nolanlab/citrus

Can not install Rclusterpp

Opened this issue · 4 comments

msuffiot commented

Dear all,

I tried to install

install_github("nolanlab/Rclusterpp")
and get:
`Downloading GitHub repo nolanlab/Rclusterpp@master
from URL https://api.github.com/repos/nolanlab/Rclusterpp/zipball/master
Installing Rclusterpp
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/nn/kbdbvshj2ms0jq1dw58lthqwpp9dng/T/RtmprDw0OI/devtools49a8744c437e/nolanlab-Rclusterpp-740cb0b'
--library='/Users/msuffiot/Library/R/3.5/library' --install-tests

  • installing source package ‘Rclusterpp’ ...
    ** libs
    clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/msuffiot/Library/R/3.5/library/Rcpp/include" -I"/Users/msuffiot/Library/R/3.5/library/RcppEigen/include" -I/usr/local/include -I../inst/include -fopenmp -fPIC -Wall -g -O2 -c hclust.cpp -o hclust.o
    clang: error: unsupported option '-fopenmp'
    make: *** [hclust.o] Error 1
    ERROR: compilation failed for package ‘Rclusterpp’
  • removing ‘/Users/msuffiot/Library/R/3.5/library/Rclusterpp’
    Installation failed: Command failed (1)`

This is my sessionInfo():

`R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] brew_1.0-6 shiny_1.1.0 samr_2.0
[4] matrixStats_0.53.1 impute_1.54.0 flowCore_1.46.1
[7] BiocInstaller_1.30.0 ggplot2_2.2.1 pamr_1.55
[10] survival_2.41-3 cluster_2.0.7-1 glmnet_2.0-16
[13] foreach_1.4.4 Matrix_1.2-14 devtools_1.13.5

loaded via a namespace (and not attached):
[1] pcaPP_1.9-73 Rcpp_0.12.17 later_0.7.3
[4] DEoptimR_1.0-8 compiler_3.5.0 pillar_1.2.3
[7] git2r_0.21.0 plyr_1.8.4 iterators_1.0.9
[10] tools_3.5.0 digest_0.6.15 jsonlite_1.5
[13] memoise_1.1.0 tibble_1.4.2 gtable_0.2.0
[16] lattice_0.20-35 rlang_0.2.1 graph_1.58.0
[19] curl_3.2 parallel_3.5.0 mvtnorm_1.0-8
[22] withr_2.1.2 httr_1.3.1 stats4_3.5.0
[25] grid_3.5.0 robustbase_0.93-0 Biobase_2.40.0
[28] rrcov_1.4-4 R6_2.2.2 tcltk_3.5.0
[31] magrittr_1.5 corpcor_1.6.9 promises_1.0.1
[34] htmltools_0.3.6 scales_0.5.0 codetools_0.2-15
[37] splines_3.5.0 BiocGenerics_0.26.0 xtable_1.8-2
[40] mime_0.5 colorspace_1.3-2 httpuv_1.4.3
[43] lazyeval_0.2.1 munsell_0.5.0 `

Could someone help me please?
Thank you very much in advance.

best,
Madeleine

DenisSch commented

Similar problem here

Installing package into ‘/Users/denis/Library/R/3.5/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘Rclusterpp’ ...
** libs
/opt/local/bin/g++-mp-4.8 -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/denis/Library/R/3.5/library/Rcpp/include" -I"/Users/denis/Library/R/3.5/library/RcppEigen/include" -I/usr/local/include  -I../inst/include -fopenmp -fPIC  -Wall -g -O2  -c hclust.cpp -o hclust.o
In file included from /opt/local/include/gcc48/c++/bits/postypes.h:40:0,
                 from /opt/local/include/gcc48/c++/bits/char_traits.h:40,
                 from /opt/local/include/gcc48/c++/string:40,
                 from /opt/local/include/gcc48/c++/stdexcept:39,
                 from hclust.cpp:1:
/opt/local/include/gcc48/c++/cwchar:44:19: fatal error: wchar.h: No such file or directory
 #include <wchar.h>
                   ^
compilation terminated.
make: *** [hclust.o] Error 1
ERROR: compilation failed for package ‘Rclusterpp’
* removing ‘/Users/denis/Library/R/3.5/library/Rclusterpp’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/var/folders/t0/mdwkshy515dfbqj16t30h9v00000gr/T//RtmpzMvqCK/file382f1723add/Rclusterpp_0.2.4.tar.gz’ had non-zero exit status
SamGG commented

Hi, I don't have a Mac. I will only point a few clues:

Best.

DenisSch commented

I have big troubles installing citrus also on Windows. Do I need to use R version 3.0?

SamGG commented

I am working on with R3.5.1 which is very stable. I can't image myself working with R < 3.0. My advice is to update R, Rtools and Bioconductor.