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qc_report cannot produce rmd due to permission issue #18

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darkcircle opened this issue Jul 9, 2021 · 0 comments
Open

qc_report cannot produce rmd due to permission issue #18

darkcircle opened this issue Jul 9, 2021 · 0 comments

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@darkcircle
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I am using fastqcr with R 4.1.0.

I tried to execute qc_report function for a single zip archive within my user's directory,
but I have met a Error msg like below

List of 3
 $ fig.width : num 4
 $ fig.height: num 3.5
 $ fig.align : chr "center"

  |..................................................................    |  94%
  ordinary text without R code

  |....................................................................  |  97%
label: kmer-content (with options) 
List of 3
 $ fig.width : num 4
 $ fig.height: num 3.5
 $ fig.align : chr "center"

Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: qc_report ... element_text -> .handleSimpleError -> h -> cat -> file
In addition: Warning messages:
1: Missing column names filled in: 'X1' [1] 
2: In file(file, ifelse(append, "a", "w")) :
  cannot open file 'sample-report.knit.md': Permission denied

Execution halted

It says "permission problem"
I could not find where above messages produced from yet.
but when I tried to run as root. "Permission denied" message is disappeared.

I guess that there is invalid setting related on knitr.
How can we resolve this problem?

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