Installation of "flowWorkspace" on Ubuntu fails
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Entering edit mode
mo • 0
@mo-12349
Last seen 4.8 years ago

Dear Members.

When trying to install the R package "flowWorkspace" on my Ubuntu 16.04, I receive the following error:

> biocLite("flowWorkspace")

...
g++ -I/usr/share/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization  -I"/home/moritz/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/moritz/R/x86_64-pc-linux-gnu-library/3.2/BH/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c boost_serialization/xml_wgrammar.cpp -o boost_serialization/xml_wgrammar.o

In file included from boost_serialization/xml_wgrammar.cpp:146:0:
boost_serialization/basic_xml_grammar.ipp:458:6: error: prototype for ‘void boost::archive::basic_xml_grammar<CharType>::windup(boost::archive::basic_xml_grammar<CharType>::IStream&)’ does not match any in class ‘boost::archive::basic_xml_grammar<CharType>’
 void basic_xml_grammar<CharType>::windup(IStream & is){
      ^
In file included from boost_serialization/xml_wgrammar.cpp:18:0:
/home/moritz/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/archive/impl/basic_xml_grammar.hpp:166:10: error: candidate is: bool boost::archive::basic_xml_grammar<CharType>::windup(boost::archive::basic_xml_grammar<CharType>::IStream&)
     bool windup(IStream & is);
/usr/lib/R/etc/Makeconf:143: recipe for target 'boost_serialization/xml_wgrammar.o' failed
make: *** [boost_serialization/xml_wgrammar.o] Error 1
ERROR: compilation failed for package ‘flowWorkspace’

...

Any suggestions?

Thanks a lot!

moritz

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=de_DE.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.20.3 httr_1.2.1          

loaded via a namespace (and not attached):
[1] magrittr_1.5 R6_2.2.0     tools_3.2.3  curl_2.3     Rcpp_0.12.9  jsonlite_1.2 purrr_0.2.2 
bioconductor R flowcytometry • 662 views
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Entering edit mode

Hi Moritz,

I am facing the same problem and I was wondering if you finally succeeded in installing flowWorkspace on ubuntu.

Thanks a lot

Pierre

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