I have been trying to compile the R package PET on Fedora 35 (fully updated). It has been archived on CRAN for the past two years or so, but has installed for me before R 4.1.2. I am wondering whether it can be fixed.
I try:
devtools::install_github('cran/PET')
and I get errors, after a bunch of non-alarming messages:
Downloading GitHub repo cran/PET#HEAD
checking for file ‘/tmp/Rtmp2To7Lw/remotesed66e3dbe79/cran-PET-9793d0d/DESCRI✔ checking for file ‘/tmp/Rtmp2To7Lw/remotesed66e3dbe79/cran-PET-9793d0d/DESCRIPTION’
─ preparing ‘PET’:
✔ 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 ‘PET_0.5.1.tar.gz’
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘PET’ ...
** using staged installation
** libs
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c Hough.c -o Hough.o
Hough.c: In function ‘Hough4’:
Hough.c:41:10: warning: variable ‘theta_min’ set but not used [-Wunused-but-set-variable]
41 | double theta_min;
| ^~~~~~~~~
Hough.c:40:38: warning: variable ‘y’ set but not used [-Wunused-but-set-variable]
40 | double *costheta,*sintheta,theta,x,y;
| ^
Hough.c: In function ‘Hough3’:
Hough.c:118:10: warning: variable ‘theta_min’ set but not used [-Wunused-but-set-variable]
118 | double theta_min;
| ^~~~~~~~~
Hough.c: In function ‘Hough2’:
Hough.c:173:10: warning: variable ‘theta_min’ set but not used [-Wunused-but-set-variable]
173 | double theta_min;
| ^~~~~~~~~
Hough.c: In function ‘Hough1’:
Hough.c:227:10: warning: variable ‘theta_min’ set but not used [-Wunused-but-set-variable]
227 | double theta_min;
| ^~~~~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c PET_init.c -o PET_init.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c amatrix.c -o amatrix.o
amatrix.c: In function ‘RegulateMatrix’:
amatrix.c:234:10: warning: variable ‘tempVv’ set but not used [-Wunused-but-set-variable]
234 | float *tempVv;
| ^~~~~~
amatrix.c: In function ‘RegulateL1Matrix’:
amatrix.c:289:10: warning: variable ‘tempVv’ set but not used [-Wunused-but-set-variable]
289 | float *tempVv;
| ^~~~~~
amatrix.c: In function ‘GenerateAMatrixColumn’:
amatrix.c:784:9: warning: variable ‘onedivsq2’ set but not used [-Wunused-but-set-variable]
784 | float onedivsq2,psi,pidivDeltaX,costheta,sintheta,of;
| ^~~~~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c art.c -o art.o
art.c: In function ‘FAST_ART’:
art.c:128:10: warning: variable ‘tempXv’ set but not used [-Wunused-but-set-variable]
128 | float *tempXv,*tempBv;
| ^~~~~~
art.c: In function ‘SLOW_ART’:
art.c:239:10: warning: variable ‘tempXv’ set but not used [-Wunused-but-set-variable]
239 | float *tempXv,*tempBv;
| ^~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c calc.c -o calc.o
calc.c: In function ‘BackFilter’:
calc.c:335:19: warning: variable ‘M’ set but not used [-Wunused-but-set-variable]
335 | int i,m,n,mm,nn,M,N,OldHeight,OldWidth;
| ^
calc.c: In function ‘CentralSliceCZ’:
calc.c:700:49: warning: variable ‘rhomin’ set but not used [-Wunused-but-set-variable]
700 | float DC,deltatheta,theta,thetaadj,*realtheta,rhomin,deltarho;
| ^~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cg.c -o cg.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c em.c -o em.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c eval.c -o eval.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c imgtools.c -o imgtools.o
imgtools.c: In function ‘ReadPET’:
imgtools.c:1005:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
1005 | size_t result;
| ^~~~~~
imgtools.c: In function ‘ReadFIFHeader’:
imgtools.c:1148:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
1148 | size_t result;
| ^~~~~~
imgtools.c: In function ‘ReadFIF’:
imgtools.c:1222:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
1222 | size_t result;
| ^~~~~~
imgtools.c: In function ‘ReadAnalyze’:
imgtools.c:1616:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
1616 | size_t result;
| ^~~~~~
imgtools.c:1614:21: warning: variable ‘OffSet’ set but not used [-Wunused-but-set-variable]
1614 | float ScaleFactor,OffSet;
| ^~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c iradon.c -o iradon.o
iradon.c: In function ‘iradon’:
iradon.c:271:5: warning: ‘spectrum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
271 | FreeImage(spectrum);
| ^~~~~~~~~~~~~~~~~~~
iradon.c: In function ‘loadFile’:
iradon.c:568:9: warning: ‘list’ may be used uninitialized in this function [-Wmaybe-uninitialized]
568 | return(list);
| ^
iradon.c:404:16: warning: ‘typeF’ may be used uninitialized in this function [-Wmaybe-uninitialized]
404 | OutImage = ReadImage(fileName, typeF);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
iradon.c: In function ‘writeFile’:
iradon.c:684:19: warning: ‘N’ may be used uninitialized in this function [-Wmaybe-uninitialized]
684 | SaveImage=NewFloatImage(fileName, M, N, _RealArray);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iradon.c:684:19: warning: ‘M’ may be used uninitialized in this function [-Wmaybe-uninitialized]
iradon.c:772:5: warning: ‘typeF’ may be used uninitialized in this function [-Wmaybe-uninitialized]
772 | WriteImage(SaveImage, typeF);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c it.c -o it.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c itreadargs.c -o itreadargs.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c misc.c -o misc.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c oradLI.c -o oradLI.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c oradNN.c -o oradNN.o
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c oradSINC.c -o oradSINC.o
oradSINC.c: In function ‘radonSINC’:
oradSINC.c:52:10: warning: variable ‘idx’ set but not used [-Wunused-but-set-variable]
52 | double idx,mintrig,psi;
| ^~~
gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sparse.c -o sparse.o
sparse.c: In function ‘ReadSIFHeader’:
sparse.c:607:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
607 | size_t result;
| ^~~~~~
sparse.c: In function ‘ReadSIF’:
sparse.c:657:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
657 | size_t result;
| ^~~~~~
sparse.c: In function ‘MeanFilterVector’:
sparse.c:1537:13: warning: variable ‘area’ set but not used [-Wunused-but-set-variable]
1537 | float sum,area,*tempVv,*tempNv,*tempKernM;
|
gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o PET.so Hough.o PET_init.o amatrix.o art.o calc.o cg.o em.o eval.o imgtools.o iradon.o it.o itreadargs.o misc.o oradLI.o oradNN.o oradSINC.o sparse.o -L/usr/lib64/R/lib -lR
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `DebugNiveau'; iradon.o (symbol from plugin):(.text+0x0): first defined here
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `IniFile'; iradon.o (symbol from plugin):(.text+0x0): first defined here
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `multtemp'; iradon.o (symbol from plugin):(.text+0x0): first defined here
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `LogFileName'; iradon.o (symbol from plugin):(.text+0x0): first defined here
/usr/bin/ld: it.o (symbol from plugin): in function `SaveIteration':
(.text+0x0): multiple definition of `LogFile'; iradon.o (symbol from plugin):(.text+0x0): first defined here
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/make/shlib.mk:10: PET.so] Error 1
ERROR: compilation failed for package ‘PET’
* removing ‘/usr/lib64/R/library/PET’
* restoring previous ‘/usr/lib64/R/library/PET’
Warning message:
In i.p(...) :
installation of package ‘/tmp/Rtmp2To7Lw/fileed67b515c13/PET_0.5.1.tar.gz’ had non-zero exit status
Any suggestions as to how i can get this to compile? I need to use the Radon transform on some images.
Thanks!
I am getting an error in installing passenger nginx in MAC 10.14.
here are the logs:
src/cxx_supportlib/vendor-modified/boost/atomic/detail/ops_gcc_x86_dcas.hpp:408:16: error:
address argument to atomic builtin cannot be const-qualified
('const volatile
boost::atomics::detail::gcc_dcas_x86_64::storage_type *' (aka
'const volatile unsigned __int128 *') invalid)
return __sync_val_compare_and_swap(&storage, value, value);
^ ~~~~~~~~
1 error generated.
rake aborted!
Command failed with status (1): [c++ -o buildout/support-binaries/AgentFundamentals.o -Isrc/agent -Isrc/cxx_supportlib -Isrc/cxx_supportlib/vendor-copy -Isrc/cxx_supportlib/vendor-modified -Isrc/cxx_supportlib/vendor-modified/libev -Wno-ambiguous-member-template -Isrc/cxx_supportlib/vendor-copy/libuv/include -Isrc/cxx_supportlib/vendor-copy/websocketpp -I/usr/local/opt/openssl/include -D_REENTRANT -I/usr/local/include -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wpointer-arith -Wwrite-strings -Wno-long-long -Wno-missing-field-initializers -Wno-ambiguous-member-template -fvisibility=hidden -DVISIBILITY_ATTRIBUTE_SUPPORTED -DHAS_ALLOCA_H -DHAS_SFENCE -DHAS_LFENCE -DPASSENGER_DEBUG -DBOOST_DISABLE_ASSERTS -g -fno-limit-debug-info -std=gnu++11 -Wno-unused-local-typedefs -Wno-format-nonliteral -DHAS_UNORDERED_MAP -c src/agent/Shared/Fundamentals/Implementation.cpp]
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/gems/passenger-6.0.2/build/support/cplusplus.rb:53:in `run_compiler'
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/gems/passenger-6.0.2/build/support/cplusplus.rb:104:in `compile_cxx'
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/gems/passenger-6.0.2/build/support/cplusplus.rb:162:in `block in define_cxx_object_compilation_task'
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/bin/ruby_executable_hooks:24:in `eval'
/Users/narendrakumawat/.rvm/gems/ruby-2.2.5#rails4115/bin/ruby_executable_hooks:24:in `<main>'
Tasks: TOP => nginx => nginx_without_native_support => buildout/support-binaries/PassengerAgent => buildout/support-binaries/AgentFundamentals.o
(See full trace by running task with --trace)
I already tried this also :
https://github.com/phusion/passenger/issues/2199
I've uploaded my R code on the company's server in order to run it. It was running smoothly on my local R studio and now when I try to run it with Rscript my_script.r I get an enormous amount of errors when trying to install very basic libraries.
if (!require("ggrepel")) {
install.packages("ggrepel", repos="http://cran.fhcrc.org")
library(ggrepel)
}
if (!require("ggplot2")) {
install.packages("ggplot2", repos="http://cran.fhcrc.org")
library("ggplot2")
}
if (!require("gridExtra")) {
install.packages("gridExtra", repos="http://cran.fhcrc.org")
library("gridExtra")
}
This is my code to install the libraries and here's the error:
Loading required package: ggrepel
Installing package into ‘/home/yoda/Rlibs’
(as ‘lib’ is unspecified)
also installing the dependencies ‘tibble’, ‘ggplot2’
trying URL 'http://cran.fhcrc.org/src/contrib/tibble_1.2.tar.gz'
Content type 'application/x-gzip' length 54517 bytes (53 KB)
==================================================
downloaded 53 KB
trying URL 'http://cran.fhcrc.org/src/contrib/ggplot2_2.2.1.tar.gz'
Content type 'application/x-gzip' length 2213308 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'http://cran.fhcrc.org/src/contrib/ggrepel_0.6.5.tar.gz'
Content type 'application/x-gzip' length 568599 bytes (555 KB)
==================================================
downloaded 555 KB
* installing *source* package ‘tibble’ ...
** package ‘tibble’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c matrixToDataFrame.cpp -o matrixToDataFrame.o
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 10; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:91:48: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<10>’
typename Matrix<RTYPE>::ConstColumn column( m.column(j) ) ;
^
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<10>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<10>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 13; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:92:48: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<13>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<13>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<13>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 14; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:93:49: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<14>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<14>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<14>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 15; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:94:49: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<15>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<15>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<15>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 16; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:95:48: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<16>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<16>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<16>’
matrixToDataFrame.cpp: In instantiation of ‘Rcpp::List copy_columns(const Rcpp::Matrix<RTYPE>&) [with int RTYPE = 19; Rcpp::List = Rcpp::Vector<19>]’:
matrixToDataFrame.cpp:96:48: required from here
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<19>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<19>’
matrixToDataFrame.cpp:71:41: error: no type named ‘ConstColumn’ in ‘class Rcpp::Matrix<19>’
make: *** [matrixToDataFrame.o] Error 1
ERROR: compilation failed for package ‘tibble’
* removing ‘/home/yoda/Rlibs/tibble’
ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
* removing ‘/home/yoda/Rlibs/ggplot2’
* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c repel_boxes.cpp -o repel_boxes.o
g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o ggrepel.so RcppExports.o repel_boxes.o -L/usr/lib64/R/lib -lR
installing to /home/yoda/Rlibs/ggrepel/libs
** R
** inst
** preparing package for lazy loading
Error : package ‘ggplot2’ 1.0.1 was found, but >= 2.0.0 is required by ‘ggrepel’
ERROR: lazy loading failed for package ‘ggrepel’
* removing ‘/home/yoda/Rlibs/ggrepel’
The downloaded source packages are in
‘/tmp/RtmpukzDll/downloaded_packages’
Error in library(ggrepel) : there is no package called ‘ggrepel’
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘ggrepel’
2: In install.packages("ggrepel", repos = "http://cran.fhcrc.org") :
installation of package ‘tibble’ had non-zero exit status
3: In install.packages("ggrepel", repos = "http://cran.fhcrc.org") :
installation of package ‘ggplot2’ had non-zero exit status
4: In install.packages("ggrepel", repos = "http://cran.fhcrc.org") :
installation of package ‘ggrepel’ had non-zero exit status
Execution halted
I have no idea what's going on, and I have to submit this. Is there any way without having sudo rights to download and install an R package?
I am trying to make qTuio(https://github.com/x29a/qTUIO) on my windows machine. However, when I try to run make, it reports: "<< was unexpected at this time"
The full output is:
cl -c -nologo -Zm200 -Zc:wchar_t- -Zi -MDd -GR -EHsc -W3 -w34100 -w34189 -DUNICO
DE -DWIN32 -DQT_LARGEFILE_SUPPORT -DOSC_HOST_LITTLE_ENDIAN -DQT_DLL -DQT_GUI_LIB
-DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_HAVE_MMX -DQT_HAVE_3DNOW -DQT_HAVE_SSE -DQT
_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_THREAD_SUPPORT -I"c:\OSGeo4W\include\qt4\QtCore
" -I"c:\OSGeo4W\include\qt4\QtNetwork" -I"c:\OSGeo4W\include\qt4\QtGui" -I"c:\OS
Geo4W\include\qt4" -I"..\..\tmp\debug" -I"..\..\tmp" -I"..\3rdparty\oscpack" -I"
..\3rdparty\tuio" -I"c:\OSGeo4W\include\qt4\ActiveQt" -I"..\tmp\debug" -I"." -I"
c:\OSGeo4W\apps\qt4\mkspecs\win32-msvc2008" -Fo..\tmp\debug\ #<<
<< was unexpected at this time.
make[1]: *** [{..}.cpp{..\tmp\debug\}.obj] Error 1
make: *** [debug] Error 2
Any help is appreciated
I installed QT 5.1 VS2012 release and installed successfuly.
I get error while compilng the project in QT Creator with the 'jom' thingy saying:
"jom: F:\tmp2\build-testprj-Desktop_Qt_5_1_0_MSVC2012_32bit-Debug\Makefile.Debug [debug\mainwindow.obj] Error 2
jom: F:\tmp2\build-testprj-Desktop_Qt_5_1_0_MSVC2012_32bit-Debug\Makefile.Debug [debug\moc_mainwindow.obj] Error 2
jom: F:\tmp2\build-testprj-Desktop_Qt_5_1_0_MSVC2012_32bit-Debug\Makefile [debug] Error 2
17:30:06: The process "C:\Qt\Qt5.1.0\Tools\QtCreator\bin\jom.exe" exited with code 2.
Error while building/deploying project testprj (kit: Desktop Qt 5.1.0 MSVC2012 32bit)
When executing step 'Make'"
"17:56:29: Running steps for project untitled...
17:56:29: Configuration unchanged, skipping qmake step.
17:56:29: Starting: "C:\Qt\Qt5.0.0\Tools\QtCreator\bin\jom.exe"
C:\Qt\Qt5.0.0\Tools\QtCreator\bin\jom.exe -f Makefile.Debug
cl -c -nologo -Zm200 -Zc:wchar_t -Zi -MDd -GR -W3 -w34100 -w34189 -EHsc -DUNICODE -DWIN32 -DQT_QML_DEBUG -DQT_DECLARATIVE_DEBUG -DQT_PRINTSUPPORT_LIB -DQT_WIDGETS_LIB -DQT_SQL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_OPENGL_ES_2 -DQT_OPENGL_ES_2_ANGLE -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtPrintSupport" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtWidgets" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtSql" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtGui" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtCore" -I"debug" -I"." -I"." -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\mkspecs\win32-msvc2010" -Fodebug\ #C:\Users\BAHADI~1.AYD\AppData\Local\Temp\main.obj.2740.16.jom
jom: F:\tmp2\untitled-build-Desktop_Qt_5_0_0_MSVC2010_32bit_SDK-Debug\Makefile.Debug [debug\main.obj] Error 2
cl -c -nologo -Zm200 -Zc:wchar_t -Zi -MDd -GR -W3 -w34100 -w34189 -EHsc -DUNICODE -DWIN32 -DQT_QML_DEBUG -DQT_DECLARATIVE_DEBUG -DQT_PRINTSUPPORT_LIB -DQT_WIDGETS_LIB -DQT_SQL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_OPENGL_ES_2 -DQT_OPENGL_ES_2_ANGLE -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtPrintSupport" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtWidgets" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtSql" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtGui" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtCore" -I"debug" -I"." -I"." -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\mkspecs\win32-msvc2010" -Fodebug\ #C:\Users\BAHADI~1.AYD\AppData\Local\Temp\qcustomplot.obj.2740.16.jom
cl -c -nologo -Zm200 -Zc:wchar_t -Zi -MDd -GR -W3 -w34100 -w34189 -EHsc -DUNICODE -DWIN32 -DQT_QML_DEBUG -DQT_DECLARATIVE_DEBUG -DQT_PRINTSUPPORT_LIB -DQT_WIDGETS_LIB -DQT_SQL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_OPENGL_ES_2 -DQT_OPENGL_ES_2_ANGLE -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtPrintSupport" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtWidgets" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtSql" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtGui" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtCore" -I"debug" -I"." -I"." -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\mkspecs\win32-msvc2010" -Fodebug\ #C:\Users\BAHADI~1.AYD\AppData\Local\Temp\dbhelper.obj.2740.16.jom
cl -c -nologo -Zm200 -Zc:wchar_t -Zi -MDd -GR -W3 -w34100 -w34189 -EHsc -DUNICODE -DWIN32 -DQT_QML_DEBUG -DQT_DECLARATIVE_DEBUG -DQT_PRINTSUPPORT_LIB -DQT_WIDGETS_LIB -DQT_SQL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_OPENGL_ES_2 -DQT_OPENGL_ES_2_ANGLE -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtPrintSupport" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtWidgets" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtSql" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtGui" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtCore" -I"debug" -I"." -I"." -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\mkspecs\win32-msvc2010" -Fodebug\ #C:\Users\BAHADI~1.AYD\AppData\Local\Temp\mainwindow.obj.2740.32.jom
cl -c -nologo -Zm200 -Zc:wchar_t -Zi -MDd -GR -W3 -w34100 -w34189 -EHsc -DUNICODE -DWIN32 -DQT_QML_DEBUG -DQT_DECLARATIVE_DEBUG -DQT_PRINTSUPPORT_LIB -DQT_WIDGETS_LIB -DQT_SQL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_OPENGL_ES_2 -DQT_OPENGL_ES_2_ANGLE -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtPrintSupport" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtWidgets" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtSql" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtGui" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtCore" -I"debug" -I"." -I"." -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\mkspecs\win32-msvc2010" -Fodebug\ #C:\Users\BAHADI~1.AYD\AppData\Local\Temp\moc_mainwindow.obj.2740.32.jom
cl -c -nologo -Zm200 -Zc:wchar_t -Zi -MDd -GR -W3 -w34100 -w34189 -EHsc -DUNICODE -DWIN32 -DQT_QML_DEBUG -DQT_DECLARATIVE_DEBUG -DQT_PRINTSUPPORT_LIB -DQT_WIDGETS_LIB -DQT_SQL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_OPENGL_ES_2 -DQT_OPENGL_ES_2_ANGLE -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtPrintSupport" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtWidgets" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtSql" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtGui" -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\include\QtCore" -I"debug" -I"." -I"." -I"C:\Qt\Qt5.0.0\5.0.0\msvc2010\mkspecs\win32-msvc2010" -Fodebug\ #C:\Users\BAHADI~1.AYD\AppData\Local\Temp\moc_qcustomplot.obj.2740.32.jom
jom: F:\tmp2\untitled-build-Desktop_Qt_5_0_0_MSVC2010_32bit_SDK-Debug\Makefile.Debug [debug\qcustomplot.obj] Error 2
jom: F:\tmp2\untitled-build-Desktop_Qt_5_0_0_MSVC2010_32bit_SDK-Debug\Makefile.Debug [debug\mainwindow.obj] Error 2
jom: F:\tmp2\untitled-build-Desktop_Qt_5_0_0_MSVC2010_32bit_SDK-Debug\Makefile.Debug [debug\moc_mainwindow.obj] Error 2
jom: F:\tmp2\untitled-build-Desktop_Qt_5_0_0_MSVC2010_32bit_SDK-Debug\Makefile.Debug [debug\moc_qcustomplot.obj] Error 2"