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Unable to install flowCore #175

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akhileshkaushal opened this issue Feb 19, 2020 · 9 comments
Closed

Unable to install flowCore #175

akhileshkaushal opened this issue Feb 19, 2020 · 9 comments

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@akhileshkaushal
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akhileshkaushal commented Feb 19, 2020 •
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Unable to install flowCore version 1.53.8, however I could install version 1.52.1. But the reason of using 1.53.8 was due to issue #98 in previous version.

devtools::install_github("RGLab/flowCore",ref="trunk")
Downloading GitHub repo RGLab/flowCore@trunk
√ checking for file 'C:\Users\akhil\AppData\Local\Temp\RtmpgbZMHZ\remotesdd07919680e\RGLab-flowCore-195ae63/DESCRIPTION' ...

  • preparing 'flowCore': (1s)
    √ checking DESCRIPTION meta-information ...
  • cleaning src
  • checking for LF line-endings in source and make files and shell scripts (689ms)
  • checking for empty or unneeded directories
  • looking to see if a 'data/datalist' file should be added
    NB: this package now depends on R (>= 3.5.0)
    WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'flowCore/data/GvHD.rda' 'flowCore/tests/testthat/expectResults.rds'
  • building 'flowCore_1.53.8.tar.gz'

Installing package into ‘C:/Program Files/R/R-3.6.1/library’
(as ‘lib’ is unspecified)

  • installing source package 'flowCore' ...
    ** using staged installation
    ** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c FastLogicle.cpp -o FastLogicle.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c Hyperlog.cpp -o Hyperlog.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c Logicle.cpp -o Logicle.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c biexponential.cpp -o biexponential.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c convertRawBytes.cpp -o convertRawBytes.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c fcsTextParse.cpp -o fcsTextParse.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c hyperlogTransform.cpp -o hyperlogTransform.o
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA1/R/R-3.6.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.6.1/library/BH/include" -I"C:/Program Files/R/R-3.6.1/library/cytolib/include" -O2 -Wall -mtune=generic -c inPolygon.cpp -o inPolygon.o
inPolygon.cpp: In function 'std::vector inPolygon(Rcpp::NumericMatrix, Rcpp::NumericMatrix)':
inPolygon.cpp:39:12: error: 'CYTO_POINT' is not a member of 'cytolib'
vectorcytolib::CYTO_POINT points(nrv);
^
inPolygon.cpp:39:12: error: 'CYTO_POINT' is not a member of 'cytolib'
inPolygon.cpp:39:31: error: template argument 1 is invalid
vectorcytolib::CYTO_POINT points(nrv);
^
inPolygon.cpp:39:31: error: template argument 2 is invalid
inPolygon.cpp:39:39: error: invalid type in declaration before '(' token
vectorcytolib::CYTO_POINT points(nrv);
^
inPolygon.cpp:42:14: error: invalid types 'int[int]' for array subscript
points[i].x = vertices[i];
^
inPolygon.cpp:43:14: error: invalid types 'int[int]' for array subscript
points[i].y = vertices[i + nrv];
^
inPolygon.cpp:52:71: error: invalid initialization of reference of type 'const std::vectorcytolib::POINT&' from expression of type 'int'
cytolib::in_polygon(xdata, ydata, points, parentInd, false, resInd);
^
In file included from inPolygon.cpp:6:0:
C:/Program Files/R/R-3.6.1/library/cytolib/include/cytolib/in_polygon.hpp:26:13: note: in passing argument 3 of 'void cytolib::in_polygon(EVENT_DATA_TYPE*, EVENT_DATA_TYPE*, const std::vectorcytolib::POINT&, INDICE_TYPE&, bool, INDICE_TYPE&)'
inline void in_polygon(EVENT_DATA_TYPE * xdata, EVENT_DATA_TYPE * ydata, const vector & vertices, INDICE_TYPE & parentInd, bool is_negated, INDICE_TYPE &res)
^
make: *** [C:/PROGRA1/R/R-3.6.2/etc/i386/Makeconf:215: inPolygon.o] Error 1
ERROR: compilation failed for package 'flowCore'

  • removing 'C:/Program Files/R/R-3.6.1/library/flowCore'
    Error: Failed to install 'flowCore' from GitHub:
    (converted from warning) installation of package ‘C:/Users/akhil/AppData/Local/Temp/RtmpgbZMHZ/filedd06f6a10e6/flowCore_1.53.8.tar.gz’ had non-zero exit status
@mikejiang
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install the latest cytolib from github

@akhileshkaushal
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Can you please direct me to the tar.gz of file RProtoBufLib >= 1.9.4 ?

install.packages("D:/Users/akaush9/Documents/R_source_file/cytolib_1.9.10.tar.gz", repos = NULL, type = "source")
Installing package into ‘C:/Program Files/R/R-3.6.1/library’
(as ‘lib’ is unspecified)

  • installing source package 'cytolib' ...
    ** using staged installation
    ** preparing to configure package 'cytolib' ...
    *** configured file: 'cytolibConfig.h.in' => 'inst/include/cytolib/cytolibConfig.h'
    ** finished configure for package 'cytolib'
    ** libs
    Error: package 'RProtoBufLib' 1.8.0 was found, but >= 1.9.4 is required by 'cytolib'
  • removing 'C:/Program Files/R/R-3.6.1/library/cytolib'
  • restoring previous 'C:/Program Files/R/R-3.6.1/library/cytolib'
    Warning in install.packages :
    installation of package ‘D:/Users/akaush9/Documents/R_source_file/cytolib_1.9.10.tar.gz’ had non-zero exit status

@mikejiang
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http://bioconductor.org/packages/3.11/bioc/html/RProtoBufLib.html

@akhileshkaushal
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Thanks it worked.

@hally166
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hally166 commented Mar 3, 2020

I am also having the same issue as Akhilesh.
I have RProtoBufLib 1.9.7 and cytolib 1.9.17 from GitHub.
As there is no longer a trunk I used the master branch. I am using Windows 10 and R3.6.3.
The error is:

> install_github("RGLab/flowCore")
Downloading GitHub repo RGLab/flowCore@master
√  checking for file 'C:\Users\chall\AppData\Local\Temp\RtmpUN2FbH\remotes34b01203702\RGLab-flowCore-486cc2c/DESCRIPTION' ...
-  preparing 'flowCore': (416ms)
√  checking DESCRIPTION meta-information ... 
-  cleaning src
-  checking for LF line-endings in source and make files and shell scripts (509ms)
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
     NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects: 'flowCore/data/GvHD.rda'  'flowCore/tests/testthat/expectResults.rds'
-  building 'flowCore_1.53.11.tar.gz'
   
Installing package into ‘C:/R363/Packages’
(as ‘lib’ is unspecified)
* installing *source* package 'flowCore' ...
** using staged installation
** libs

*** arch - i386
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c biexponential.cpp -o biexponential.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c convertRawBytes.cpp -o convertRawBytes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c fcsTextParse.cpp -o fcsTextParse.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c hyperlogTransform.cpp -o hyperlogTransform.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c logicleTransform.cpp -o logicleTransform.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c poly_centroid.cpp -o poly_centroid.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c sortBytes.cpp -o sortBytes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R363/include" -DNDEBUG  -I"C:/R363/Packages/Rcpp/include" -I"C:/R363/Packages/RcppArmadillo/include" -I"C:/R363/Packages/BH/include" -I"C:/R363/Packages/cytolib/include" -I"C:/R363/Packages/RProtoBufLib/include"        -O2 -Wall  -mtune=core2 -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o poly_centroid.o sortBytes.o uint2double.o zeroin.o C:/R363/Packages/cytolib/lib/i386/libcytolib.a -LC:/R363/bin/i386 -lR
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0x26): undefined reference to `google::protobuf::internal::fixed_address_empty_string'
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0x47): undefined reference to `google::protobuf::internal::fixed_address_empty_string'
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0x68): undefined reference to `google::protobuf::internal::fixed_address_empty_string'
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0x89): undefined reference to `google::protobuf::internal::fixed_address_empty_string'
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0xaa): undefined reference to `google::protobuf::internal::fixed_address_empty_string'
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0x107): undefined reference to `google::protobuf::RepeatedPtrField<std::string>::Add()'
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0x13f): undefined reference to `google::protobuf::RepeatedField<float>::Reserve(int)'
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0x52e): undefined reference to `google::protobuf::RepeatedPtrField<std::string>::size() const'
C:/R363/Packages/cytolib/lib/i386/libcytolib.a(compensation.o):compensation.cpp:(.text+0x53c): undefined reference to `google::protobuf::RepeatedPtrField<std::string>::Get(int) const'
collect2.exe: error: ld returned 1 exit status
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
no DLL was created
ERROR: compilation failed for package 'flowCore'
* removing 'C:/R363/Packages/flowCore'
* restoring previous 'C:/R363/Packages/flowCore'
Error: Failed to install 'flowCore' from GitHub:
  (converted from warning) installation of package ‘C:/Users/chall/AppData/Local/Temp/RtmpUN2FbH/file34b01c9c435b/flowCore_1.53.11.tar.gz’ had non-zero exit status

Thank you for your help.

@mikejiang
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mikejiang commented Mar 3, 2020 •
edited
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Since you are using windows/mac, I'd recommend to re-install all the packages directly from Bioconductor (either the latest release or development version, depends on your R version)

@hally166
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hally166 commented Mar 4, 2020 •
edited
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As I'm sure you guessed, I was installing from GitHub in order to give Dillon's CytoExploreR a go.
Thanks for your help. Using the devel version of bioconductor worked.

@mikejiang
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Yes, bioc devel should be in sync with github version

mikejiang pushed a commit that referenced this issue Mar 6, 2020
link to RProtoBufLib. #175
4569510
@mikejiang
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@hally166 flowCore should compile Now.

@mikejiang mikejiang mentioned this issue Mar 6, 2020
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@mikejiang @akhileshkaushal @hally166