Closed makimenkova closed 4 years ago
Hi Maria,
We have some ideas as to why this occurred. However, in order to help us to diagnose the problem, could you run
devtools::session_info()
and post the relevant lines for scMerge
?
Many thanks,
Kevin
Hello! Here is my session_info:
─ setting value
version R version 3.6.1 (2019-07-05)
os Ubuntu 18.04.2 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
─ Packages
scMerge 1.0.0 2019-05-02 [1] Bioconductor
Thanks
Hi Maria,
That is very helpful, thank you.
Could I ask you to try to install the latest version using devtools::install_github("SydneyBioX/scMerge, force = TRUE)
?
This should install Version 1.1.3 which might already provided a fix.
Thanks,
Kevin
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From: makimenkova notifications@github.com Sent: Thursday, July 25, 2019 10:13:36 PM To: SydneyBioX/scMerge scMerge@noreply.github.com Cc: Kevin Wang kevin.wang@sydney.edu.au; Comment comment@noreply.github.com Subject: Re: [SydneyBioX/scMerge] Unexpected error in specifying kmeansK parameters (#13)
Hello! Here is my session_info:
─ setting value
version R version 3.6.1 (2019-07-05)
os Ubuntu 18.04.2 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
─ Packages
scMerge 1.0.0 2019-05-02 [1] Bioconductor
Thanks
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Thanks! I did it, but it didn't help unfortunately
V scMerge 1.0.0 2019-07-25 [1] Github (SydneyBioX/scMerge@1936764)
Error in igraph::fastgreedy.community(g) :
At fast_community.c:639 : fast-greedy community finding works only on graphs without multiple edges, Invalid value```
Hi,
It seems like you still have scMerge V1.0.0 installed. This is an outdated version, so you should try to run (edit) devtools::install_github("SydneyBioX/scMerge, force = TRUE)
BiocManager::install("scMerge", version = "3.10)
, restart R and try to load scMerge again. You should have (edit) V1.1.4 V1.1.3 installed after this.
As for the error itself, I wonder if you see a plot that looks somewhat like this one before the error occur. If so, could you share that with us?
Thanks, Kevin
... 1.0.0 ... is an outdated version ...
Not really. Almost all end-users should be using the release branch, which is at 1.0.0. The development branch is for the package's developer and early adopters / testers. Are there changes to the developer branch which ought to be ported to the release branch? Installing using devtools::install_github
just annoys Martin Morgan on the mailing list when users end up with a mix of incompatible R and R package versions, which wouldn't happen if BiocManager is used.
@DarioS, scMerge V1.0.0
is fine as is. But after the BioC release this year, we went on to expand scMerge
's capabilities in V1.1.z, including resolving this issue.
Maybe for the sake of consistency, @makimenkova, could you try BiocManager::install("scMerge", version = "3.10)
instead? Once we resolve this issue, I will push the patched version to BioC.
Hi,
I'm interested in integrating sc-RNA data sets and your package seems very suitable for this. However I get this error while running scMerge.
sce_mESC_mg <- scMerge::scMerge(sce_combine = sce_combine, ctl = ctl, kmeansK = c(1, 2), assay_name = 'scMerge')
For any other value of the kmeansK parameter everything works, but I need exactly kmeansK = c(1, 2). I tried to change data sets order and specify kmeansK = c(2, 1), but it didn't work
Thanks in advance, Maria