Question

Could it be possible to get an older version of ChIPQC?

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etiennedanis • 0

@8f9d24cc

Last seen 3 months ago

United States

Hello creators of ChIPQC,

Could it be possible to have access to an older version of ChIPQC (version 1.31 for example) instead of the current version 1.32?

ChIPQC worked great for me till I updated it to the latest version. I got an error message described here: BiocParallel error with ChIPQC

I managed to downgrade R and use an older version of ChIPQC I had on my machine (which solved my issue) till by mistake, I upgraded R and ChIPQC again and following a bad idea, I deleted all my previous versions of R packages...

If you could post an older version of ChIPQC on Github or somewhere else, that would be greatly appreciated.

Thank you very much in advance.

Best, Etienne

ChIPQC ChIP-seq DiffBind Rory_Stark • 1.2k views

ADD COMMENT • link 2.3 years ago etiennedanis • 0

score 1 · Answer 1 · 2022-08-02

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Rory Stark ★ 5.2k

@rory-stark-5741

Last seen 28 days ago

Cambridge, UK

I have submitted two fixes for ChIPQC. One addresses the issues where an error is generated with the message:

Error in if (is.na(peaks)) peaks = NULL: the condition has length > 1

The other makes the use of BiocParallel more explicit, checking for installed backends and reporting information on how ChIPQC will be executed.

These fixes will be in effect from version ChIPQC_1.32.1 in the main Release branch. There are related fixes in DiffBind_3.6.2 so these should be updated together.

ADD COMMENT • link 2.3 years ago Rory Stark ★ 5.2k

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Thank you so much, Rory!!! It worked!!! For some weird reason, I had to install the package using the tar.gz file:

install.packages("/home/<your_username>/tools/ChIPQC_1.32.1.tar.gz", repos = NULL, type="source")

for it to be updated to the 1.32.1 version (instead of staying at 1.32.0). And after loading the library and launching ChIPQC, I got the following error message when I tried to generate the ChIPQC report using ChIPQCreport() :

Error in f(...) : Graphics API version mismatch

But after installing the ragg package:

install.packages("ragg")

it fixed the error. Now, everything perfectly works!

I can finally use your fantastic ChIPQC package again. :-)

ADD REPLY • link 2.3 years ago etiennedanis • 0