Failed Installation of fastRPCA

[TJCooperIL]

I'm trying to install fastRPCA (for use with SeuratWrappers) but i'm encountering errors:

Package KlugerLab/rpca-mkl/fastRPCA is not yet installed
Install now?

1: yes
2: no

Selection: yes
Downloading GitHub repo KlugerLab/rpca-mkl@master
✓  checking for file ‘/tmp/RtmpLWpzW2/remotes39cf56b0e209e/KlugerLab-rpca-mkl-4eb4e22/fastRPCA/DESCRIPTION’ ...
─  preparing ‘fastRPCA’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to process help pages
         -----------------------------------
─  installing *source* package ‘fastRPCA’ ...
   ** using staged installation
   ** libs
   g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tjcooper/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Do_dS_/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
   g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fastRPCA.so RcppExports.o -L../inst/libs/ -Wl,-rpath,/tmp/RtmpVYp8ep/Rinst3bb172366e8f4/00LOCK-fastRPCA/00new/fastRPCA/libs -lfastpca -L/usr/lib/R/lib -lR
   installing via 'install.libs.R' to /tmp/RtmpVYp8ep/Rinst3bb172366e8f4/00LOCK-fastRPCA/00new/fastRPCA
   ** R
   ** inst
   ** byte-compile and prepare package for lazy loading
   ** help
   *** installing help indices
   ** building package indices
   ** testing if installed package can be loaded from temporary location
   Error: package or namespace load failed for ‘fastRPCA’ in dyn.load(file, DLLpath = DLLpath, ...):
    unable to load shared object '/tmp/RtmpVYp8ep/Rinst3bb172366e8f4/00LOCK-fastRPCA/00new/fastRPCA/libs/fastRPCA.so':
     libfastpca_custommkl.so: cannot open shared object file: No such file or directory
   Error: loading failed
   Execution halted
   ERROR: loading failed
─  removing ‘/tmp/RtmpVYp8ep/Rinst3bb172366e8f4/fastRPCA’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'fastRPCA' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> ** testing if installed package can be loaded from temporary location
E> Error: package or namespace load failed for ‘fastRPCA’ in dyn.load(file, DLLpath = DLLpath, ...):
E>  unable to load shared object '/tmp/RtmpVYp8ep/Rinst3bb172366e8f4/00LOCK-fastRPCA/00new/fastRPCA/libs/fastRPCA.so':
E>   libfastpca_custommkl.so: cannot open shared object file: No such file or directory
E> Error: loading failed
E> Execution halted
E> ERROR: loading failed
E> * removing ‘/tmp/RtmpVYp8ep/Rinst3bb172366e8f4/fastRPCA’
E>       -----------------------------------
E> ERROR: package installation failed

How can I fix this?

[TJCooperIL]

OS: Ubuntu 20.04
R: 4.0.0
SeuratWrappers: 0.1.0

[TJCooperIL]

Let me know if you need any further information. Could really use a fix for this.

[linqiaozhi]

If I recall correctly, the "staged installation" that has become standard for newer versions of R cause trouble for fastRPCA. Can you try installing as per the instructions in the README of this repository? When I use that --no-staged-install flag it works for me on Ubuntu 16 and R 3.6.

[TJCooperIL]

Same error:

git clone https://github.com/KlugerLab/rpca-mkl
Cloning into 'rpca-mkl'...
remote: Enumerating objects: 225, done.
remote: Total 225 (delta 0), reused 0 (delta 0), pack-reused 225
Receiving objects: 100% (225/225), 13.69 MiB | 1.39 MiB/s, done.
Resolving deltas: 100% (101/101), done.
cd rpca-mkl
cd fastRPCA
R CMD INSTALL . --no-staged-install
* installing to library ‘/home/tjcooper/R/x86_64-pc-linux-gnu-library/4.0’
* installing *source* package ‘fastRPCA’ ...
** using non-staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/tjcooper/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Do_dS_/r-base-4.0.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fastRPCA.so RcppExports.o -L../inst/libs/ -Wl,-rpath,/home/tjcooper/R/x86_64-pc-linux-gnu-library/4.0/fastRPCA/libs -lfastpca -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /home/tjcooper/R/x86_64-pc-linux-gnu-library/4.0/fastRPCA
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘fastRPCA’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/tjcooper/R/x86_64-pc-linux-gnu-library/4.0/fastRPCA/libs/fastRPCA.so':
  libfastpca_custommkl.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed

[TJCooperIL]

It errors if using an ordinary, staged install too.

[kaizen89]

I have the same error