FindConservedMarker() metap package installation gave a nonzero status

satijalab / seurat

R toolkit for single cell genomics

http://www.satijalab.org/seurat

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FindConservedMarker() metap package installation gave a nonzero status #5957

Closed Skrueger09 closed 2 years ago

Skrueger09 commented 2 years ago

I am processing my Single Cell RNA seq data and I am at Cluster Analysis: FindConservedMarkers(seurat_integrated, ident.1 = cluster, grouping.var = "sample", only.pos = TRUE, min.diff.pct = 0.25, min.pct = 0.25, logfc.threshold = 0.25)

But I get an error of Error: Please install the metap package to use FindConservedMarkers. This can be accomplished with the following commands:

install.packages('BiocManager') BiocManager::install('multtest') install.packages('metap')

Then when I try to install metap I get the following message: ERROR: dependency ‘qqconf’ is not available for package ‘metap’

removing ‘/home/shawn/R/x86_64-pc-linux-gnu-library/4.1/metap’ Warning in install.packages : installation of package '/extDataS/class/BIMD514_2021/project/ShawnK/DarlandSC/DarlandSC/Sc_RNA_Seq/data/metap_1.8.tar.gz' had non-zero exit status

samuel-marsh commented 2 years ago

Hi,

Not member of the dev team but hopefully can be helpful. Did you try running:

install.packages("qqconf")

Best, Sam

Skrueger09 commented 2 years ago

@samuel-marsh I have tried manually installing qqconf as well and I have the same error

samuel-marsh commented 2 years ago

So the error above is saying qqconf is not available (which is strange because it appears to be good for R3+). What is the error when attempting direct qqconf install?

Skrueger09 commented 2 years ago

samuel-marsh commented 2 years ago

Hi,

so ya looks like some sort of compilation issue related to qqconf package and not Seurat directly. I would suggest posting to their repo for help solving the install issue. https://github.com/eweine/qqconf

Best, Sam

saketkc commented 2 years ago

Hi @Skrueger09, the latest qqconf seems to require fftw3 headers, which needs to be installed on the system: apt-get install libfftw3-dev

AngCamp commented 2 years ago

No offense but this is a pretty important function and it seems like this should be something Seurat handles automatically. This is not an obscure part of the seurat workflow, it makes seurat functional for scRNA-seq of any kind of intervention done to the tissue or organism. I just had this same issue now in october.