installation error

[tamerbio]

Hi There,
I am trying to install shaman on macOS monterey using:

devtools::install_github('tanaylab/shaman', 
                            vignette = TRUE, 
                            repos=c(getOption('repos'), 'https://tanaylab.bitbucket.io/repo'))

but getting this error:

Downloading GitHub repo tanaylab/shaman@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/tanaylab/shaman/tarball/HEAD' failed
Error in `action()`:
! `class` is absent but must be supplied.
Run `rlang::last_error()` to see where the error occurred.

then i tried:
install.packages("http://www.wisdom.weizmann.ac.il/~nettam/shaman/shaman_2.0.tar.gz", , repos=NULL)
and getting this error:

trying URL 'http://www.wisdom.weizmann.ac.il/~nettam/shaman/shaman_2.0.tar.gz'
Content type 'application/x-gzip' length 213509957 bytes (203.6 MB)
===========
downloaded 46.1 MB

Warning in install.packages :
  downloaded length 48313856 != reported length 213509957
Warning in install.packages :
  URL 'https://www.wisdom.weizmann.ac.il/~nettam/shaman/shaman_2.0.tar.gz': Timeout of 60 seconds was reached
Error in download.file(p, destfile, method, mode = "wb", ...) : 
  download from 'http://www.wisdom.weizmann.ac.il/~nettam/shaman/shaman_2.0.tar.gz' failed

in addition, i tried also:
devtools::install_local("~/Desktop/shaman-master.zip")
but again getting this error:

* installing *source* package ‘shaman’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ContactShuffler.cpp -o ContactShuffler.o
ContactShuffler.cpp:34:4: warning: field 'm_decay_smooth' will be initialized after field 'm_regularization' [-Wreorder-ctor]
   m_decay_smooth(decay_smooth),
   ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c GenomeGridLog.cpp -o GenomeGridLog.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Parser.cpp -o Parser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Random.cpp -o Random.o
In file included from Random.cpp:1:
./Random.h:17:16: error: unknown type name 'uint'; did you mean 'int'?
        static uint bits_data;
               ^~~~
               int
./Random.h:22:16: error: unknown type name 'uint'; did you mean 'int'?
        static uint bits();
               ^~~~
               int
./Random.h:23:16: error: unknown type name 'uint'; did you mean 'int'?
        static uint bits(int num);
               ^~~~
               int
./Random.h:32:8: error: unknown type name 'uint'; did you mean 'int'?
inline uint Random::bits() {
       ^~~~
       int
./Random.h:33:9: error: use of undeclared identifier 'uint'; did you mean 'int'?
        uint raw = mrand48();
        ^~~~
        int
Random.cpp:5:14: error: redefinition of 'bits_data' with a different type: 'uint' (aka 'unsigned int') vs 'int'
uint Random::bits_data = 0;
             ^
./Random.h:17:21: note: previous declaration is here
        static uint bits_data;
                    ^
Random.cpp:88:14: error: return type of out-of-line definition of 'Random::bits' differs from that in the declaration
uint Random::bits(int num) {
~~~~         ^
./Random.h:23:21: note: previous declaration is here
        static uint bits(int num);
               ~~~~ ^
7 errors generated.
make: *** [Random.o] Error 1
ERROR: compilation failed for package ‘shaman’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/shaman’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/tz/vb7vv98d2_bfq_t4zbrypvl40000gn/T//Rtmp9N4v2a/remotes13843b12eafb/shaman-master’ had non-zero exit status

any help!
thx

[aviezerl]

Hi @tamerbio

Indeed the installation instructions pointed to the old bitbucket repository, it was changed now. Could you try running:

devtools::install_github('tanaylab/shaman')

And see if the problem persists?

The compilation problem is related to headers on MAC. If the you still get the error - could you try running:

xcode-select --install

And then re-install?

Aviezer

[tamerbio]

Hi @aviezerl
I did already, still the same error!

> devtools::install_github('tanaylab/shaman')
Downloading GitHub repo tanaylab/shaman@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/tanaylab/shaman/tarball/HEAD' failed