Back to Multiple platform build/check report for BioC 3.12
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CHECK report for scruff on tokay1

This page was generated on 2020-11-23 12:23:09 -0500 (Mon, 23 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE scruff PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1660/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scruff 1.8.2
Zhe Wang
Snapshot Date: 2020-11-22 14:42:09 -0500 (Sun, 22 Nov 2020)
URL: https://git.bioconductor.org/packages/scruff
Branch: RELEASE_3_12
Last Commit: eef2cdd
Last Changed Date: 2020-11-19 17:29:00 -0500 (Thu, 19 Nov 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: scruff
Version: 1.8.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scruff.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings scruff_1.8.2.tar.gz
StartedAt: 2020-11-23 07:14:09 -0500 (Mon, 23 Nov 2020)
EndedAt: 2020-11-23 07:29:05 -0500 (Mon, 23 Nov 2020)
EllapsedTime: 895.9 seconds
RetCode: 0
Status:  OK  
CheckDir: scruff.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scruff.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings scruff_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/scruff.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scruff/DESCRIPTION' ... OK
* this is package 'scruff' version '1.8.2'
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
tenxBamqc 6.02   1.33   80.42
rview     6.36   0.02    6.37
qcplots   5.24   0.83    6.07
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
rview     7.41   0.03   11.08
tenxBamqc 6.07   0.65   91.85
qcplots   6.39   0.05    6.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/scruff.Rcheck/00check.log'
for details.



Installation output

scruff.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/scruff_1.8.2.tar.gz && rm -rf scruff.buildbin-libdir && mkdir scruff.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scruff.buildbin-libdir scruff_1.8.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL scruff_1.8.2.zip && rm scruff_1.8.2.tar.gz scruff_1.8.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4402k  100 4402k    0     0  18.3M      0 --:--:-- --:--:-- --:--:-- 18.6M

install for i386

* installing *source* package 'scruff' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scruff'
    finding HTML links ... done
    alignRsubread                           html  
    bamExample                              html  
    barcodeExample                          html  
    cbtop10000                              html  
    countUMI                                html  
    demultiplex                             html  
    gview                                   html  
    qcplots                                 html  
    rview                                   html  
    sceExample                              html  
    scruff                                  html  
    tenxBamqc                               html  
    validCb                                 html  
** 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

install for x64

* installing *source* package 'scruff' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scruff' as scruff_1.8.2.zip
* DONE (scruff)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'scruff' successfully unpacked and MD5 sums checked

Tests output

scruff.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
> 
> proc.time()
   user  system elapsed 
  16.48    2.01   25.12 

scruff.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
> 
> proc.time()
   user  system elapsed 
  25.04    1.00   34.92 

Example timings

scruff.Rcheck/examples_i386/scruff-Ex.timings

nameusersystemelapsed
alignRsubread000
countUMI0.020.000.02
demultiplex3.810.424.24
gview1.951.002.98
qcplots5.240.836.07
rview6.360.026.37
scruff0.010.000.02
tenxBamqc 6.02 1.3380.42

scruff.Rcheck/examples_x64/scruff-Ex.timings

nameusersystemelapsed
alignRsubread000
countUMI0.020.000.02
demultiplex3.730.103.84
gview1.780.222.00
qcplots6.390.056.44
rview 7.41 0.0311.08
scruff0.010.000.01
tenxBamqc 6.07 0.6591.85