I've been corresponding with the package author about an error I'm getting in the HLMdiag package. He suggested that I install the development version [https://github.com/aloy/HLMdiag]. So, I'm trying to install the development version from both GitHub and a local version that he sent me. I'm running into errors for both my work computer and personal computer. I'm hoping someone in the user community who is more knowledgeable about such things can help solve this.
My initial thought was that there might be some security protocol on my work machine that was causing problems, which is why I attempted the install on a personal machine. I am getting different error messages on the different machines; but still unable to install on either. Any help would be very much appreciated.
Sorry in advance for the post length. I wanted to give as much of the error messages / log as possible.
Machine 1 -- personal
sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] devtools_1.6.1 tools_3.1.2
Attempt (A) - direct from GitHub
devtools::install_github("aloy/HLMdiag")
Downloading github repo aloy/HLMdiag#master
Installing HLMdiag
"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" --vanilla CMD INSTALL \
"C:\Users\crossfit_al1985\AppData\Local\Temp\Rtmp8o4p3s\devtools24b871ace19\aloy-HLMdiag-3f7977d" \
--library="C:/Users/crossfit_al1985/Documents/R/win-library/3.1" --install-tests
* installing *source* package 'HLMdiag' ...
** libs
*** arch - i386
C:\RBuildTools\3.1\gcc-4.6.3\bin\nm.exe: cooksd_obs.o: File format not recognized
C:\RBuildTools\3.1\gcc-4.6.3\bin\nm.exe: cooksd_subset.o: File format not recognized
C:\RBuildTools\3.1\gcc-4.6.3\bin\nm.exe: covratio.o: File format not recognized
C:\RBuildTools\3.1\gcc-4.6.3\bin\nm.exe: covtrace.o: File format not recognized
C:\RBuildTools\3.1\gcc-4.6.3\bin\nm.exe: linear_algebra_fnc.o: File format not recognized
C:\RBuildTools\3.1\gcc-4.6.3\bin\nm.exe: mdffits_subset.o: File format not recognized
g++ -m32 -shared -s -static-libgcc -o HLMdiag.dll tmp.def cooksd_obs.o cooksd_subset.o covratio.o covtrace.o linear_algebra_fnc.o mdffits_subset.o -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lRlapack -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lR
cooksd_obs.o: file not recognized: File format not recognized
collect2: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'HLMdiag'
* removing 'C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag'
* restoring previous 'C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag'
Error: Command failed (1)
Attempt (B) - via install.packages() from local
setwd(...)
install.packages("./HLMdiag_0.3.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘C:/Users/crossfit_al1985/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
* installing *source* package 'HLMdiag' ...
** libs
*** arch - i386
cygwin warning:
MS-DOS style path detected: C:/PROGRA~1/R/R-31~1.2/etc/i386/Makeconf
Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-31~1.2/etc/i386/Makeconf
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cooksd_obs.cpp -o cooksd_obs.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cooksd_subset.cpp -o cooksd_subset.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c covratio.cpp -o covratio.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c covtrace.cpp -o covtrace.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c linear_algebra_fnc.cpp -o linear_algebra_fnc.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c mdffits_subset.cpp -o mdffits_subset.o
g++ -m32 -shared -s -static-libgcc -o HLMdiag.dll tmp.def cooksd_obs.o cooksd_subset.o covratio.o covtrace.o linear_algebra_fnc.o mdffits_subset.o -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lRlapack -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lR
installing to C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag/libs/i386
*** arch - x64
cygwin warning:
MS-DOS style path detected: C:/PROGRA~1/R/R-31~1.2/etc/x64/Makeconf
Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-31~1.2/etc/x64/Makeconf
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cooksd_obs.cpp -o cooksd_obs.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cooksd_subset.cpp -o cooksd_subset.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c covratio.cpp -o covratio.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c covtrace.cpp -o covtrace.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c linear_algebra_fnc.cpp -o linear_algebra_fnc.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c mdffits_subset.cpp -o mdffits_subset.o
g++ -m64 -shared -s -static-libgcc -o HLMdiag.dll tmp.def cooksd_obs.o cooksd_subset.o covratio.o covtrace.o linear_algebra_fnc.o mdffits_subset.o -LC:/PROGRA~1/R/R-31~1.2/bin/x64 -lRlapack -LC:/PROGRA~1/R/R-31~1.2/bin/x64 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/x64 -lR
installing to C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function from function 'adjust_lmList' in package 'HLMdiag'
Error in setMethod("lmList", signature(formula = "formula", data = "data.frame"), :
no existing definition for function 'lmList'
Error : unable to load R code in package 'HLMdiag'
ERROR: lazy loading failed for package 'HLMdiag'
* removing 'C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag'
* restoring previous 'C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\crossfit_al1985\Documents\R\win-library\3.1" "./HLMdiag_0.3.0.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘./HLMdiag_0.3.0.tar.gz’ had non-zero exit status
Attempt (C) - via unzipping and devtools::install()
setwd(...)
devtools::install("HLMdiag")
Installing HLMdiag
"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" --vanilla CMD INSTALL \
"C:\Users\crossfit_al1985\Downloads\HLMdiag" \
--library="C:/Users/crossfit_al1985/Documents/R/win-library/3.1" --install-tests
* installing *source* package 'HLMdiag' ...
** libs
*** arch - i386
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cooksd_obs.cpp -o cooksd_obs.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cooksd_subset.cpp -o cooksd_subset.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c covratio.cpp -o covratio.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c covtrace.cpp -o covtrace.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c linear_algebra_fnc.cpp -o linear_algebra_fnc.o
g++ -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c mdffits_subset.cpp -o mdffits_subset.o
g++ -m32 -shared -s -static-libgcc -o HLMdiag.dll tmp.def cooksd_obs.o cooksd_subset.o covratio.o covtrace.o linear_algebra_fnc.o mdffits_subset.o -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lRlapack -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lR
installing to C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag/libs/i386
*** arch - x64
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cooksd_obs.cpp -o cooksd_obs.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cooksd_subset.cpp -o cooksd_subset.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c covratio.cpp -o covratio.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c covtrace.cpp -o covtrace.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c linear_algebra_fnc.cpp -o linear_algebra_fnc.o
g++ -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/crossfit_al1985/Documents/R/win-library/3.1/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c mdffits_subset.cpp -o mdffits_subset.o
g++ -m64 -shared -s -static-libgcc -o HLMdiag.dll tmp.def cooksd_obs.o cooksd_subset.o covratio.o covtrace.o linear_algebra_fnc.o mdffits_subset.o -LC:/PROGRA~1/R/R-31~1.2/bin/x64 -lRlapack -LC:/PROGRA~1/R/R-31~1.2/bin/x64 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/x64 -lR
installing to C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function from function 'adjust_lmList' in package 'HLMdiag'
Error in setMethod("lmList", signature(formula = "formula", data = "data.frame"), :
no existing definition for function 'lmList'
Error : unable to load R code in package 'HLMdiag'
ERROR: lazy loading failed for package 'HLMdiag'
* removing 'C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag'
* restoring previous 'C:/Users/crossfit_al1985/Documents/R/win-library/3.1/HLMdiag'
Error: Command failed (1)
Machine 2 -- work
sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_1.5
loaded via a namespace (and not attached):
[1] digest_0.6.4 evaluate_0.5.5 formatR_0.10 htmltools_0.2.4 httr_0.6.1 knitr_1.6
[7] memoise_0.2.1 parallel_3.1.1 RCurl_1.95-4.1 rmarkdown_0.4.2 stringr_0.6.2 tools_3.1.1
[13] whisker_0.3-2
Attempt (A) -- direct from github
devtools::install_github("aloy/HLMdiag")
Installing github repo HLMdiag/master from aloy
Downloading master.zip from https://github.com/aloy/HLMdiag/archive/master.zip
Installing package from C:\Users\alewit\AppData\Local\Temp\RtmpATVjSy/master.zip
Installing HLMdiag
"C:/PROGRA~1/R/R-31~1.1/bin/x64/R" --vanilla CMD INSTALL \
"C:\Users\alewit\AppData\Local\Temp\RtmpATVjSy\devtoolsc745bf04fbd\HLMdiag-master" \
--library="C:/Users/alewit/Documents/R/win-library/3.1" --install-tests
* installing *source* package 'HLMdiag' ...
** libs
*** arch - i386
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-31~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-31~1.1/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="HLMdiag.dll" OBJECTS="cooksd_obs.o cooksd_subset.o covratio.o covtrace.o linear_algebra_fnc.o mdffits_subset.o"' had status 127
ERROR: compilation failed for package 'HLMdiag'
* removing 'C:/Users/alewit/Documents/R/win-library/3.1/HLMdiag'
* restoring previous 'C:/Users/alewit/Documents/R/win-library/3.1/HLMdiag'
Error: Command failed (1)
Attempt (B) -- via install.packages() from local
setwd(...)
install.packages("./HLMdiag_0.3.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘C:/Users/alewit/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
* installing *source* package 'HLMdiag' ...
** libs
*** arch - i386
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-31~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-31~1.1/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="HLMdiag.dll" OBJECTS="cooksd_obs.o cooksd_subset.o covratio.o covtrace.o linear_algebra_fnc.o mdffits_subset.o"' had status 127
ERROR: compilation failed for package 'HLMdiag'
* removing 'C:/Users/alewit/Documents/R/win-library/3.1/HLMdiag'
* restoring previous 'C:/Users/alewit/Documents/R/win-library/3.1/HLMdiag'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\alewit\Documents\R\win-library\3.1" "C:/Users/alewit/Downloads/HLMdiag_0.3.0.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/alewit/Downloads/HLMdiag_0.3.0.tar.gz’ had non-zero exit status
Attempt (C) -- via devtools::install()
setwd(...)
install("HLMdiag")
Installing HLMdiag
"C:/PROGRA~1/R/R-31~1.1/bin/x64/R" --vanilla CMD INSTALL "C:\Users\alewit\Downloads\HLMdiag" \
--library="C:/Users/alewit/Documents/R/win-library/3.1" --install-tests
* installing *source* package 'HLMdiag' ...
** libs
*** arch - i386
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-31~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-31~1.1/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="HLMdiag.dll" OBJECTS="cooksd_obs.o cooksd_subset.o covratio.o covtrace.o linear_algebra_fnc.o mdffits_subset.o"' had status 127
ERROR: compilation failed for package 'HLMdiag'
* removing 'C:/Users/alewit/Documents/R/win-library/3.1/HLMdiag'
* restoring previous 'C:/Users/alewit/Documents/R/win-library/3.1/HLMdiag'
Error: Command failed (1)
The .o files in the src directory were messing things up. I submitted a pull request so hopefully Adam will incorporate those fixes soon and your problem should go away. You could test if this works by using
install_github("Dasonk/HLMdiag")
until the pull request is accepted.
Edit: And Adam was quick to merge. Test out installing from github again install_github("aloy/HLMdiag") and it should work for you.
Related
I am trying to set up R on a Mac and the installation of the cluster package is failing, possibly due to gfortran (or its library path). Below is the output for the failing package installation (sorry about the partly german output).
> install.packages("cluster", type = "source")
versuche URL 'https://cran.rstudio.com/src/contrib/cluster_2.1.4.tar.gz'
Content type 'application/x-gzip' length 352076 bytes (343 KB)
==================================================
downloaded 343 KB
* installing *source* package ‘cluster’ ...
** Paket ‘cluster’ erfolgreich entpackt und MD5 Summen überprüft
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clara.c -o clara.o
gfortran -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c daisy.f -o daisy.o
gfortran -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c dysta.f -o dysta.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fanny.c -o fanny.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mona.c -o mona.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pam.c -o pam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sildist.c -o sildist.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spannel.c -o spannel.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c twins.c -o twins.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -L/usr/local/gfortran/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
ld: warning: ignoring file dysta.o, building for macOS-arm64 but attempting to link with file built for unknown-x86_64
ld: warning: ignoring file daisy.o, building for macOS-arm64 but attempting to link with file built for unknown-x86_64
installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-cluster/00new/cluster/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: Laden von Paket oder Namensraum für ‘cluster’ in dyn.load(file, DLLpath = DLLpath, ...): fehlgeschlagen
kann shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-cluster/00new/cluster/libs/cluster.so' nicht laden:
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-cluster/00new/cluster/libs/cluster.so, 0x0006): symbol not found in flat namespace '_dysta_'
Fehler: Laden fehlgeschlagen
Ausführung angehalten
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cluster’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/cluster’
Warning in install.packages :
Installation des Pakets ‘cluster’ hatte Exit-Status ungleich 0
Die heruntergeladenen Quellpakete sind in
‘/private/var/folders/vg/kjdqgj4j4d949_p782bz80rm0000gn/T/RtmpsJedpT/downloaded_packages’
Could this be related to the architecture arm64?
gfortran is also installed.
Here is the output of sessionInfo() and the setting in ~/.R/Makevars
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2
# Makevars
FC = gfortran
F77 = gfortran
FLIBS = -L/usr/local/gfortran/lib
I had to set gfortran in ~/.R/Makevars, otherwise R searches in an inconclusive place for gfortran and cannot find it. I checked the FLIBS path with gfortran -print-search-dirs, not sure if this is the correct setting.
Actually, the output seems as the package could be installed but not loaded. Does anybody have any ideas or faced a similar problem?
Thank you!
I am trying to build a package but the Cpp bit is causing an error. This package is very similar to another one which also has a cpp bit and I do manage to build it without problems.
I have checked usual errors like:
Not having the linkingTo Rccp in the DESCRIPTION as here.
Remove xxx.o and xxx.so files in the src/ and try to compile and also
the RccpExports.R as here.
I tried Compile(".") and
tools::package_native_routine_registration_skeleton(".") although I
do not really understand what they mean...
The error
* installing to library 'C:/Program Files/R/R-3.4.0/library'
* installing *source* package 'PackageName' ...
** libs
c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_64/bin/gcc -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o
c:/Rtools/mingw_64/bin/g++ -I"C:/PROGRA~1/R/R-34~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.4.0/library/Rcpp/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c rcpp_hello.cpp -o rcpp_hello.o
c:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o PackageName.dll tmp.def RcppExports.o init.o rcpp_hello.o -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/PROGRA~1/R/R-34~1.0/bin/x64 -lR
init.o:init.c:(.rdata+0x28): undefined reference to `PackageName_rcpp_hello'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'PackageName'
* removing 'C:/Program Files/R/R-3.4.0/library/PackageName'
Exited with status 1.
Details on my session:
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Rstudio: 1.1.383
Rcpp: Rcpp_0.12.12
I'm trying to install the deldir package in R via install.packages("deldir",type = 'source') but am getting the following error message (this is OSX Mavericks):
* installing *source* package ‘deldir’ ...
** package ‘deldir’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8 -fPIC -g -O2 -c acchk.f -o acchk.o
make: gfortran-4.8: No such file or directory
make: *** [acchk.o] Error 1
ERROR: compilation failed for package ‘deldir’
gfortran 4.8 does seem to be available on my system, however:
> gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin13/4.8.2/lto-wrapper
Target: x86_64-apple-darwin13
Configured with: ../gcc-4.8.2/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/deps-static/x86_64 --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin13
Thread model: posix
gcc version 4.8.2 (GCC)
After symlinking gfortran-4.8 to gfortran I get a bit further but fail nonetheless:
* installing *source* package ‘deldir’ ...
** package ‘deldir’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8 -fPIC -g -O2 -c acchk.f -o acchk.o
gfortran-4.8 -fPIC -g -O2 -c addpt.f -o addpt.o
gfortran-4.8 -fPIC -g -O2 -c adjchk.f -o adjchk.o
gfortran-4.8 -fPIC -g -O2 -c binsrt.f -o binsrt.o
gfortran-4.8 -fPIC -g -O2 -c circen.f -o circen.o
gfortran-4.8 -fPIC -g -O2 -c cross.f -o cross.o
gfortran-4.8 -fPIC -g -O2 -c delet.f -o delet.o
gfortran-4.8 -fPIC -g -O2 -c delet1.f -o delet1.o
gfortran-4.8 -fPIC -g -O2 -c delout.f -o delout.o
gfortran-4.8 -fPIC -g -O2 -c delseg.f -o delseg.o
gfortran-4.8 -fPIC -g -O2 -c dirout.f -o dirout.o
gfortran-4.8 -fPIC -g -O2 -c dirseg.f -o dirseg.o
gfortran-4.8 -fPIC -g -O2 -c dldins.f -o dldins.o
gfortran-4.8 -fPIC -g -O2 -c initad.f -o initad.o
gfortran-4.8 -fPIC -g -O2 -c insrt.f -o insrt.o
gfortran-4.8 -fPIC -g -O2 -c insrt1.f -o insrt1.o
gfortran-4.8 -fPIC -g -O2 -c intri.f -o intri.o
gfortran-4.8 -fPIC -g -O2 -c locn.f -o locn.o
gfortran-4.8 -fPIC -g -O2 -c master.f -o master.o
gfortran-4.8 -fPIC -g -O2 -c mnnd.f -o mnnd.o
gfortran-4.8 -fPIC -g -O2 -c pred.f -o pred.o
gfortran-4.8 -fPIC -g -O2 -c qtest.f -o qtest.o
gfortran-4.8 -fPIC -g -O2 -c qtest1.f -o qtest1.o
gfortran-4.8 -fPIC -g -O2 -c stoke.f -o stoke.o
gfortran-4.8 -fPIC -g -O2 -c succ.f -o succ.o
gfortran-4.8 -fPIC -g -O2 -c swap.f -o swap.o
gfortran-4.8 -fPIC -g -O2 -c testeq.f -o testeq.o
gfortran-4.8 -fPIC -g -O2 -c triar.f -o triar.o
gfortran-4.8 -fPIC -g -O2 -c trifnd.f -o trifnd.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout .o delseg.o dirout.o dirseg.o dldins.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 - lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [deldir.so] Error 1
ERROR: compilation failed for package ‘deldir’
Note that /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.3 exists, /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 does not
sessionInfo():
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Sys.getenv():
> Sys.getenv()
__CF_USER_TEXT_ENCODING
"0x1F5:0:0"
__CHECKFIX1436934
"1"
Apple_PubSub_Socket_Render
"/tmp/launch-jCxLku/Render"
DISPLAY
":0"
DYLD_FALLBACK_LIBRARY_PATH
"/Users/<myusername>/lib:/usr/local/lib:/usr/lib::/Library/Frameworks/R.framework/Resources/lib"
EDITOR
"vi"
GIT_ASKPASS
"rpostback-askpass"
HOME
"/Users/<myusername>"
LANG
"en_US.UTF-8"
LC_CTYPE
"en_US.UTF-8"
LN_S
"ln -s"
LOGNAME
"<myusername>"
MAKE
"make"
PAGER
"/usr/bin/less"
PATH
"/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin"
R_BROWSER
"/usr/bin/open"
R_BZIPCMD
"/usr/bin/bzip2"
R_DOC_DIR
"/Library/Frameworks/R.framework/Resources/doc"
R_GZIPCMD
"/usr/bin/gzip"
R_HOME
"/Library/Frameworks/R.framework/Resources"
R_INCLUDE_DIR
"/Library/Frameworks/R.framework/Resources/include"
R_LIBS_SITE
""
R_LIBS_USER
"~/Library/R/3.1/library"
R_PAPERSIZE
"a4"
R_PDFVIEWER
"/usr/bin/open"
R_PLATFORM
"x86_64-apple-darwin13.1.0"
R_PRINTCMD
"lpr"
R_QPDF
"/Library/Frameworks/R.framework/Resources/bin/qpdf"
R_RD4PDF
"times,inconsolata,hyper"
R_SESSION_TMPDIR
"/var/folders/jf/ds4sdyys44xckz_7f9zhrvsh0000gn/T//RtmpXaPpYF"
R_SHARE_DIR
"/Library/Frameworks/R.framework/Resources/share"
R_SYSTEM_ABI
"osx,gcc,gxx,gfortran,?"
R_TEXI2DVICMD
"/usr/bin/texi2dvi"
R_UNZIPCMD
"/usr/bin/unzip"
R_ZIPCMD
"/usr/bin/zip"
RS_RPOSTBACK_PATH
"/Applications/RStudio.app/Contents/MacOS/rpostback"
RS_SHARED_SECRET
<removed>
RSTUDIO
"1"
RSTUDIO_PANDOC
"/Applications/RStudio.app/Contents/MacOS/pandoc"
RSTUDIO_SESSION_PORT
"10153"
RSTUDIO_USER_IDENTITY
"<myusername>"
SED
"/usr/bin/sed"
SHELL
"/bin/bash"
SSH_AUTH_SOCK
"/tmp/launch-Shnu2H/Listeners"
TAR
"/usr/bin/tar"
TMPDIR
"/var/folders/jf/ds4sdyys44xckz_7f9zhrvsh0000gn/T/"
USER
"<myusername>"
I was getting the same error when installing the igraph package in R on Manjaro Linux.
It was due to the absence of a Fortran compiler (gfortran I think). I found out that gfortran package is named as gcc-fortran in Manjaro repo and many other (GNU) Linux repos. So, I just installed gcc-fortran package and then restarted RStudio and igraph package installed without any issues.
I found a solution here: https://support.rstudio.com/hc/communities/public/questions/201688563-Problem-with-Mac-Yosemite-Beta-and-RStudio-not-finding-TeX-distribution
It turns out that Adam Maxwell noted that Yosemite beta has a significant bug in passing environment variables to subprocesses.
After installing gfortran as in OS X package installation depends on gfortran-4.8 .
This works: create an alias in your .bash_profile
alias fixrs="launchctl setenv PATH /usr/texbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin"
Then close and open the terminal.
And execute the fixrs command in the terminal before launching RStudio.
Then I could build igraph successfully.
I was using a linux machine and RStudio server. I had a similar problem. I knew already that gfortran was on the machine thanks to the system administrator.
To solve, in the shell, I typed which gfortran, which gave me a path.
Then, following this SO posting, I entered the following in the shell to create a new Makevars file
# create a file called ~/.R/Makevars:
mkdir -p ~/.R
touch ~/.R/Makevars
Then, in that new file, I wrote the following
F77 = /usr/local/bin/gfortran #this was the path that I got from typing which gfortran in the shell
FC = $F77
FLIBS = -L/usr/local/bin/gfortran
From there, I was able to install the package that wasn't compiling properly (in my case vegan instead of igraph using install.packages("vegan")
I had your same problem (in OS X Yosemite), and (unfortunately) painstakingly recreated your symlink "partial solution". Finally, I was able to solve the issue by forgetting about linking or aliasing and just downgrading to gfortran-4.8.
I had installed the newer version with brew, so for me this entailed uninstalling
brew uninstall gcc
and then following the instructions here to install 4.8.2, i.e.
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
It still threw up some warnings but at least I got a successful installation of deldir, which I needed to run pgirmess.
I am installing lme4 using the README.md file on their github account and I fail during installing the dependencies. I tried to install them separately and still crash at installing the minqa package. I'm using R/3.0.2 on RHEL6. During the build the compiler argues about RScript not existing which as I check it is in the R/bin folder.
Here is the log to the R INSTALL:
$ R CMD INSTALL minqa_1.2.2.tar.gz
* installing to library ‘/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library’
* installing *source* package ‘minqa’ ...
** package ‘minqa’ successfully unpacked and MD5 sums checked
** libs
gfortran -fpic -g -O2 -c altmov.f -o altmov.o
gfortran -fpic -g -O2 -c bigden.f -o bigden.o
gfortran -fpic -g -O2 -c biglag.f -o biglag.o
gfortran -fpic -g -O2 -c bobyqa.f -o bobyqa.o
gfortran -fpic -g -O2 -c bobyqb.f -o bobyqb.o
gfortran -fpic -g -O2 -c lagmax.f -o lagmax.o
g++ -I/gpfs/apps/x86_64-rhel6/R/3.0.2/R/include -DNDEBUG -I/usr/local/include -I"/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/Rcpp/include" -fpic -g -O2 -c minqa.cpp -o minqa.o
gfortran -fpic -g -O2 -c newuoa.f -o newuoa.o
gfortran -fpic -g -O2 -c newuob.f -o newuob.o
gfortran -fpic -g -O2 -c prelim.f -o prelim.o
gfortran -fpic -g -O2 -c rescue.f -o rescue.o
gfortran -fpic -g -O2 -c trsapp.f -o trsapp.o
gfortran -fpic -g -O2 -c trsbox.f -o trsbox.o
gfortran -fpic -g -O2 -c trstep.f -o trstep.o
gfortran -fpic -g -O2 -c uobyqa.f -o uobyqa.o
gfortran -fpic -g -O2 -c uobyqb.f -o uobyqb.o
gfortran -fpic -g -O2 -c update.f -o update.o
gfortran -fpic -g -O2 -c updatebobyqa.f -o updatebobyqa.o
Rscript execution error: No such file or directory
g++ -shared -L/usr/local/lib64 -o minqa.so altmov.o bigden.o biglag.o bobyqa.o bobyqb.o lagmax.o minqa.o newuoa.o newuob.o prelim.o rescue.o trsapp.o trsbox.o trstep.o uobyqa.o uobyqb.o update.o updatebobyqa.o -lgfortran -lm -L/gpfs/apps/x86_64-rhel6/R/3.0.2/R/lib -lR
Rscript execution error: No such file or directory
installing to /gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/minqa/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/minqa/libs/minqa.so':
/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/minqa/libs/minqa.so: undefined symbol: _ZTIN4Rcpp7RObjectE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/gpfs/apps/x86_64-rhel6/R/3.0.2/R/library/minqa’
A similar error also occurs when trying to upgrade lme4 from 1.0-5 to 1.0-6. The error message is something like:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/minqa/libs/minqa.so':
libRcpp.so: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘lme4’
To resolve this install the packages in the order below:
install.packages('Rcpp')
install.packages('RcppEigen')
install.packages('minqa')
install.packages('lme4')
I guess it's related to RCpp; just upgrade the version from 0.10.6 to 0.11.0 and some ABI break change happens?
Credit from dmbates
/usr/share/R/share/make/shlib.mk:6: recipe for target 'minqa.so' failed make: *** [minqa.so] Error 1
I got the same error when installing minqa (needed for lme4). It was due to modify .First() in /etc/R/Rprofile.site
Desactive .First or use R --vanilla.
I am trying to install an R shiny server on my local Ubuntu 12.04 machine, and I followed the instructions here https://github.com/rstudio/shiny-server/wiki/Ubuntu-step-by-step-install-instructions:
When trying to do a:
install.packages('shiny', repos='http://cran.rstudio.com/')
It goes through the dependencies, but fails to install Rcpp. See error log below:
* installing *source* package 'Rcpp' ...
* package 'Rcpp' successfully unpacked and MD5 sums checked
* libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Module.cpp -o Module.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Rcpp_init.c -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Timer.cpp -o Timer.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c barrier.cpp -o barrier.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c exceptions.cpp -o exceptions.o
g++ -shared -o Rcpp.so Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o barrier.o exceptions.o -L/usr/lib/R/lib -lR
g++ -o libRcpp.so Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o barrier.o exceptions.o -shared -L/usr/lib/R/lib -lR
ar qc libRcpp.a Date.o Module.o Rcpp_init.o Timer.o api.o attributes.o barrier.o exceptions.o
cp libRcpp.so ../inst/lib
cp libRcpp.a ../inst/lib
rm libRcpp.so libRcpp.a
installing to /usr/local/lib/R/site-library/Rcpp/libs
* R
* inst
* preparing package for lazy loading
Error : package 'codetools' was built before R 3.0.0: please re-install it
Error : unable to load R code in package 'Rcpp'
ERROR: lazy loading failed for package 'Rcpp'
* removing '/usr/local/lib/R/site-library/Rcpp'
* installing *source* package 'httpuv' ...
* package 'httpuv' successfully unpacked and MD5 sums checked
* libs
g++ -I/usr/share/R/include -DNDEBUG -I./libuv/include -I./http-parser -I./sha1 -I./base64 -I"/usr/lib/R/site-library/Rcpp/include" -fpic -O3 -pipe -g -c RcppExports.cpp -o RcppExports.o
RcppExports.cpp:75:10: error: 'uint32_t' was not declared in this scope
RcppExports.cpp: In function 'SEXPREC* httpuv_run(SEXP)':
RcppExports.cpp:79:5: error: 'uint32_t' was not declared in this scope
RcppExports.cpp:79:14: error: expected ';' before 'timeoutMillis'
RcppExports.cpp:80:25: error: 'timeoutMillis' was not declared in this scope
RcppExports.cpp:80:38: error: 'run' cannot be used as a function
make: * [RcppExports.o] Error 1
ERROR: compilation failed for package 'httpuv'
* removing '/usr/local/lib/R/site-library/httpuv'
ERROR: dependency 'httpuv' is not available for package 'shiny'
* removing '/usr/local/lib/R/site-library/shiny'
EDITED:
Manually downloading and installing Rcpp gives me:
sudo R CMD INSTALL Rcpp_0.10.6.tar.gz
Error : package 'codetools' was built before R 3.0.0: please re-install it
So I manually downloaded and installed codetools and re-tried Rcpp:
sudo R CMD INSTALL codetools_0.2-8.tar.gz
sudo R CMD INSTALL Rcpp_0.10.6.tar.gz
Then followed the instructions again from the Shiny webpage from "Install R" and "Install shiny" and got a similar error but now with caTools, bitops and xtable, so I did the manual installation of each of them. The shiny was installed correctly.
Then followed the next steps in the instructions.
Any ideas why I got this 'was built before R 3.0.0' errors?
Ubuntu 12.04 is a pre-R 3.0.0 release. You have to decide whether you want its long-term support and stability "as is", or if you want newer software.
You can mix and match. Read the CRAN Ubuntu README, adjust your apt settings and enjoy updated r-cran-* packages. With those you can then install shiny and its dependencies.
Manually downloading and installing Rcpp gives me:
sudo R CMD INSTALL Rcpp_0.10.6.tar.gz
Error : package 'codetools' was built before R 3.0.0: please re-install it
So I manually downloaded and installed codetools and re-tried Rcpp:
sudo R CMD INSTALL codetools_0.2-8.tar.gz
sudo R CMD INSTALL Rcpp_0.10.6.tar.gz
Then followed the instructions again from the Shiny webpage from "Install R" and "Install shiny" and got a similar error but now with caTools, bitops and xtable, so I did the manual installation of each of them. The shiny was installed correctly.
Then followed the next steps in the instructions. All went well from there. Not sure why I was getting these was built before 3.0.0 errors.