Closed Giu1ia closed 3 years ago
prisilveira
commented
4 years ago [windows] I've also tried to install from both CRAN and github... followed the step-by-step on the page and R (v 3.5.1, 4.0.1, 3.6.3) hasn't been able to install the package.
dpasqualin
commented
4 years ago Hi, sorry it took so long to answer. I haven't updated CRAN with recent changes in the package, so I'd suggest using the source on github from now. @Giu1ia , unfortunately I don't have OSX and don't know any one who has it, also the message given by R is not so clear on what steps to do so at this point I don't know how to help you :(
@prisilveira I recently made an update to fix installation issues on Windows. Could you please provide the error message you are receiving? I'll try to fix as soon as possible.
prisilveira
commented
4 years ago pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.[v. 3.6.1] & [v.3.6.3] I noticed there is also a problem with the package‘mnormt’ I've tried many different R version and the Error message I get is below:
Downloading GitHub repo dpasqualin/sfreemap@master Skipping 1 packages not available: mnormt Installing 36 packages: RcppArmadillo, ape, phytools, reshape2, ggplot2, phangorn, seqinr, magick, quadprog, igraph, fastmatch, farver, labeling, munsell, RColorBrewer, viridisLite, colorspace, pixmap, sp, maps, animation, clusterGeneration, coda, combinat, expm, gtools, mnormt, numDeriv, plotrix, scatterplot3d, plyr, gtable, isoband, scales, ade4, segmented Installing packages into ‘C:/Users/piken/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) Error: Failed to install 'sfreemap' from GitHub: (converted from warning) package ‘mnormt’ is not available (for R version 3.6.1)
| >
dpasqualin
commented
3 years ago @prisilveira , I just installed sfreemap on windows using rtools 3.5 and R 3.6.2. Also worked with R 4.0.3 and Rtools 4.0. I used Rstudio to install it, but I don't think it is necessary. Only the commands below were necessary in both cases:
install.packages('devtools')
require(devtools)
install_github('dpasqualin/sfreemap')I guess you just need to make sure you have the Rtools version installed compatible with R.
dpasqualin
commented
3 years ago @sam217pa , you managed to install sfreemap on OSX, did you have the same problem as @Giu1ia ? Would you know how to solve it? I don't have OSX so I can't reproduce the error. Thank you very much.
sam217pa
commented
3 years ago @dpasqualin I did not have any problem installing; I use clang from the latest LLVM however, installed with homebrew;
here is the content of my ~/.R/Makevars:
# -*- conf -*-
LLVM_LOC=/usr/local/opt/llvm
CC=$(LLVM_LOC)/bin/clang #-fopenmp
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXX=$(LLVM_LOC)/bin/clang++ -fopenmp
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/libAnd here is the output of R CMD INSTALL sfreemap:
✦ ❯ R CMD INSTALL sfreemap_1.1.tar.gz
* installing to library '/Users/samuelbarreto/.local/share/R'
* installing *source* package 'sfreemap' ...
** using staged installation
** libs
/usr/local/opt/llvm/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/samuelbarreto/.local/share/R/Rcpp/include" -I"/Users/samuelbarreto/.local/share/R/RcppArmadillo/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fopenmp -fPIC -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c RcppExports.cpp -o RcppExports.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/samuelbarreto/.local/share/R/Rcpp/include" -I"/Users/samuelbarreto/.local/share/R/RcppArmadillo/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fopenmp -fPIC -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c sfreemap.cpp -o sfreemap.o
sfreemap.cpp:46:9: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
if (fabsf(diff) < TOL) {
^
sfreemap.cpp:46:9: note: use function 'std::abs' instead
if (fabsf(diff) < TOL) {
^~~~~
std::abs
1 warning generated.
/usr/local/opt/llvm/bin/clang++ -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o sfreemap.so RcppExports.o sfreemap.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/samuelbarreto/.local/share/R/00LOCK-sfreemap/00new/sfreemap/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (sfreemap)To me it looks like a clang version related problem, but I can't be sure.
dpasqualin
commented
3 years ago Thank you very much again @sam217pa . As I could install sfreemap on windows and it works on osx too I'm closing this issue.
Hi, I am trying to install sfreemap on a OS 10.13.6, R 3.6.3, from GitHub but I got this error:
I tried also to install it from CRAN, but the response is that "package ‘sfreemap’ is not available (for R version 3.6.3)". I tried with earlier versions (3.1 and 3.3) same error.
Do you have any solution to bypass these errors?
Thanks