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IMB-Computational-Genomics-Lab / scGPS

A framework for clustering (CORE) and estimation of relationship between pairs of clusters (scGPS) from single cell data
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error when installing scGPS #3

Open lixin4306ren opened 5 years ago

lixin4306ren commented 5 years ago

command I used: devtools::install_github("IMB-Computational-Genomics-Lab/scGPS")

Error: package or namespace load failed for ‘scGPS’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/share/apps/anaconda3/envs/r3.5/lib/R/library/scGPS/libs/scGPS.so': /share/apps/anaconda3/envs/r3.5/lib/R/library/scGPS/libs/scGPS.so: undefined symbol: dgesvd_ Error: loading failed Execution halted ERROR: loading failed

quanaibn commented 5 years ago

You may try the followings: git clone https://github.com/IMB-Computational-Genomics-Lab/scGPS

then check in scGPS/src if any of the precompiled (e.g. those with .so and .o) files exist and delete them before recompiling

create a Makevars file in the scGPS/src with one line: PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

then with the scGPS as the R working directory, manually recompile scGPS in R using devtools to load and install functions devtools::document() update the NAMESPACE using the update_NAMESPACE.sh by sh update_NAMESPACE.sh

for window system, to update the NAMESPACE: copy and paste the content of the file NAMESPACE_toAdd_cpp_links to end of the file NAMESPACE

load the package to the workspace

devtools::load_all()