Question: how to get the lastest version of tximport
0
20 months ago by
matrs10
matrs10 wrote:
packageVersion("tximport")
[1] '1.6.0'

I'm following this guide and when testing with a single table from stringtie, I get the following error:

txi <- tximport(files, type = "stringtie", tx2gene = tx2gene)
Error in match.arg(type, c("none", "salmon", "sailfish", "kallisto", "rsem")) :
'arg' should be one of “none”, “salmon”, “sailfish”, “kallisto”, “rsem”

After checking the github repo, the NEWS file states that  stringtie support was added in 1.8, which isn't available in bioconductor and the development version is 1.7.13. It would be useful if that guide adds some info regarding the tximport version used to carry out all those analyses.  I can try installing from github, but i wanted to know what is the preferred way to get the last stable version of this package.

Cheers

stringtie tximport • 528 views
modified 17 months ago • written 20 months ago by matrs10

Which version of R and Bioconductor are you running? You seem to be using the Bioconductor version 3.4

Answer: how to get the last version of tximport
2
20 months ago by
Michael Love25k
United States
Michael Love25k wrote:

The vignette shows the information about the session (package versions etc.) in the last section called Session Info.

Usually, the only way to use development branch code on Bioconductor is to use R-devel, and to install a complete set of development Bioconductor packages, only using biocLite(). This is a rare exception, where I can tell you as the maintainer, that tximport has no upstream Bioconductor dependencies, and the current devel branch doesn't change the "API" for downstream packages, so it's safe to install v1.7 from Github to replace v1.6. Usually, installing from Github instead of using biocLite() would "void the warranty" with respect to making sure that Bioconductor packages function together without error.

Answer: how to get the last version of tximport
0
20 months ago by
matrs10
matrs10 wrote:

Thanks, it worked as expected. I didn't see the last part of the guide before, so i missed  the sessionInfo() output, my fault.  If anybody wants to try the last version:

library(devtools)

options(unzip = 'internal')

install_github("mikelove/tximport")


By the way, there is a small mistake in the guide. For kallisto, salmon and rsem (maybe the others too), when you create the variable files, you pass the string with the .gz extesion, but the actual files aren't gzipped so all(file.exists(files)) returns FALSE.