Installation problems related to udunits2

akitepowell commented 7 years ago

Hi, In our Rstudio server pro (redhat linux) environment we can't seem to install ggforce or ggraph because of configuration failures for the udunits2 package. I realize you aren't the maintainer of udunits2, but was curious if you've heard this before and/or knew of some solution. I've been in touch with udunits2 maintainer, but haven't heard back from them.

ERROR: configuration failed for package ‘udunits2’

removing ‘/mnt/enc1/home/R/x86_64-redhat-linux-gnu-library/3.3/udunits2’ Warning in install.packages : installation of package ‘udunits2’ had non-zero exit status ERROR: dependency ‘udunits2’ is not available for package ‘units’
removing ‘/mnt/enc1/home/R/x86_64-redhat-linux-gnu-library/3.3/units’ Warning in install.packages : installation of package ‘units’ had non-zero exit status ERROR: dependency ‘units’ is not available for package ‘ggforce’
removing ‘/mnt/enc1/home/R/x86_64-redhat-linux-gnu-library/3.3/ggforce’ Warning in install.packages : installation of package ‘ggforce’ had non-zero exit status

Thankfully this doesn't appear to be a problem on local windows desktop installations, but it would be nice to have this working on Rstudio server pro too.

Thanks, Aaron

thomasp85 commented 7 years ago

In Linux you need the udunits2 library installed - check the travis script in ggforce for the correct command

akitepowell commented 7 years ago

Ok, thank you. The library for udunits2 is installed now, but we are still getting the errors in Rstudio. I've used the config args to try to get it to work, but to no avail as of yet. We'll troubleshoot more tomorrow. install.packages("ggforce", configure.args="--with-udunits2-lib=/usr/lib64--with-udunits2-include=/usr/including/udunits2")

Deleetdk commented 7 years ago

Installing ggforce fails on Windows 8.1 too. It seems there is a call to the udunits2 library without it being listed as a requirement and thus may not be installed. I installed udunits2 manually, but ggraph still fails with a weird error:

> devtools::install_github('thomasp85/ggraph')
Downloading GitHub repo thomasp85/ggraph@master
from URL https://api.github.com/repos/thomasp85/ggraph/zipball/master
Installing ggraph
"C:/PROGRA~1/R/R-3.3.2/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  "C:/Users/Emil/AppData/Local/Temp/Rtmp6ZxnXj/devtools20784fd71113/thomasp85-ggraph-777a81d"  \
  --library="C:/Users/Emil/Documents/R/win-library/3.3" --install-tests 

* installing *source* package 'ggraph' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-3.3.2/include" -DNDEBUG    -I"C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-3.3.2/include" -DNDEBUG    -I"C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c circlePack.cpp -o circlePack.o
circlePack.cpp: In function 'std::vector<NodePack*> createHierarchy(std::vector<int>, std::vector<double>)':
circlePack.cpp:378:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < parent.size(); ++i) {
                   ^
circlePack.cpp:382:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < parent.size(); ++i) {
                   ^
circlePack.cpp: In function 'int findTopNode(std::vector<NodePack*>&)':
circlePack.cpp:392:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < nodes.size(); ++i) {
                   ^
circlePack.cpp: In function 'Rcpp::NumericMatrix pack(Rcpp::NumericVector)':
circlePack.cpp:444:73: warning: narrowing conversion of '(circles.std::deque<_Tp, _Alloc>::size<Circle, std::allocator<Circle> >() + 1u)' from 'std::deque<Circle>::size_type {aka unsigned int}' to 'int' inside { } is ill-formed in C++11 [-Wnarrowing]
         Circle c = {0, 0, std::sqrt(float(*itr / M_PI)), circles.size() + 1};
                                                                         ^
circlePack.cpp: In function 'Rcpp::NumericMatrix circlePackLayout(Rcpp::IntegerVector, Rcpp::NumericVector)':
circlePack.cpp:476:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < nodes.size(); ++i) {
                   ^
c:/Rtools/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-3.3.2/include" -DNDEBUG    -I"C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c iciclePlot.cpp -o iciclePlot.o
In file included from iciclePlot.cpp:2:0:
nodes.h: In member function 'std::vector<Node*> Node::getChildren()':
nodes.h:45:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < children.size(); ++i) {
                           ^
iciclePlot.cpp: In function 'std::vector<Node*> createHierarchy(std::vector<int>, std::vector<int>, std::vector<double>, std::vector<double>)':
iciclePlot.cpp:8:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < parent.size(); ++i) {
                   ^
iciclePlot.cpp:12:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < parent.size(); ++i) {
                   ^
iciclePlot.cpp: In function 'void icicleLayout(Node*, double, double)':
iciclePlot.cpp:26:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < children.size(); i++) {
                           ^
iciclePlot.cpp: In function 'Rcpp::NumericMatrix partitionTree(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector)':
iciclePlot.cpp:40:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < nodes.size(); ++i) {
                   ^
iciclePlot.cpp:47:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < nodes.size(); ++i) {
                   ^
c:/Rtools/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-3.3.2/include" -DNDEBUG    -I"C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2 -c lineCutter.cpp -o lineCutter.o
lineCutter.cpp: In function 'Point ellipsis_intersection(Point, Point, double, double)':
lineCutter.cpp:90:9: error: 'copysign' is not a member of 'std'
     x = std::copysign(x, pX);
         ^
lineCutter.cpp:90:9: note: suggested alternative:
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/cmath:44:0,
                 from C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include/Rcpp/r/headers.h:48,
                 from C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include/RcppCommon.h:29,
                 from C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include/Rcpp.h:27,
                 from lineCutter.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:913:31: note:   'copysign'
   __CRT_INLINE double __cdecl copysign (double x, double y)
                               ^
lineCutter.cpp:91:9: error: 'copysign' is not a member of 'std'
     y = std::copysign(y, pY);
         ^
lineCutter.cpp:91:9: note: suggested alternative:
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/cmath:44:0,
                 from C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include/Rcpp/r/headers.h:48,
                 from C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include/RcppCommon.h:29,
                 from C:/Users/Emil/Documents/R/win-library/3.3/Rcpp/include/Rcpp.h:27,
                 from lineCutter.cpp:1:
C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:913:31: note:   'copysign'
   __CRT_INLINE double __cdecl copysign (double x, double y)
                               ^
make: *** [lineCutter.o] Error 1
Warning: running command 'make -f "C:/PROGRA~1/R/R-3.3.2/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-3.3.2/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="ggraph.dll" OBJECTS="RcppExports.o circlePack.o iciclePlot.o lineCutter.o pathAttr.o treemap.o"' had status 2
ERROR: compilation failed for package 'ggraph'
* removing 'C:/Users/Emil/Documents/R/win-library/3.3/ggraph'
Error: Command failed (1)

I tried installing treemap manually too. Did not change anything. I tried googling various parts of this error. No hits.

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252    LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C                   
[5] LC_TIME=Danish_Denmark.1252    

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

loaded via a namespace (and not attached):
[1] httr_1.2.1      R6_2.2.0        tools_3.3.2     withr_1.0.2     curl_2.3        memoise_1.0.0   git2r_0.18.0    digest_0.6.12  
[9] devtools_1.12.0

thomasp85 commented 7 years ago

@akitepowell I suggest you take this to the units developers as it is now too complicated an issue for me to help with.

@Deleetdk Another time please start a new issue instead of adding unrelated problems to this. In this particular case it was related to different compilers on different systems and should've been fixed now

Deleetdk commented 7 years ago

I thought it might be related that's why I added it here.

thomasp85 commented 7 years ago

No worries - has the issue been fixed?

Deleetdk commented 7 years ago

@thomasp85 no. Here's the new issue. https://github.com/thomasp85/ggraph/issues/37

atongsa commented 6 years ago

ubuntu 18.04 LTS --from coder atongsa ^_^

sudo apt update
sudo apt install libudunits2-dev

zyxdef commented 6 years ago

Just to corroborate, it worked like a charm for me on ububtu 18.04 and R 3.5.1

gvdr commented 6 years ago

To add a tad of knowledge: in Arch based systems, the units library is called udunits (without the 2). Once installed, everything is smooth and happy.

thomasp85 / ggraph

Installation problems related to udunits2 #34