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decomverse / ACTIONet

ACTIONet single-cell analysis framework
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Can't install anymore #35

Open f6v opened 1 year ago

f6v commented 1 year ago

Hi,

I can't install the package anymore. I tried building a docker image from the Dockerfile you have in the repository. Here's part of the log:

 building ‘ACTIONetExperiment_1.0.2.tar.gz’

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘ACTIONetExperiment’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -
fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-libra
ry/RcppArmadillo/include' -I/usr/local/include  `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m
64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -
Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -
fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-libra
ry/RcppArmadillo/include' -I/usr/local/include  `find ../inst/include -type d -print | sed s/^/-I/` -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m
64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -
Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RCpp_util.cpp -o RCpp_util.o
g++ -std=gnu++14 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o ACTIONetExperiment.so RcppExports.o RCpp_util.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-ACTIONetExperiment/00new/ACTIONetExperiment/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ACTIONetExperiment)
Downloading GitHub repo shmohammadi86/ACTIONet@R-release
'/usr/bin/git' clone --depth 1 --no-hardlinks --recurse-submodules --branch core https://github.com/shmohammadi86/ACTIONet.git /tmp/Rtmphc8IaJ/remotes25d77cd02
/shmohammadi86-ACTIONet-a14d783/src/ACTIONet
Cloning into '/tmp/Rtmphc8IaJ/remotes25d77cd02/shmohammadi86-ACTIONet-a14d783/src/ACTIONet'...
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmphc8IaJ/remotes25d77cd02/shmohammadi86-ACTIONet-a14d783/DESCRIPTION’ ... OK
* preparing ‘ACTIONet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘ACTIONet_3.0.1.tar.gz’

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘ACTIONet’ ...
** using staged installation
** libs
Using Linux configurations
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanAlgorithm.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanAlgorithm.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/ManhattanDistance.cc -o ACTIONet/src/misc/HDBSCAN/ManhattanDistance.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanConstraint.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanConstraint.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/outlierScore.cc -o ACTIONet/src/misc/HDBSCAN/outlierScore.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/undirectedGraph.cc -o ACTIONet/src/misc/HDBSCAN/undirectedGraph.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/cluster.cc -o ACTIONet/src/misc/HDBSCAN/cluster.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscan.cc -o ACTIONet/src/misc/HDBSCAN/hdbscan.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/bitSet.cc -o ACTIONet/src/misc/HDBSCAN/bitSet.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanRunner.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanRunner.o
In file included from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/arma/armadillo_bits/Mat_meat.hpp:9921,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/arma/armadillo:616,
                 from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:56,
                 from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/clustering/HDBSCAN/hdbscan.hpp:2,
                 from ACTIONet/src/misc/HDBSCAN/hdbscan.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h: In constructor ‘arma::Mat<eT>::Mat(const Rcpp::VectorBase<RTYPE, NA, VEC
TOR>&)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h:104:11: error: class ‘arma::Mat<eT>’ does not have any field named ‘n_all
oc’
  104 |         , n_alloc(0)
      |           ^~~~~~~
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h: In constructor ‘arma::Mat<eT>::Mat(const Rcpp::MatrixBase<RTYPE, NA, VEC
TOR>&)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h:124:11: error: class ‘arma::Mat<eT>’ does not have any field named ‘n_all
oc’
  124 |         , n_alloc(0)
      |           ^~~~~~~
In file included from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/clustering/HDBSCAN/hdbscan.hpp:2,
                 from ACTIONet/src/misc/HDBSCAN/hdbscan.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h: At global scope:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:67:51: error: ‘subview_cols’ in namespace ‘arma’ does not na
me a template type; did you mean ‘subview_col’?
   67 |     template <typename T> SEXP wrap ( const arma::subview_cols<T>& ) ;
      |                                                   ^~~~~~~~~~~~
      |                                                   subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:67:63: error: expected ‘,’ or ‘...’ before ‘<’ token
   67 |     template <typename T> SEXP wrap ( const arma::subview_cols<T>& ) ;
      |                                                               ^
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanParameters.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanParameters.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/EuclideanDistance.cc -o ACTIONet/src/misc/HDBSCAN/EuclideanDistance.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/hdbscanResult.cc -o ACTIONet/src/misc/HDBSCAN/hdbscanResult.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/HDBSCAN/IDistanceCalculator.cc -o ACTIONet/src/misc/HDBSCAN/IDistanceCalculator.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I.
./inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -m64 -fno-strict-aliasing -fomit-frame-pointer -funroll-loops -I/usr/include/suitesparse -I'/usr/l
ocal/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include  `find /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/AC
TIONet/src/ACTIONet/include -type d -print | sed s/^/-I/` -I../inst/include -w -m64 -DINT_64BITS -DARMA_64BIT_WORD -O3 -w -std=c++14 -m64 -fno-strict-aliasing 
-fomit-frame-pointer -funroll-loops -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ACTIONet/src
/misc/my_utils.cc -o ACTIONet/src/misc/my_utils.o
In file included from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:35,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/clustering/HDBSCAN/hdbscan.hpp:2,
                 from ACTIONet/src/misc/HDBSCAN/hdbscan.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:57:45: error: ‘subview_cols’ in namespace ‘arma’ does not name 
a template type; did you mean ‘subview_col’?
   57 |         SEXP arma_subview_wrap( const arma::subview_cols<T>& data, int nrows, int ncols ){
      |                                             ^~~~~~~~~~~~
      |                                             subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:57:57: error: expected ‘,’ or ‘...’ before ‘<’ token
   57 |         SEXP arma_subview_wrap( const arma::subview_cols<T>& data, int nrows, int ncols ){
      |                                                         ^
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: In function ‘SEXPREC* Rcpp::RcppArmadillo::arma_subview_wrap(i
nt)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:59:38: error: ‘nrows’ was not declared in this scope; did you m
ean ‘row’?
   59 |             Rcpp::Matrix<RTYPE> mat( nrows, ncols ) ;
      |                                      ^~~~~
      |                                      row
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:59:45: error: ‘ncols’ was not declared in this scope; did you m
ean ‘cos’?
   59 |             Rcpp::Matrix<RTYPE> mat( nrows, ncols ) ;
      |                                             ^~~~~
      |                                             cos
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:61:31: error: ‘data’ was not declared in this scope
   61 |             const T* svcmem = data.colptr(0);
      |                               ^~~~
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: At global scope:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:99:50: error: ‘subview_cols’ in namespace ‘arma’ does not name 
a template type; did you mean ‘subview_col’?
   99 |     template <typename T> SEXP wrap( const arma::subview_cols<T>& data ){
      |                                                  ^~~~~~~~~~~~
      |                                                  subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:99:62: error: expected ‘,’ or ‘...’ before ‘<’ token
   99 |     template <typename T> SEXP wrap( const arma::subview_cols<T>& data ){
      |                                                              ^
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: In function ‘SEXPREC* Rcpp::wrap(int)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:100:53: error: ‘data’ was not declared in this scope
  100 |         return RcppArmadillo::arma_subview_wrap<T>( data, data.n_rows, data.n_cols ) ;
      |                                                     ^~~~
make: *** [/usr/local/lib/R/etc/Makeconf:176: ACTIONet/src/misc/HDBSCAN/hdbscan.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/arma/armadillo_bits/Mat_meat.hpp:9921,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/arma/armadillo:616,
                 from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:56,
                 from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/misc/my_utils.h:4,
                 from ACTIONet/src/misc/my_utils.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h: In constructor ‘arma::Mat<eT>::Mat(const Rcpp::VectorBase<RTYPE, NA, VEC
TOR>&)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h:104:11: error: class ‘arma::Mat<eT>’ does not have any field named ‘n_all
oc’
  104 |         , n_alloc(0)
      |           ^~~~~~~
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h: In constructor ‘arma::Mat<eT>::Mat(const Rcpp::MatrixBase<RTYPE, NA, VEC
TOR>&)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/internal/Mat_meat.h:124:11: error: class ‘arma::Mat<eT>’ does not have any field named ‘n_all
oc’
  124 |         , n_alloc(0)
      |           ^~~~~~~
In file included from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/misc/my_utils.h:4,
                 from ACTIONet/src/misc/my_utils.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h: At global scope:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:67:51: error: ‘subview_cols’ in namespace ‘arma’ does not na
me a template type; did you mean ‘subview_col’?
   67 |     template <typename T> SEXP wrap ( const arma::subview_cols<T>& ) ;
      |                                                   ^~~~~~~~~~~~
      |                                                   subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:67:63: error: expected ‘,’ or ‘...’ before ‘<’ token
   67 |     template <typename T> SEXP wrap ( const arma::subview_cols<T>& ) ;
      |                                                               ^
In file included from /usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo.h:35,
                 from ../inst/include/ACTIONet.h:13,
                 from /tmp/RtmpVmxLbv/R.INSTALLfc8fb1874/ACTIONet/src/ACTIONet/include/misc/my_utils.h:4,
                 from ACTIONet/src/misc/my_utils.cc:1:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:57:45: error: ‘subview_cols’ in namespace ‘arma’ does not name 
a template type; did you mean ‘subview_col’?
   57 |         SEXP arma_subview_wrap( const arma::subview_cols<T>& data, int nrows, int ncols ){
      |                                             ^~~~~~~~~~~~
      |                                             subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:57:57: error: expected ‘,’ or ‘...’ before ‘<’ token
   57 |         SEXP arma_subview_wrap( const arma::subview_cols<T>& data, int nrows, int ncols ){
      |                                                         ^
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: In function ‘SEXPREC* Rcpp::RcppArmadillo::arma_subview_wrap(i
nt)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:59:38: error: ‘nrows’ was not declared in this scope; did you m
ean ‘row’?
   59 |             Rcpp::Matrix<RTYPE> mat( nrows, ncols ) ;
      |                                      ^~~~~
      |                                      row
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:59:45: error: ‘ncols’ was not declared in this scope; did you m
ean ‘cos’?
   59 |             Rcpp::Matrix<RTYPE> mat( nrows, ncols ) ;
      |                                             ^~~~~
      |                                             cos
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:61:31: error: ‘data’ was not declared in this scope
   61 |             const T* svcmem = data.colptr(0);
      |                               ^~~~
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: At global scope:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:99:50: error: ‘subview_cols’ in namespace ‘arma’ does not name 
a template type; did you mean ‘subview_col’?
   99 |     template <typename T> SEXP wrap( const arma::subview_cols<T>& data ){
      |                                                  ^~~~~~~~~~~~
      |                                                  subview_col
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:99:62: error: expected ‘,’ or ‘...’ before ‘<’ token
   99 |     template <typename T> SEXP wrap( const arma::subview_cols<T>& data ){
      |                                                              ^
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h: In function ‘SEXPREC* Rcpp::wrap(int)’:
/usr/local/lib/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloWrap.h:100:53: error: ‘data’ was not declared in this scope
  100 |         return RcppArmadillo::arma_subview_wrap<T>( data, data.n_rows, data.n_cols ) ;
      |                                                     ^~~~
make: *** [/usr/local/lib/R/etc/Makeconf:176: ACTIONet/src/misc/my_utils.o] Error 1
ERROR: compilation failed for package ‘ACTIONet’
* removing ‘/usr/local/lib/R/site-library/ACTIONet’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmphc8IaJ/file229c8f86b/ACTIONet_3.0.1.tar.gz’ had non-zero exit status
--> 8bdc1fca966
STEP 8/8: CMD ["/init"]
COMMIT actionnet_minidocker
--> b2ac55511a4
Successfully tagged localhost/actionnet_minidocker:latest
ekokrek commented 1 year ago

I have almost the same error and installation failure when trying to install with

devtools::install_github("shmohammadi86/ACTIONet", ref = "R-devel")

joonlee3 commented 1 year ago

Me too. I ran devtools::install_github("shmohammadi86/ACTIONet", ref = "R-devel") but failed to install ACTIONet.

ninakhera commented 1 year ago

I had the exact same issue!

shmohammadi86 commented 1 year ago

Hi everyone and sorry for the late reply. RcppArmadillo had a major update recently that we needed to incorporate with our codebase. It has been done last night, but we are still testing it to make sure everything is still working with the new package. Technically, the package should install at the very least now. Thank you all for the issue report.

biotein1 commented 1 year ago

Thank you! I am trying to install it now, but I am still getting the same error.. I'm using the command 'install_github("shmohammadi86/ACTIONet", ref = "R-devel")'. Should I just use the past RcppArmadillo version?

On Sun, Dec 18, 2022 at 7:27 AM Shahin Mohammadi @.***> wrote:

Hi everyone and sorry for the late reply. RcppArmadillo had a major update recently that we needed to incorporate with our codebase. It has been done last night, but we are still testing it to make sure everything is still working with the new package. Technically, the package should install at the very least now. Thank you all for the issue report.

— Reply to this email directly, view it on GitHub https://github.com/shmohammadi86/ACTIONet/issues/35#issuecomment-1356787814, or unsubscribe https://github.com/notifications/unsubscribe-auth/AL72FVIDQLH6M4T2DV7DGE3WN37LZANCNFSM6AAAAAASOWONYE . You are receiving this because you commented.Message ID: @.***>

-- Thank you, Nina Khera Grade 12 Student at BB&N Co-founder of Biotein https://ninakhera.com

shmohammadi86 commented 1 year ago

There was a minor issue in the code that was introduced last night (independent of RcppArmadillo). That is fixed now and it installs properly on both my Mac and Linux machines. Please let us know if you still have problems and post the updates.

On Sun, Dec 18, 2022 at 1:34 PM Shahin Mohammadi @.***> wrote:

It works with the old version, but we should be able to fix it to work with new version too. Which RcppArmadillo version are you using?

On Sun, Dec 18, 2022, 1:30 PM biotein1 @.***> wrote:

Thank you! I am trying to install it now, but I am still getting the same error.. I'm using the command 'install_github("shmohammadi86/ACTIONet", ref = "R-devel")'. Should I just use the past RcppArmadillo version?

On Sun, Dec 18, 2022 at 7:27 AM Shahin Mohammadi @.***> wrote:

Hi everyone and sorry for the late reply. RcppArmadillo had a major update recently that we needed to incorporate with our codebase. It has been done last night, but we are still testing it to make sure everything is still working with the new package. Technically, the package should install at the very least now. Thank you all for the issue report.

— Reply to this email directly, view it on GitHub < https://github.com/shmohammadi86/ACTIONet/issues/35#issuecomment-1356787814 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AL72FVIDQLH6M4T2DV7DGE3WN37LZANCNFSM6AAAAAASOWONYE

. You are receiving this because you commented.Message ID: @.***>

-- Thank you, Nina Khera Grade 12 Student at BB&N Co-founder of Biotein https://ninakhera.com

— Reply to this email directly, view it on GitHub https://github.com/shmohammadi86/ACTIONet/issues/35#issuecomment-1356788337, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABYB6H6IXKQMRBC5IUVDBOLWN37X7ANCNFSM6AAAAAASOWONYE . You are receiving this because you commented.Message ID: @.***>

ninakhera commented 1 year ago

Thanks! I'm getting an odd issue with the following code in my R client though. I'm not sure if this is related to RcppArmadillo!

ACTIONet/src/misc/cholmod_wrappers.cc:2:10: fatal error: 'cholmod.h' file not found
#include <cholmod.h>
         ^~~~~~~~~~~
1 error generated.
shmohammadi86 commented 1 year ago

You need to install the suitesparse package.

On Sun, Dec 18, 2022, 3:03 PM ninakhera @.***> wrote:

Thanks! I'm getting an odd issue with the following code in my R client though.

ACTIONet/src/misc/cholmod_wrappers.cc:2:10: fatal error: 'cholmod.h' file not found

include 

     ^~~~~~~~~~~

1 error generated.

— Reply to this email directly, view it on GitHub https://github.com/shmohammadi86/ACTIONet/issues/35#issuecomment-1356805881, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABYB6HZXVVTQIVVWVGWV3U3WN4KRHANCNFSM6AAAAAASOWONYE . You are receiving this because you commented.Message ID: @.***>

yuweisong-uab commented 1 year ago

Is this problem solved? i'm still not able to install the package.

samvidk commented 4 months ago

Is this problem solved? i'm still not able to install the package.

I am having trouble installing ACTIOnet as well - getting the cholmod.h error even after installing suitesparse