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campbio / scruff

Single Cell RNA-seq UMI Filtering Facilitator
http://bioconductor.org/packages/scruff/
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Release 3 12 #174

Closed zhewa closed 3 years ago

lintr-bot commented 3 years ago

data-raw/10x/cbWhitelist737KAugust2016.R:5:1: style: Trailing blank lines are superfluous.

​
^

data-raw/exampleFastqs.R:16:1: style: Lines should not be more than 80 characters.

​ShortRead::writeFastq(v1r1fastq[seq(500)], "vandenBrink_1h1_L001_R1_001.fastq.gz")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

data-raw/exampleFastqs.R:17:1: style: Lines should not be more than 80 characters.

​ShortRead::writeFastq(v1r2fastq[seq(500)], "vandenBrink_1h1_L001_R2_001.fastq.gz")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

data-raw/Mus_musculus/barcodeExample.R:3:64: style: Commas should always have a space after.

​    "data-raw/Mus_musculus/GSE85755_CEL-Seq_barcodes_96.txt")[,2])
                                                               ^

data-raw/Mus_musculus/barcodeExample.R:6:1: style: Trailing blank lines are superfluous.

​
^

vignettes/scruff.Rmd:184:5: style: Use <-, not =, for assignment.

​sce = countUMI(al,
    ^

vignettes/scruff.Rmd:225:42: style: Commas should always have a space after.

​g <- ggbio::tracks(g1, g2, heights = c(4,1), xlab = "chr MT")
                                         ^
codecov-io commented 3 years ago

Codecov Report

:exclamation: No coverage uploaded for pull request base (RELEASE_3_12@09ac176). Click here to learn what that means. The diff coverage is n/a.

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@@              Coverage Diff               @@
##             RELEASE_3_12    #174   +/-   ##
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  Coverage                ?   0.00%           
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  Files                   ?       9           
  Lines                   ?    1763           
  Branches                ?       0           
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  Hits                    ?       0           
  Misses                  ?    1763           
  Partials                ?       0

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