex15.319 7.51112.550
gview9.9392.7114.585
qcplots9.5100.0719.600
rview14.959 0.23515.206
scruff0.0370.0010.040
tenxBamqc22.920 6.26724.462