How to include shell command results in Sweave PDF report?

Asked May 01 '15 at 14:09

Active May 28 '16 at 23:21

Viewed 82 times

I need to include the results and reports of shell calls in a Sweave PDF report, but I can't find any parameter for that in the chunk parameters.

For example, when I apply the code below:

> system(" makeblastdb -in mouseX.fasta -dbtype nucl -parse_seqids -out mouseXdb")

It reports:

Building a new DB, current time: 05/01/2015 18:31:57
New DB name:   mouseXdb
New DB title:  mouseX.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 1 sequences in 1.08783 seconds.

but it doesn't show up in Sweave Report when I use parameters like print or echo...

As another example, I might want to include the header of a file in my report using a shell call to the header command.

edited May 28 '16 at 23:21

Cel Skeggs

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asked May 01 '15 at 14:09

ameerosein

Did you try using `rep – Rentrop May 01 '15 at 14:22
@Floo0 sorry but not working... it returns zero... – ameerosein May 01 '15 at 19:33
Does [this previous SO post](http://stackoverflow.com/questions/7014081/capture-both-exit-status-and-output-from-a-system-call-in-r) answer your question? – Jthorpe May 01 '15 at 19:48
@Jthorpe Unfortunately No .. I want the execution message not the output of the system call, when i done that, it just take me a null character – ameerosein May 02 '15 at 04:31

How to include shell command results in Sweave PDF report?

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