Installation failed: Timeout was reached

[ankhnesmerira]

Trying to install the Laurae2/sparsity package so i can convert from sparse matrix to SVMLight. however, i keep getting this error message Installation failed: Timeout was reached.
I am behind no proxy, and have all dependent packages installed.
I've also tweaked around with options(download.file.method = "") with various methods but to no avail. Searched the web, tried everything and still no success. Is the package still available for download and installation? I'm using R version:

platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 4.0
year 2017
month 04
day 21
svn rev 72570
language R
version.string R version 3.4.0 (2017-04-21)
nickname You Stupid Darkness

[Laurae2]

@ankhnesmerira Try install_git instead of install_github.

[ankhnesmerira]

Now I'm getting this error:
Downloading git repo Laurae2/sparsity
Installation failed: Error in 'git2r_clone': Unsupported URL protocol

thanks for your help.

[Laurae2]

You can download the repository and install locally if your OS does not support install_git from GitHub.

[ankhnesmerira]

Sure. Do I need the three following files in R folder of sparsity depository for installation:
sparsity-io.R
liblinear.r
RcppExports.R

Sorry, I've never done this before and my skills in R are a bit rudimentary

[Laurae2]

Use

setwd(<your R package directory>)
devtools::install()

[ankhnesmerira]

I apologise for pestering but this hasn't been working for me. I downloaded all files and folders in sparsity, and copied them to a folder called sparsity in the libraries folder of my R installation (Windows 7 x64 ).
The sparsity folder on my computer has five folders (inst, man, R, src, tests --> each with files in the folders) and four files (DESCRIPTION, gitignore, NAMESPACE, README.md)

Then I did:
setwd('C:\Program Files\R\R-3.4.0\library\sparsity')
devtools::install()

but i get the following error message:
Error in read.dcf(path_desc) :
Line starting ' ...' is malformed!

I'm using latest version of R (R-3.4.0)

[Laurae2]

supposing you have download the .zip from GitHub of Laurae2/sparsity and extracted it into C:\sparsity such as the folders are like this:

-- C:/
------ sparsity/
----------------- R/
----------------- inst/
----------------- man/
...

Then in R, do that:

setwd("C:/sparsity")
devtools::install()

[ankhnesmerira]

I think I've never been closer to installing this sparsity package! :-D
I installed the latest version of RTools and it actually started installing using the zip file. But at the very end it failed giving me this long message:

> devtools::install()

> Installing sparsity
> "C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
>   "C:/Users/User/Downloads/sparsity-master/sparsity-master" --library="C:/Program Files/R/R-3.4.0/library" --install-tests 
> 
> * installing *source* package 'sparsity' ...
> ** libs
> c:/Rtools/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG  -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"C:/Program Files/R/R-3.4.0/library/RcppEigen/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
> c:/Rtools/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG  -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"C:/Program Files/R/R-3.4.0/library/RcppEigen/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c readSvmLight.cpp -o readSvmLight.o
> readSvmLight.cpp: In function 'Rcpp::List readSvmLight(std::string)':
> readSvmLight.cpp:23:58: warning: typedef 'SpRMat' locally defined but not used [-Wunused-local-typedefs]
>      typedef Eigen::SparseMatrix<double, Eigen::RowMajor> SpRMat;
>                                                           ^
> c:/Rtools/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG  -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"C:/Program Files/R/R-3.4.0/library/RcppEigen/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c writeSvmLight.cpp -o writeSvmLight.o
> In file included from C:/Program Files/R/R-3.4.0/library/Rcpp/include/RcppCommon.h:179:0,
>                  from C:/Program Files/R/R-3.4.0/library/RcppEigen/include/RcppEigenForward.h:26,
>                  from C:/Program Files/R/R-3.4.0/library/RcppEigen/include/RcppEigen.h:25,
>                  from writeSvmLight.cpp:2:
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h: In instantiation of 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown_iterable(const T&, Rcpp::traits::false_type) [with T = long long int; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]':
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:732:98:   required from 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown(const T&, Rcpp::traits::false_type) [with T = long long int; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:770:96:   required from 'SEXPREC* Rcpp::internal::wrap_dispatch_eigen(const T&, Rcpp::traits::false_type) [with T = long long int; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:787:80:   required from 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown_importable(const T&, Rcpp::traits::false_type) [with T = long long int; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:807:99:   required from 'SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_unknown_tag) [with T = long long int; SEXP = SEXPREC*]'
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap_end.h:30:110:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/vector/Vector.h:529:44:   required from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>; Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >; SEXP = SEXPREC*; R_xlen_t = long long int]'
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/vector/Vector.h:522:110:   required from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage; Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>; Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >; SEXP = SEXPREC*; R_xlen_t = long long int]'
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/vector/Vector.h:512:56:   required from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >; SEXP = SEXPREC*; R_xlen_t = long long int]'
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/generated/Vector__create.h:139:40:   required from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T1&, const T2&) [with T1 = Rcpp::traits::named_object<std::basic_string<char> >; T2 = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage; Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>]'
> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/generated/Vector__create.h:112:21:   required from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&) [with T1 = Rcpp::traits::named_object<std::basic_string<char> >; T2 = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
> writeSvmLight.cpp:53:13:   required from here
**> C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:525:11: error: invalid conversion from 'long long int' to 'SEXP' [-fpermissive]
>   SEXP x = object ;
>            ^
> make: *** [writeSvmLight.o] Error 1
> Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-34~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-34~1.0/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="sparsity.dll" WIN=64 TCLBIN=64 OBJECTS="RcppExports.o readSvmLight.o writeSvmLight.o"' had status 2
> ERROR: compilation failed for package 'sparsity'
> * removing 'C:/Program Files/R/R-3.4.0/library/sparsity'
> Error: Command failed (1)**

[Laurae2]

@ankhnesmerira Try reinstalling Rcpp and RcppEigen, wipe your sparsity folder temporary files (or delete the folder and redownload it), and try installing again.

[ankhnesmerira]

no luck. i get the same error :(

well, actually, not sure if it's exactly the same, but it seems the same:

* installing *source* package 'sparsity' ...
** libs
c:/Rtools/mingw_64/bin/g++  -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG  -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"C:/Program Files/R/R-3.4.0/library/RcppEigen/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c writeSvmLight.cpp -o writeSvmLight.o
In file included from C:/Program Files/R/R-3.4.0/library/Rcpp/include/RcppCommon.h:179:0,
                 from C:/Program Files/R/R-3.4.0/library/RcppEigen/include/RcppEigenForward.h:26,
                 from C:/Program Files/R/R-3.4.0/library/RcppEigen/include/RcppEigen.h:25,
                 from writeSvmLight.cpp:2:
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h: In instantiation of 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown_iterable(const T&, Rcpp::traits::false_type) [with T = long long int; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]':
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:732:98:   required from 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown(const T&, Rcpp::traits::false_type) [with T = long long int; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:770:96:   required from 'SEXPREC* Rcpp::internal::wrap_dispatch_eigen(const T&, Rcpp::traits::false_type) [with T = long long int; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:787:80:   required from 'SEXPREC* Rcpp::internal::wrap_dispatch_unknown_importable(const T&, Rcpp::traits::false_type) [with T = long long int; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]'
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:807:99:   required from 'SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_unknown_tag) [with T = long long int; SEXP = SEXPREC*]'
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap_end.h:30:110:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/vector/Vector.h:529:44:   required from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>; Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >; SEXP = SEXPREC*; R_xlen_t = long long int]'
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/vector/Vector.h:522:110:   required from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage; Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>; Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >; SEXP = SEXPREC*; R_xlen_t = long long int]'
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/vector/Vector.h:512:56:   required from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(Rcpp::Vector<RTYPE, StoragePolicy>::iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYPE, StoragePolicy>::iterator = Rcpp::internal::Proxy_Iterator<Rcpp::internal::generic_proxy<19> >; SEXP = SEXPREC*; R_xlen_t = long long int]'
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/generated/Vector__create.h:139:40:   required from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T1&, const T2&) [with T1 = Rcpp::traits::named_object<std::basic_string<char> >; T2 = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage; Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>]'
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/generated/Vector__create.h:112:21:   required from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&) [with T1 = Rcpp::traits::named_object<std::basic_string<char> >; T2 = Rcpp::traits::named_object<long long int>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
writeSvmLight.cpp:53:13:   required from here
C:/Program Files/R/R-3.4.0/library/Rcpp/include/Rcpp/internal/wrap.h:525:11: error: invalid conversion from 'long long int' to 'SEXP' [-fpermissive]
  SEXP x = object ;
           ^
make: *** [writeSvmLight.o] Error 1
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-34~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-34~1.0/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="sparsity.dll" WIN=64 TCLBIN=64 OBJECTS="RcppExports.o readSvmLight.o writeSvmLight.o"' had status 2
ERROR: compilation failed for package 'sparsity'
* removing 'C:/Program Files/R/R-3.4.0/library/sparsity'
Error: Command failed (1)
>