Cannot install CytoML

[JimboMahoney]

Hi Jacob!

Thanks for fixing the previous issue on gating. I'm trying to update the packages, and flowWorkspace installs fine, but CytoML fails.

I'm pretty new to R, so maybe I'm doing something wrong. Here's what I get:

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

Gives this output / error:

Downloading GitHub repo RGLab/CytoML@trunk
Skipping 16 packages ahead of CRAN: flowCore, openCyto, RBGL, ncdfFlow, Rgraphviz, Biobase, graph, ggcyto, RProtoBufLib, cytolib, BiocGenerics, flowViz, flowStats, flowClust, zlibbioc, Rhdf5lib
√ checking for file 'C:\Users\3054270\AppData\Local\Temp\RtmpINQsh2\remotesb25c7d4657f7\RGLab-CytoML-1bf2d5d/DESCRIPTION' ...

• preparing 'CytoML':
  √ checking DESCRIPTION meta-information ...
• cleaning src
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'CytoML_1.11.10.tar.gz'
  Warning: file 'CytoML/configure' did not have execute permissions: corrected

Installing package into ‘C:/Users/3054270/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

• installing source package 'CytoML' ...
  ** using staged installation

  ---

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

  ---

** libs

*** arch - i386
C:/RBuildTools/3.5/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -DROUT -I../inst/include/ -I//i386/include/libxml2 -DLIBXML_STATIC -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/3054270/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/3054270/Documents/R/win-library/3.6/BH/include" -I"C:/Users/3054270/Documents/R/win-library/3.6/RProtoBufLib/include" -I"C:/Users/3054270/Documents/R/win-library/3.6/cytolib/include" -I"C:/Users/3054270/Documents/R/win-library/3.6/RcppParallel/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.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 ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
../inst/include/flowWorkspace/workspace.hpp:12:26: fatal error: libxml/xpath.h: No such file or directory
#include <libxml/xpath.h>
^
compilation terminated.
make: *** [C:/PROGRA1/R/R-361.1/etc/i386/Makeconf:215: RcppExports.o] Error 1
ERROR: compilation failed for package 'CytoML'

• removing 'C:/Users/3054270/Documents/R/win-library/3.6/CytoML'
  Error: Failed to install 'CytoML' from GitHub:
  (converted from warning) installation of package ‘C:/Users/3054270/AppData/Local/Temp/RtmpINQsh2/fileb25cea727e7/CytoML_1.11.10.tar.gz’ had non-zero exit status

Any ideas?

Let me know if you need more info.

Thanks!

[mikejiang]

Looks like the libxml2 library is missing from your pc. It may be easier for you to install directly from bioconductor development branch , which I just pushed over and its prebuilt binary should be available within 2 days so that you don't need to worry about compiling the package by your self and its dependencies.

[jacobpwagner]

Thanks, @mikejiang . Agreed, it just looks like you're missing the libxml2 dependency.

[JimboMahoney]

Sorry for the delay in confiming that this (installing from Bioconductor) works great - thanks!