Install error

[kharchenkolab]

Install error

[gxg2002cn]

R3.5 works!
The problem shows up to me in R3.6.
Anyway, working in R3.5 now.

[gxg2002cn]

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

decompose, spectrum

The following object is masked from ‘package:base’:

union

g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conos.so RcppExports.o checkfunctions.o cpca.o deltacut.o edgeFilter.o edge_rebalancing.o edgeweights.o gradients.o graph_embedding.o largeVis.o leiden.o n2knn.o propagate_labels.o spColSum.o spcov.o -L/usr/lib/ -L. -lpthread -lstdc++ -ln2 -lleidenalg -lm -llapack -lblas -lgfortran -lm -lquadmath -fopenmp /home/niels/R/x86_64-pc-linux-gnu-library/3.6/igraph/libs/igraph.so -L/usr/lib/R/lib -lR

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

decompose, spectrum

The following object is masked from ‘package:base’:

union

installing to /home/niels/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-conos/00new/conos/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘getPca’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getPca’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getOverdispersedGenes’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getOverdispersedGenes’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getCellNames’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getCellNames’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getGenes’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getGenes’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘edgeMat<-’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘edgeMat<-’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘edgeMat’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘edgeMat’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getCountMatrix’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getCountMatrix’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getRawCountMatrix’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getRawCountMatrix’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getEmbedding’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getEmbedding’ with signature ‘"seurat"’: no definition for class “seurat”
in method for ‘getClustering’ with signature ‘"Pagoda2"’: no definition for class “Pagoda2”
in method for ‘getClustering’ with signature ‘"seurat"’: no definition for class “seurat”
Note: wrong number of arguments to '*'
Note: wrong number of arguments to 'exp'
** help
Error : (converted from warning) /tmp/RtmpthJJoM/R.INSTALL11ed7d25582c/conos/man/getClusterPrivacy.Rd:6: unexpected section header '\usage'
ERROR: installing Rd objects failed for package ‘conos’

• removing ‘/home/niels/R/x86_64-pc-linux-gnu-library/3.6/conos’
  Error in i.p(...) :
  (converted from warning) installation of package ‘/tmp/Rtmp2TOrID/filebe57e70ca57/conos_1.0.1.tar.gz’ had non-zero exit status

[VPetukhov]

Interesting. Thanks for sharing solution!