Question: Unable to install flowWorkspace from github
0
gravatar for anders.tondell
20 months ago by
anders.tondell30 wrote:

I am trying to install dev version of flowWorkspace to be able to install cytoUtils, but this fails. I do not have adm. rights on the system (at my univerisity, Windows), but Rtools was installed yesterday. Any help would be highly appreciated. (I need cytoUtils for MFI of flow data).

install_github("RGLab/RProtoBufLib", ref="trunk")

install_github("RGLab/flowCore", ref="trunk")

install_github("RGLab/cytolib", ref="trunk")#all worked fine.

install_github("RGLab/flowWorkspace", ref="trunk")#Failed!

Se error and sessioninfo:

> library(devtools) #load it
> install_github("RGLab/cytolib", ref="trunk")
Skipping install of 'cytolib' from a github remote, the SHA1 (bb553196) has not changed since last install.
  Use `force = TRUE` to force installation
> install_github("RGLab/flowWorkspace", ref="trunk")
Downloading GitHub repo RGLab/flowWorkspace@trunk
from URL https://api.github.com/repos/RGLab/flowWorkspace/zipball/trunk
Installing flowWorkspace
"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  "C:/Users/anderto/AppData/Local/Temp/35/RtmpCsUPtj/devtoolsc5f822b84407/RGLab-flowWorkspace-1e73500"  \
  --library="M:/Documents/Temp" --install-tests

* installing *source* package 'flowWorkspace' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs

*** arch - i386
c:/Programs/RTools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.3/include" -DNDEBUG -DROUT -I../inst/include/ -I//i386/include/libxml2 -DLIBXML_STATIC -I"M:/Documents/Temp/Rcpp/include" -I"M:/Documents/Temp/BH/include" -I"M:/Documents/Temp/RProtoBufLib/include" -I"M:/Documents/Temp/cytolib/include"        -O2 -Wall  -mtune=generic -c R_API.cpp -o R_API.o
In file included from M:/Documents/Temp/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from M:/Documents/Temp/cytolib/include/cytolib/populationTree.hpp:11,
                 from M:/Documents/Temp/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from M:/Documents/Temp/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
M:/Documents/Temp/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
M:/Documents/Temp/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
M:/Documents/Temp/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
M:/Documents/Temp/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
c:/Programs/RTools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.3/include" -DNDEBUG -DROUT -I../inst/include/ -I//i386/include/libxml2 -DLIBXML_STATIC -I"M:/Documents/Temp/Rcpp/include" -I"M:/Documents/Temp/BH/include" -I"M:/Documents/Temp/RProtoBufLib/include" -I"M:/Documents/Temp/cytolib/include"        -O2 -Wall  -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from M:/Documents/Temp/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from M:/Documents/Temp/cytolib/include/cytolib/populationTree.hpp:11,
                 from M:/Documents/Temp/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
M:/Documents/Temp/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
M:/Documents/Temp/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
M:/Documents/Temp/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
M:/Documents/Temp/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
c:/Programs/RTools/mingw_32/bin/g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-34~1.3/include" -DNDEBUG -DROUT -I../inst/include/ -I//i386/include/libxml2 -DLIBXML_STATIC -I"M:/Documents/Temp/Rcpp/include" -I"M:/Documents/Temp/BH/include" -I"M:/Documents/Temp/RProtoBufLib/include" -I"M:/Documents/Temp/cytolib/include"        -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/workspace.hpp:12:26: fatal error: libxml/xpath.h: No such file or directory
 #include <libxml/xpath.h>
                          ^
compilation terminated.
make: *** [R_GatingSet.o] Error 1
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-34~1.3/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.3/share/make/winshlib.mk" CXX='$(CXX11) $(CXX11STD)' CXXFLAGS='$(CXX11FLAGS)' CXXPICFLAGS='$(CXX11PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX11LDFLAGS)' SHLIB_LD='$(SHLIB_CXX11LD)' SHLIB="flowWorkspace.dll" OBJECTS="R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getSingleCellExpression.o setCounts.o"' had status 2
ERROR: compilation failed for package 'flowWorkspace'
* removing 'M:/Documents/Temp/flowWorkspace'
* restoring previous 'M:/Documents/Temp/flowWorkspace'
In R CMD INSTALL
Installation failed: Command failed (1)
>

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=Norwegian Bokmål_Norway.1252
[2] LC_CTYPE=Norwegian Bokmål_Norway.1252  
[3] LC_MONETARY=Norwegian Bokmål_Norway.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=Norwegian Bokmål_Norway.1252   

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

other attached packages:
[1] devtools_1.13.5

loaded via a namespace (and not attached):
 [1] httr_1.3.1           compiler_3.4.3       R6_2.2.2           
 [4] BiocInstaller_1.28.0 tools_3.4.3          withr_2.1.2        
 [7] curl_3.1             memoise_1.1.0        git2r_0.21.0       
[10] digest_0.6.15      
>

flowworkspace cytoutils • 338 views
ADD COMMENTlink modified 20 months ago by Martin Morgan ♦♦ 24k • written 20 months ago by anders.tondell30
Answer: Unable to install flowWorkspace from github
1
gravatar for Martin Morgan
20 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Installing from github on Windows is a source installation, compared to installing via biocLite() where the binaries have been built. You're likely to face significant challenges in getting the source code to compile. The immediate problem is

./inst/include/flowWorkspace/workspace.hpp:12:26: fatal error: libxml/xpath.h: No such file or directory
 #include <libxml/xpath.h>
                          ^
compilation terminated.

which requires that the libxml library and headers be available on your platform. The Bioconductor build system is documented and includes instructions for installing this software, but that document is primarily for our internal use so may be incomplete or highly specific to our situation.

As an additional minimum, you will likely need to use the 'devel' version of R and hence 'devel' version of Bioconductor. Note that admin rights are not needed to install R.

ADD COMMENTlink written 20 months ago by Martin Morgan ♦♦ 24k

All our github 'trunk' branch is in sync with the 'devel' version of BioC. So as Martin said, install them from BioC devel is the easiest way to go. `cytoUtils` is not in BioC yet, but once you get the other flow tool chains installed, you can install its the `pureR` branch install_github("RGLab/cytolib", ref="pureR") if you still have compiling error.

ADD REPLYlink written 20 months ago by Jiang, Mike1.2k
Thanx to both of you for clarifying answers. I will look into this. With regards,
ADD REPLYlink written 20 months ago by anders.tondell30
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