Package: scruff

Version: 1.2.5

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scruff.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scruff_1.2.5.tar.gz

StartedAt: 2019-10-16 04:52:28 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:00:00 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 451.4 seconds

RetCode: 0

Status:  OK

CheckDir: scruff.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:scruff.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings scruff_1.2.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/scruff.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
gview       67.404  0.540  14.853
tenxBamqc   15.260  2.779  16.507
demultiplex 10.327  1.688   7.358
rview       11.452  0.023  11.477
qcplots      6.904  0.012   6.916
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/scruff.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL scruff
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 
 19.764   0.717  20.466 

name	user	system	elapsed
alignRsubread	0	0	0
countUMI	0.037	0.020	0.057
demultiplex	10.327	1.688	7.358
gview	67.404	0.540	14.853
qcplots	6.904	0.012	6.916
rview	11.452	0.023	11.477
scruff	0.070	0.020	0.089
tenxBamqc	15.260	2.779	16.507