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

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###
### 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
###
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* 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.

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

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 

name	user	system	elapsed
alignRsubread	0.001	0.001	0.001
countUMI	0.034	0.004	0.038
demultiplex	15.319	7.511	12.550
gview	9.939	2.711	4.585
qcplots	9.510	0.071	9.600
rview	14.959	0.235	15.206
scruff	0.037	0.001	0.040
tenxBamqc	22.920	6.267	24.462