############################################################################## ############################################################################## ### ### 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/scruff.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 ‘scruff/DESCRIPTION’ ... OK * this is package ‘scruff’ version ‘1.10.0’ * 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: .git_fetch_output.txt .git_merge_output.txt 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 (user + system) or elapsed time > 5s user system elapsed tenxBamqc 11.964 2.327 13.329 rview 7.278 0.046 7.327 qcplots 5.329 0.034 5.413 * 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-3.13-bioc/meat/scruff.Rcheck/00check.log’ for details.