Having trouble installing R package httpuv - r

I am using R 3.3.3 on Debian/Linux 8 and I am having trouble installing the package httpuv, which is a dependency for another package I want to use. The installing error message is shown below. It seems like there are problems with libuv, but I am not sure about this.
How can I figure out where the problem is and how to fix it?
> install.packages("httpuv")
Installing package into ‘/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.cnr.berkeley.edu/src/contrib/httpuv_1.5.1.tar.gz'
Content type 'unknown' length 1758514 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
* installing *source* package ‘httpuv’ ...
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** libs
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports-legacy.cpp -o RcppExports-legacy.o
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c callback.cpp -o callback.o
g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -Ilibuv/include -pthread -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -I"/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/later/include" -DSTRICT_R_HEADERS -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c callbackqueue.cpp -o callbackqueue.o
In file included from libuv/include/uv.h:62:0,
from thread.h:4,
from tqueue.h:7,
from callbackqueue.h:4,
from callbackqueue.cpp:1:
libuv/include/uv/unix.h:103:28: error: ‘sem_t’ does not name a type
# define UV_PLATFORM_SEM_T sem_t
^
libuv/include/uv/unix.h:135:9: note: in expansion of macro ‘UV_PLATFORM_SEM_T’
typedef UV_PLATFORM_SEM_T uv_sem_t;
^
In file included from thread.h:4:0,
from tqueue.h:7,
from callbackqueue.h:4,
from callbackqueue.cpp:1:
libuv/include/uv.h:1562:27: error: ‘uv_sem_t’ was not declared in this scope
UV_EXTERN int uv_sem_init(uv_sem_t* sem, unsigned int value);
^
libuv/include/uv.h:1562:37: error: ‘sem’ was not declared in this scope
UV_EXTERN int uv_sem_init(uv_sem_t* sem, unsigned int value);
^
libuv/include/uv.h:1562:42: error: expected primary-expression before ‘unsigned’
UV_EXTERN int uv_sem_init(uv_sem_t* sem, unsigned int value);
^
libuv/include/uv.h:1562:60: error: expression list treated as compound expression in initializer [-fpermissive]
UV_EXTERN int uv_sem_init(uv_sem_t* sem, unsigned int value);
^
libuv/include/uv.h:1563:31: error: variable or field ‘uv_sem_destroy’ declared void
UV_EXTERN void uv_sem_destroy(uv_sem_t* sem);
^
libuv/include/uv.h:1563:31: error: ‘uv_sem_t’ was not declared in this scope
libuv/include/uv.h:1563:41: error: ‘sem’ was not declared in this scope
UV_EXTERN void uv_sem_destroy(uv_sem_t* sem);
^
libuv/include/uv.h:1564:28: error: variable or field ‘uv_sem_post’ declared void
UV_EXTERN void uv_sem_post(uv_sem_t* sem);
^
libuv/include/uv.h:1564:28: error: ‘uv_sem_t’ was not declared in this scope
libuv/include/uv.h:1564:38: error: ‘sem’ was not declared in this scope
UV_EXTERN void uv_sem_post(uv_sem_t* sem);
^
libuv/include/uv.h:1565:28: error: variable or field ‘uv_sem_wait’ declared void
UV_EXTERN void uv_sem_wait(uv_sem_t* sem);
^
libuv/include/uv.h:1565:28: error: ‘uv_sem_t’ was not declared in this scope
libuv/include/uv.h:1565:38: error: ‘sem’ was not declared in this scope
UV_EXTERN void uv_sem_wait(uv_sem_t* sem);
^
libuv/include/uv.h:1566:30: error: ‘uv_sem_t’ was not declared in this scope
UV_EXTERN int uv_sem_trywait(uv_sem_t* sem);
^
libuv/include/uv.h:1566:40: error: ‘sem’ was not declared in this scope
UV_EXTERN int uv_sem_trywait(uv_sem_t* sem);
^
/usr/lib/R/etc/Makeconf:141: recipe for target 'callbackqueue.o' failed
make: *** [callbackqueue.o] Error 1
ERROR: compilation failed for package ‘httpuv’
* removing ‘/data/home/yh362/R/x86_64-pc-linux-gnu-library/3.3/httpuv’
The downloaded source packages are in
‘/tmp/Rtmpqg62zZ/downloaded_packages’
Warning message:
In install.packages("httpuv") :
installation of package ‘httpuv’ had non-zero exit status

I had the same error and tried several installations to make it work:
Install Java jre and jdk
Install devtools install.packages("devtools")
In the console, run .libPaths() to see where packages are installed.
Make sure to get full permission from your library directory
Run devtools::install_github("rstudio/httpuv", lib = "directory from 3.") in the console.

Related

Local package install with undefined reference error

I am very new to the R extension with C.
The scenario is:
I want to implement the code in one package from one paper which is quite old (2007 or earlier).
I first tried to install the package with the commend
install.packages("~/ppmx_1.0.tar.gz", repos = NULL, type = "source")
Then I got errors and warnings (I am sorry it it quite long)
** libs
*** arch - i386
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bayes.c -o bayes.o
bayes.c: In function 'nn_bayes1':
bayes.c:107:5: warning: variable 'sd' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c cdf.c -o cdf.o
cdf.c:3:1: warning: "/*" within comment [-Wcomment]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c com.c -o com.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dcdflib.c -o dcdflib.o
dcdflib.c: In function 'cdfbin':
dcdflib.c:1889:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c: In function 'cdfgam':
dcdflib.c:3551:9: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c: In function 'E0000':
dcdflib.c:6410:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c:6434:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c:6475:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
dcdflib.c:6342:56: warning: variable 'qok' set but not used [-Wunused-but-set-variable]
dcdflib.c: In function 'E0001':
dcdflib.c:6877:5: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fortif.c -o fortif.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c interface.c -o interface.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ipmpar.c -o ipmpar.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c matrix.c -o matrix.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mess.c -o mess.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c nrutil.c -o nrutil.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ppmx.c -o ppmx.o
ppmx.c: In function 'init':
ppmx.c:69:8: warning: unused variable 'line' [-Wunused-variable]
ppmx.c:68:10: warning: unused variable 'r' [-Wunused-variable]
ppmx.c: In function 'init_config':
ppmx.c:382:13: warning: unused variable 'ct' [-Wunused-variable]
ppmx.c: In function 'gibbs':
ppmx.c:426:7: warning: unused variable 'time' [-Wunused-variable]
ppmx.c: In function 'sample_config':
ppmx.c:470:11: warning: unused variable 'j' [-Wunused-variable]
ppmx.c:470:7: warning: unused variable 'si' [-Wunused-variable]
ppmx.c: In function 'loglik':
ppmx.c:589:11: warning: unused variable 'offset' [-Wunused-variable]
ppmx.c:589:9: warning: unused variable 'k' [-Wunused-variable]
ppmx.c:589:7: warning: unused variable 'j' [-Wunused-variable]
ppmx.c: In function 'make_Sk':
ppmx.c:725:10: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
ppmx.c:724:12: warning: unused variable 'j2' [-Wunused-variable]
ppmx.c:724:9: warning: unused variable 'j1' [-Wunused-variable]
ppmx.c: In function 'make_Sk1':
ppmx.c:742:10: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
ppmx.c:741:12: warning: unused variable 'j2' [-Wunused-variable]
ppmx.c:741:9: warning: unused variable 'j1' [-Wunused-variable]
ppmx.c: In function 'sample_V':
ppmx.c:838:9: warning: unused variable 'j2' [-Wunused-variable]
ppmx.c:838:6: warning: unused variable 'j1' [-Wunused-variable]
ppmx.c:837:5: warning: unused variable 'V11' [-Wunused-variable]
ppmx.c: In function 'sample_S':
ppmx.c:894:23: warning: unused variable 'S1' [-Wunused-variable]
ppmx.c:894:18: warning: unused variable 'Vinv' [-Wunused-variable]
ppmx.c:892:12: warning: unused variable 'j2' [-Wunused-variable]
ppmx.c:892:9: warning: unused variable 'j1' [-Wunused-variable]
ppmx.c: In function 'setup_mj1':
ppmx.c:1070:20: warning: unused variable 'mu' [-Wunused-variable]
ppmx.c: In function 'setup_aj4':
ppmx.c:1147:13: warning: unused variable 'b1' [-Wunused-variable]
ppmx.c:1147:10: warning: unused variable 'a1' [-Wunused-variable]
ppmx.c: In function 'print_pars':
ppmx.c:1267:7: warning: too many arguments for format [-Wformat-extra-args]
ppmx.c: In function 'write_nclass':
ppmx.c:1401:7: warning: unused variable 'j' [-Wunused-variable]
ppmx.c:1407:1: warning: control reaches end of non-void function [-Wreturn-type]
ppmx.c: In function 'update_nclass':
ppmx.c:1396:1: warning: control reaches end of non-void function [-Wreturn-type]
ppmx.c: In function 'print_allpars':
ppmx.c:1344:1: warning: control reaches end of non-void function [-Wreturn-type]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c predict2.c -o predict2.o
predict2.c: In function 'py_update':
predict2.c:173:5: warning: unused variable 'y' [-Wunused-variable]
predict2.c:169:22: warning: unused variable 'lpr' [-Wunused-variable]
predict2.c:169:10: warning: variable 'kd' set but not used [-Wunused-but-set-variable]
predict2.c: In function 'print_pyvec':
predict2.c:343:5: warning: too many arguments for format [-Wformat-extra-args]
predict2.c: In function 'pyvec_update':
predict2.c:366:9: warning: unused variable 'sx' [-Wunused-variable]
predict2.c:364:9: warning: unused variable 'lgr' [-Wunused-variable]
predict2.c:364:5: warning: unused variable 'hC' [-Wunused-variable]
predict2.c:363:5: warning: unused variable 'r' [-Wunused-variable]
predict2.c:360:22: warning: unused variable 'lpr' [-Wunused-variable]
predict2.c:360:10: warning: variable 'kd' set but not used [-Wunused-but-set-variable]
predict2.c:358:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
predict2.c: In function 'py_update':
predict2.c:213:11: warning: 'mxh' may be used uninitialized in this function [-Wuninitialized]
predict2.c:171:5: warning: 'wmx' may be used uninitialized in this function [-Wuninitialized]
predict2.c: In function 'pyvec_update':
predict2.c:438:16: warning: 'V' may be used uninitialized in this function [-Wuninitialized]
predict2.c:438:16: warning: 'm' may be used uninitialized in this function [-Wuninitialized]
predict2.c:361:5: warning: 'wmx' may be used uninitialized in this function [-Wuninitialized]
predict2.c:427:12: warning: 'k0' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rand-nr.c -o rand-nr.o
rand-nr.c:5:1: warning: "/*" within comment [-Wcomment]
rand-nr.c:65:1: warning: "/*" within comment [-Wcomment]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rand.c -o rand.o
In file included from rand.c:60:0:
mathconst.h:23:0: warning: "M_PI" redefined [enabled by default]
c:\rtools\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:45:0: note: this is the location of the previous definition
rand.c:77:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
rand.c: In function 'pdf_norm_trunc':
rand.c:380:28: warning: variable 'lpdf' set but not used [-Wunused-but-set-variable]
rand.c:380:10: warning: unused variable 'u' [-Wunused-variable]
rand.c: In function 'cdfbeta':
rand.c:491:20: warning: variable 'x1' set but not used [-Wunused-but-set-variable]
rand.c: In function 'expdev':
rand.c:737:5: warning: variable 'b' set but not used [-Wunused-but-set-variable]
rand.c: At top level:
cdflib.h:45:13: warning: 'E0000' declared 'static' but never defined [-Wunused-function]
cdflib.h:52:13: warning: 'E0001' declared 'static' but never defined [-Wunused-function]
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ranlib.c -o ranlib.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c regr.c -o regr.o
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c unixrep.c -o unixrep.o
In file included from unixrep.c:31:0:
mathconst.h:23:0: warning: "M_PI" redefined [enabled by default]
c:\rtools\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:45:0: note: this is the location of the previous definition
gcc -m32 -I"C:/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c vector.c -o vector.o
gcc -m32 -shared -s -static-libgcc -o ppmx.dll tmp.def bayes.o cdf.o com.o dcdflib.o fortif.o interface.o ipmpar.o matrix.o mess.o nrutil.o ppmx.o predict2.o rand-nr.o rand.o ranlib.o regr.o unixrep.o vector.o -LC:/R-31~1.0/bin/i386 -lRlapack -LC:/R-31~1.0/bin/i386 -lRblas -lm -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R-31~1.0/bin/i386 -lR
fortif.o:fortif.c:(.text+0x38): undefined reference to `DPOTRF#24'
fortif.o:fortif.c:(.text+0x88): undefined reference to `DPOTRI#24'
fortif.o:fortif.c:(.text+0xf9): undefined reference to `DTRTRI#32'
fortif.o:fortif.c:(.text+0x181): undefined reference to `DSYEV#44'
collect2: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'ppmx'
* removing 'C:/R-3.1.0/library/ppmx'
Warning in install.packages :
running command '"C:/R-31~1.0/bin/x64/R" CMD INSTALL -l "C:\R-3.1.0\library" "C:/Users/kutrds11/Documents/ppmx_1.3.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/kutrds11/Documents/ppmx_1.3.tar.gz’ had non-zero exit status
I doubt the problem is the way to call .c file too old?
I know the problem is quite complicated. Is there anyone could help me please. I guess it is about the link problem bec of
fortif.o:fortif.c:(.text+0x38): undefined reference to `DPOTRF#24'
fortif.o:fortif.c:(.text+0x88): undefined reference to `DPOTRI#24'
fortif.o:fortif.c:(.text+0xf9): undefined reference to `DTRTRI#32'
fortif.o:fortif.c:(.text+0x181): undefined reference to `DSYEV#44'
I think I need toensure that my program is linked with a Lapack
library.. But I dont know how..
The fortif.c code is
static const char fortif_c_sccs_id[] = "%W%";
/*+
* fortif.c - Fortran Interface
*
* Version: %I%
*
* Description:
* Handles the interface between FORTRAN and C on the two platforms, by
* providing a single C interface to the Fortran routine, and dispatching
* according to the platform.
*
* This particular file only contains Win32 interface routines for FORTRAN
* subroutines that have a character arguments. When a FORTRAN routine is
* compiled, for each character argument in the signature the compiler
* adds another unsigned long argument immediately following it, that
* holds the length of the char array being passed to it.
*
* In Response\01, we have C routines calling FORTRAN ones, and the size
* of the char array is generally unknown (it may be passed in from the
* caller's caller). However, for the FORTRAN routines we are interested
* in, the character argument is input only, not being changed by the
* routine. Therefore, we can use the length of the string represented by
* the "char*" argument as a suitable length to pass to the FORTRAN code.
*
* Note that this ".c" file does not contain interfaces for routines that
* do not pass in character arguments; these interfaces can be handled
* by simple definitions in the associated header file.
*
* Modification History:
* 10-JUN-1999 1.1 Stephen Morris (Tessella Support Services plc)
* Created.
-*/
#include <string.h>
#define FORTIF_H_SCCS_ID
#include "fortif.h"
#if defined(_WIN32)
/*+
* dpotrf - Lapack Routine
-*/
extern void __stdcall DPOTRF(char *uplo, unsigned int uplo_length, int *n,
double *a, int *ncol_a, int *info);
void dpotrf(char *uplo, int *n, double *a, int *ncol_a, int *info)
{
DPOTRF(uplo, (unsigned int) strlen(uplo), n, a, ncol_a, info);
}
/*+
* dpotri - Lapack Routine
-*/
extern void __stdcall DPOTRI(char *uplo, unsigned int uplo_length, int *n,
double *a, int *ncol_a, int *info);
void dpotri(char *uplo, int *n, double *a, int *ncol_a, int *info)
{
DPOTRI(uplo, (unsigned int) strlen(uplo), n, a, ncol_a, info);
}
/*+
* dtrtri - Lapack Routine
-*/
extern void __stdcall DTRTRI(char *uplo, unsigned int uplo_length,
char *diag, unsigned int diag_len, int *n, double *a, int *ncol_a, int *info);
void dtrtri(char *uplo, char *diag, int *n, double *a, int *ncol_a, int *info)
{
DTRTRI(uplo, (unsigned int) strlen(uplo), diag, (unsigned int) strlen(diag),
n, a, ncol_a, info);
}
/*+
* dsyev - Lapack Routine
*/
extern void __stdcall DSYEV(char *jobz, unsigned int jobz_length,
char *uplo, unsigned int uplo_length, int *n, double *a, int *lda,
double *w, double *work, int *lwork, int *info);
void dsyev(char *jobz, char *uplo, int *n, double *a, int *lda, double *w, double *work,
int *lwork, int *info)
{
DSYEV(jobz, (unsigned int) strlen(jobz), uplo, (unsigned int) strlen(uplo),
n, a, lda, w, work, lwork, info);
}
#endif
Please help me.
I have put the link of the code below just in case:
https://www.tandfonline.com/doi/suppl/10.1198/jcgs.2011.09066?scroll=top
Please let me know if you need more specific information
Thank you so much in advance

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$ sudo apt-get install r-cran-curl r-cran-openssl r-cran-xml2
$ R
> install.packages("tidyverse")
Following the above procedure ends with the following as output in the R interactive terminal:
Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.0.tar.gz'
Content type 'application/x-gzip' length 712837 bytes (696 KB)
==================================================
downloaded 696 KB
* installing *source* package ‘tidyverse’ ...
** package ‘tidyverse’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘$.rlang_ctxt_pronoun’, ‘$.rlang_data_pronoun’, ‘$.rlang_fake_data_pronoun’, ‘$<-.quosures’, ‘$<-.rlang_ctxt_pronoun’, ‘$<-.rlang_data_pronoun’, ‘[.quosure’, ‘[.quosures’, ‘[.rlang_data_pronoun’, ‘[.rlang_envs’, ‘[.stack’, ‘[<-.quosures’, ‘[[.quosure’, ‘[[.rlang_ctxt_pronoun’, ‘[[.rlang_data_pronoun’, ‘[[.rlang_fake_data_pronoun’, ‘[[<-.quosures’, ‘[[<-.rlang_ctxt_pronoun’, ‘[[<-.rlang_data_pronoun’, ‘Math.quosure’, ‘Ops.quosure’, ‘Summary.quosure’, ‘as.character.quosure’, ‘as.list.quosures’, ‘c.quosures’, ‘c.rlang_envs’, ‘cnd_footer.default’, ‘cnd_header.default’, ‘conditionMessage.rlang_error’, ‘format.rlang_error’, ‘format.rlang_trace’, ‘length.rlang_ctxt_pronoun’, ‘length.rlang_data_pronoun’, ‘length.rlang_fake_data_pronoun’, ‘mean.quosure’, ‘median.quosure’, ‘names.rlang_ctxt_pronoun’, ‘names.rlang_data_pronoun’, ‘name [... truncated]
Error in namespaceExport(ns, exports) :
undefined exports: !!!, !!, %#%, %#%<-, %|%, %||%, :=, f_env<-, f_lhs<-, f_rhs<-, fn_body<-, fn_env<-, fn_fmls<-, fn_fmls_names<-, .data, UQ, UQS, abort, are_na, arg_match, as_box, as_box_if, as_bytes, as_character, as_closure, as_complex, as_data_mask, as_data_pronoun, as_double, as_env, as_environment, as_function, as_integer, as_label, as_list, as_logical, as_name, as_overscope, as_pairlist, as_quosure, as_quosures, as_string, as_utf8_character, base_env, bytes, bytes_along, bytes_len, call2, call_args, call_args_names, call_depth, call_fn, call_frame, call_inspect, call_modify, call_name, call_ns, call_stack, call_standardise, caller_env, caller_fn, caller_frame, calling, catch_cnd, child_env, chr, chr_along, chr_len, chr_unserialise_unicode, cnd, cnd_body, cnd_entrace, cnd_footer, cnd_header, cnd_message, cnd_muffle, cnd_signal, cnd_type, coerce_class, coerce_type, cpl, cpl_along, cpl_len, ctxt_depth, ctxt_frame, ctxt_stack, current_env, current_fn, current_frame, dbl, dbl_along, dbl_len, done, dots_definitions, dots_list, dots_n, dots_splice, dots_values, duplicate, empty_env, enexpr, enexprs, enquo, enquos, ensym, ensyms, entrace, env, env_bind, env_bind_active, env_bind_exprs, env_bind_fns, env_bind_lazy, env_binding_are_active, env_binding_are_lazy, env_binding_are_locked, env_binding_lock, env_binding_unlock, env_bury, env_clone, env_depth, env_get, env_get_list, env_has, env_inherits, env_is_locked, env_label, env_length, env_lock, env_name, env_names, env_parent, env_parents, env_poke, env_poke_parent, env_print, env_tail, env_unbind, env_unlock, error_cnd, eval_bare, eval_tidy, exec, exiting, expr, expr_deparse, expr_interp, expr_label, expr_name, expr_print, expr_text, exprs, exprs_auto_name, f_env, f_label, f_lhs, f_name, f_rhs, f_text, flatten, flatten_chr, flatten_cpl, flatten_dbl, flatten_if, flatten_int, flatten_lgl, flatten_raw, fn_body, fn_env, fn_fmls, fn_fmls_names, fn_fmls_syms, format_error_bullets, frame_position, friendly_type, get_env, get_expr, global_env, global_frame, has_length, has_name, have_name, inform, inherits_all, inherits_any, inherits_only, int, int_along, int_len, interrupt, invoke, is_atomic, is_attached, is_bare_atomic, is_bare_bytes, is_bare_character, is_bare_double, is_bare_env, is_bare_environment, is_bare_formula, is_bare_integer, is_bare_integerish, is_bare_list, is_bare_logical, is_bare_numeric, is_bare_raw, is_bare_string, is_bare_vector, is_binary_lang, is_bool, is_box, is_bytes, is_call, is_call_stack, is_callable, is_character, is_chr_na, is_closure, is_condition, is_copyable, is_cpl_na, is_dbl_na, is_definition, is_dictionaryish, is_done_box, is_double, is_empty, is_env, is_environment, is_eval_stack, is_expr, is_expression, is_false, is_formula, is_formulaish, is_frame, is_function, is_installed, is_int_na, is_integer, is_integerish, is_interactive, is_lambda, is_lang, is_lgl_na, is_list, is_logical, is_missing, is_na, is_named, is_namespace, is_node, is_node_list, is_null, is_pairlist, is_primitive, is_primitive_eager, is_primitive_lazy, is_quosure, is_quosures, is_raw, is_reference, is_scalar_atomic, is_scalar_bytes, is_scalar_character, is_scalar_double, is_scalar_integer, is_scalar_integerish, is_scalar_list, is_scalar_logical, is_scalar_raw, is_scalar_vector, is_scoped, is_spliced, is_spliced_bare, is_stack, is_string, is_symbol, is_symbolic, is_syntactic_literal, is_true, is_unary_lang, is_vector, is_weakref, is_zap, lang, lang_args, lang_args_names, lang_fn, lang_head, lang_modify, lang_name, lang_standardise, lang_tail, last_error, last_trace, lgl, lgl_along, lgl_len, list2, list_along, list_len, ll, local_bindings, local_interactive, local_options, locally, maybe_missing, message_cnd, missing_arg, modify, mut_attrs, mut_node_caar, mut_node_cadr, mut_node_car, mut_node_cdar, mut_node_cddr, mut_node_cdr, mut_node_tag, na_chr, na_cpl, na_dbl, na_int, na_lgl, names2, new_box, new_call, new_character, new_character_along, new_complex, new_complex_along, new_data_mask, new_definition, new_double, new_double_along, new_environment, new_formula, new_function, new_integer, new_integer_along, new_language, new_list, new_list_along, new_logical, new_logical_along, new_node, new_overscope, new_quosure, new_quosures, new_raw, new_raw_along, new_weakref, node, node_caar, node_cadr, node_car, node_cdar, node_cddr, node_cdr, node_poke_caar, node_poke_cadr, node_poke_car, node_poke_cdar, node_poke_cddr, node_poke_cdr, node_poke_tag, node_tag, ns_env, ns_env_name, ns_imports_env, overscope_clean, overscope_eval_next, pairlist2, parse_expr, parse_exprs, parse_quo, parse_quos, parse_quosure, parse_quosures, peek_option, peek_options, pkg_env, pkg_env_name, prepend, prim_name, push_options, qq_show, quo, quo_expr, quo_get_env, quo_get_expr, quo_is_call, quo_is_lang, quo_is_missing, quo_is_null, quo_is_symbol, quo_is_symbolic, quo_label, quo_name, quo_set_env, quo_set_expr, quo_squash, quo_text, quos, quos_auto_name, raw_along, raw_len, rep_along, rep_named, restarting, return_from, return_to, rst_abort, rst_exists, rst_jump, rst_list, rst_maybe_jump, scoped_bindings, scoped_env, scoped_envs, scoped_interactive, scoped_names, scoped_options, search_env, search_envs, seq2, seq2_along, set_attrs, set_env, set_expr, set_names, signal, splice, squash, squash_chr, squash_cpl, squash_dbl, squash_if, squash_int, squash_lgl, squash_raw, stack_trim, string, switch_class, switch_type, sym, syms, trace_back, trace_length, type_of, unbox, vec_poke_n, vec_poke_range, warn, warning_cnd, with_abort, with_bindings, with_env, with_handlers, with_interactive, with_options, with_restarts, wref_key, wref_value, zap
ERROR: lazy loading failed for package ‘tidyverse’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/tidyverse’
The downloaded source packages are in
‘/tmp/RtmpXT3xFS/downloaded_packages’
Warning message:
In install.packages("tidyverse") :
installation of package ‘tidyverse’ had non-zero exit status
It is clear from the output that the binary matches the checksum, and that the issue is related to exporting what appear to be method names from a namespace. While I am familiar with the general problem of namespace conflicts, I am unsure what is exactly happening here.
I've also tried changing step 5 to install.packages("tidyverse", dependencies = TRUE), which instead gives the following output:
Installing package into ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
also installing the dependencies ‘rex’, ‘covr’, ‘feather’
trying URL 'https://cloud.r-project.org/src/contrib/rex_1.1.2.tar.gz'
Content type 'application/x-gzip' length 89430 bytes (87 KB)
==================================================
downloaded 87 KB
trying URL 'https://cloud.r-project.org/src/contrib/covr_3.4.0.tar.gz'
Content type 'application/x-gzip' length 144119 bytes (140 KB)
==================================================
downloaded 140 KB
trying URL 'https://cloud.r-project.org/src/contrib/feather_0.3.5.tar.gz'
Content type 'application/x-gzip' length 73812 bytes (72 KB)
==================================================
downloaded 72 KB
trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.0.tar.gz'
Content type 'application/x-gzip' length 712837 bytes (696 KB)
==================================================
downloaded 696 KB
* installing *source* package ‘rex’ ...
** package ‘rex’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘[.fseq’, ‘[[.fseq’, ‘print.fseq’ were declared in NAMESPACE but not found
Error in namespaceExport(ns, exports) :
undefined exports: %$%, %<>%, %>%, %T>%, n'est pas, add, and, debug_fseq, debug_pipe, divide_by, divide_by_int, equals, extract, extract2, freduce, functions, inset, inset2, is_greater_than, is_in, is_less_than, is_weakly_greater_than, is_weakly_less_than, mod, multiply_by, multiply_by_matrix, not, or, raise_to_power, set_colnames, set_names, set_rownames, subtract, undebug_fseq, use_series
ERROR: lazy loading failed for package ‘rex’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/rex’
* installing *source* package ‘feather’ ...
** package ‘feather’ successfully unpacked and MD5 sums checked
Platform is little endian. Good.
** libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-read.cpp -o feather-read.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-types.cpp -o feather-types.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather-write.cpp -o feather-write.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/buffer.cc -o feather/buffer.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/feather-c.cc -o feather/feather-c.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/io.cc -o feather/io.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/metadata.cc -o feather/metadata.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/reader.cc -o feather/reader.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/status.cc -o feather/status.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/types.cc -o feather/types.o
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I. -I"/home/galen/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c feather/writer.cc -o feather/writer.o
ar rcs libfeather.a feather/buffer.o feather/feather-c.o feather/io.o feather/metadata.o feather/reader.o feather/status.o feather/types.o feather/writer.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o feather.so RcppExports.o feather-read.o feather-types.o feather-write.o -L. -lfeather -L/usr/lib/R/lib -lR
installing to /home/galen/R/x86_64-pc-linux-gnu-library/3.4/feather/libs
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘.DollarNames.C++Object’, ‘.DollarNames.Module’, ‘print.bytes’, ‘format.Rcpp_stack_trace’, ‘str.Rcpp_stack_trace’, ‘print.Rcpp_stack_trace’ were declared in NAMESPACE but not found
Error in namespaceExport(ns, exports) :
undefined exports: Module, Rcpp.package.skeleton, populate, loadRcppModules, setRcppClass, loadRcppClass, loadModule, cppFunction, exposeClass, evalCpp, sourceCpp, compileAttributes, registerPlugin, RcppLdFlags, LdFlags, demangle, sizeof, cpp_object_initializer, cpp_object_dummy, Rcpp.plugin.maker, getRcppVersion
ERROR: lazy loading failed for package ‘feather’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/feather’
* installing *source* package ‘tidyverse’ ...
** package ‘tidyverse’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning: S3 methods ‘$.rlang_ctxt_pronoun’, ‘$.rlang_data_pronoun’, ‘$.rlang_fake_data_pronoun’, ‘$<-.quosures’, ‘$<-.rlang_ctxt_pronoun’, ‘$<-.rlang_data_pronoun’, ‘[.quosure’, ‘[.quosures’, ‘[.rlang_data_pronoun’, ‘[.rlang_envs’, ‘[.stack’, ‘[<-.quosures’, ‘[[.quosure’, ‘[[.rlang_ctxt_pronoun’, ‘[[.rlang_data_pronoun’, ‘[[.rlang_fake_data_pronoun’, ‘[[<-.quosures’, ‘[[<-.rlang_ctxt_pronoun’, ‘[[<-.rlang_data_pronoun’, ‘Math.quosure’, ‘Ops.quosure’, ‘Summary.quosure’, ‘as.character.quosure’, ‘as.list.quosures’, ‘c.quosures’, ‘c.rlang_envs’, ‘cnd_footer.default’, ‘cnd_header.default’, ‘conditionMessage.rlang_error’, ‘format.rlang_error’, ‘format.rlang_trace’, ‘length.rlang_ctxt_pronoun’, ‘length.rlang_data_pronoun’, ‘length.rlang_fake_data_pronoun’, ‘mean.quosure’, ‘median.quosure’, ‘names.rlang_ctxt_pronoun’, ‘names.rlang_data_pronoun’, ‘name [... truncated]
Error in namespaceExport(ns, exports) :
undefined exports: !!!, !!, %#%, %#%<-, %|%, %||%, :=, f_env<-, f_lhs<-, f_rhs<-, fn_body<-, fn_env<-, fn_fmls<-, fn_fmls_names<-, .data, UQ, UQS, abort, are_na, arg_match, as_box, as_box_if, as_bytes, as_character, as_closure, as_complex, as_data_mask, as_data_pronoun, as_double, as_env, as_environment, as_function, as_integer, as_label, as_list, as_logical, as_name, as_overscope, as_pairlist, as_quosure, as_quosures, as_string, as_utf8_character, base_env, bytes, bytes_along, bytes_len, call2, call_args, call_args_names, call_depth, call_fn, call_frame, call_inspect, call_modify, call_name, call_ns, call_stack, call_standardise, caller_env, caller_fn, caller_frame, calling, catch_cnd, child_env, chr, chr_along, chr_len, chr_unserialise_unicode, cnd, cnd_body, cnd_entrace, cnd_footer, cnd_header, cnd_message, cnd_muffle, cnd_signal, cnd_type, coerce_class, coerce_type, cpl, cpl_along, cpl_len, ctxt_depth, ctxt_frame, ctxt_stack, current_env, current_fn, current_frame, dbl, dbl_along, dbl_len, done, dots_definitions, dots_list, dots_n, dots_splice, dots_values, duplicate, empty_env, enexpr, enexprs, enquo, enquos, ensym, ensyms, entrace, env, env_bind, env_bind_active, env_bind_exprs, env_bind_fns, env_bind_lazy, env_binding_are_active, env_binding_are_lazy, env_binding_are_locked, env_binding_lock, env_binding_unlock, env_bury, env_clone, env_depth, env_get, env_get_list, env_has, env_inherits, env_is_locked, env_label, env_length, env_lock, env_name, env_names, env_parent, env_parents, env_poke, env_poke_parent, env_print, env_tail, env_unbind, env_unlock, error_cnd, eval_bare, eval_tidy, exec, exiting, expr, expr_deparse, expr_interp, expr_label, expr_name, expr_print, expr_text, exprs, exprs_auto_name, f_env, f_label, f_lhs, f_name, f_rhs, f_text, flatten, flatten_chr, flatten_cpl, flatten_dbl, flatten_if, flatten_int, flatten_lgl, flatten_raw, fn_body, fn_env, fn_fmls, fn_fmls_names, fn_fmls_syms, format_error_bullets, frame_position, friendly_type, get_env, get_expr, global_env, global_frame, has_length, has_name, have_name, inform, inherits_all, inherits_any, inherits_only, int, int_along, int_len, interrupt, invoke, is_atomic, is_attached, is_bare_atomic, is_bare_bytes, is_bare_character, is_bare_double, is_bare_env, is_bare_environment, is_bare_formula, is_bare_integer, is_bare_integerish, is_bare_list, is_bare_logical, is_bare_numeric, is_bare_raw, is_bare_string, is_bare_vector, is_binary_lang, is_bool, is_box, is_bytes, is_call, is_call_stack, is_callable, is_character, is_chr_na, is_closure, is_condition, is_copyable, is_cpl_na, is_dbl_na, is_definition, is_dictionaryish, is_done_box, is_double, is_empty, is_env, is_environment, is_eval_stack, is_expr, is_expression, is_false, is_formula, is_formulaish, is_frame, is_function, is_installed, is_int_na, is_integer, is_integerish, is_interactive, is_lambda, is_lang, is_lgl_na, is_list, is_logical, is_missing, is_na, is_named, is_namespace, is_node, is_node_list, is_null, is_pairlist, is_primitive, is_primitive_eager, is_primitive_lazy, is_quosure, is_quosures, is_raw, is_reference, is_scalar_atomic, is_scalar_bytes, is_scalar_character, is_scalar_double, is_scalar_integer, is_scalar_integerish, is_scalar_list, is_scalar_logical, is_scalar_raw, is_scalar_vector, is_scoped, is_spliced, is_spliced_bare, is_stack, is_string, is_symbol, is_symbolic, is_syntactic_literal, is_true, is_unary_lang, is_vector, is_weakref, is_zap, lang, lang_args, lang_args_names, lang_fn, lang_head, lang_modify, lang_name, lang_standardise, lang_tail, last_error, last_trace, lgl, lgl_along, lgl_len, list2, list_along, list_len, ll, local_bindings, local_interactive, local_options, locally, maybe_missing, message_cnd, missing_arg, modify, mut_attrs, mut_node_caar, mut_node_cadr, mut_node_car, mut_node_cdar, mut_node_cddr, mut_node_cdr, mut_node_tag, na_chr, na_cpl, na_dbl, na_int, na_lgl, names2, new_box, new_call, new_character, new_character_along, new_complex, new_complex_along, new_data_mask, new_definition, new_double, new_double_along, new_environment, new_formula, new_function, new_integer, new_integer_along, new_language, new_list, new_list_along, new_logical, new_logical_along, new_node, new_overscope, new_quosure, new_quosures, new_raw, new_raw_along, new_weakref, node, node_caar, node_cadr, node_car, node_cdar, node_cddr, node_cdr, node_poke_caar, node_poke_cadr, node_poke_car, node_poke_cdar, node_poke_cddr, node_poke_cdr, node_poke_tag, node_tag, ns_env, ns_env_name, ns_imports_env, overscope_clean, overscope_eval_next, pairlist2, parse_expr, parse_exprs, parse_quo, parse_quos, parse_quosure, parse_quosures, peek_option, peek_options, pkg_env, pkg_env_name, prepend, prim_name, push_options, qq_show, quo, quo_expr, quo_get_env, quo_get_expr, quo_is_call, quo_is_lang, quo_is_missing, quo_is_null, quo_is_symbol, quo_is_symbolic, quo_label, quo_name, quo_set_env, quo_set_expr, quo_squash, quo_text, quos, quos_auto_name, raw_along, raw_len, rep_along, rep_named, restarting, return_from, return_to, rst_abort, rst_exists, rst_jump, rst_list, rst_maybe_jump, scoped_bindings, scoped_env, scoped_envs, scoped_interactive, scoped_names, scoped_options, search_env, search_envs, seq2, seq2_along, set_attrs, set_env, set_expr, set_names, signal, splice, squash, squash_chr, squash_cpl, squash_dbl, squash_if, squash_int, squash_lgl, squash_raw, stack_trim, string, switch_class, switch_type, sym, syms, trace_back, trace_length, type_of, unbox, vec_poke_n, vec_poke_range, warn, warning_cnd, with_abort, with_bindings, with_env, with_handlers, with_interactive, with_options, with_restarts, wref_key, wref_value, zap
ERROR: lazy loading failed for package ‘tidyverse’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/tidyverse’
ERROR: dependency ‘rex’ is not available for package ‘covr’
* removing ‘/home/galen/R/x86_64-pc-linux-gnu-library/3.4/covr’
The downloaded source packages are in
‘/tmp/RtmpGxNQPL/downloaded_packages’
Warning messages:
1: In install.packages("tidyverse", dependencies = TRUE) :
installation of package ‘rex’ had non-zero exit status
2: In install.packages("tidyverse", dependencies = TRUE) :
installation of package ‘feather’ had non-zero exit status
3: In install.packages("tidyverse", dependencies = TRUE) :
installation of package ‘tidyverse’ had non-zero exit status
4: In install.packages("tidyverse", dependencies = TRUE) :
installation of package ‘covr’ had non-zero exit status
Given the above context, how can I change the above installation procedure such that it is easily maintained with package managers?
Additional Notes:
RStudio is not installed on my system.
R version information after installation with apt-get:
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
You should probably first update R (currently it is version 3.6.1-2). The documentation on how to set new repositories for R in Ubuntu is here: https://cran.r-project.org/bin/linux/ubuntu/

R Rstudio problems installing packages mapdeck and googlePolylines

When I try to install the package mapdeck in Rstudio, it appears a message in the console saying that I need to install the package googlePolylines, but I can't install this one. The error that appears in the console is the following:
package ‘googlePolylines’ successfully unpacked and MD5 sums checked
libs
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I../inst/include -I"/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I../inst/include -I"/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c encode.cpp -o encode.o
encode.cpp: In function ‘void encode_vector(std::ostringstream&, std::ostringstream&, Rcpp::List, Rcpp::CharacterVector&, int)’:
encode.cpp:175: error: conversion from ‘Rcpp::internal::generic_proxy<19, Rcpp::PreserveStorage>’ to ‘double’ is ambiguous
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:73: note: candidates are: Rcpp::internal::generic_proxy::operator int() const [with int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:72: note: Rcpp::internal::generic_proxy::operator bool() const [with int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:67: note: Rcpp::internal::generic_proxy::operator U() const [with U = double, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
encode.cpp:176: error: conversion from ‘Rcpp::internal::generic_proxy<19, Rcpp::PreserveStorage>’ to ‘double’ is ambiguous
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:73: note: candidates are: Rcpp::internal::generic_proxy::operator int() const [with int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:72: note: Rcpp::internal::generic_proxy::operator bool() const [with int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/Rcpp/include/Rcpp/vector/generic_proxy.h:67: note: Rcpp::internal::generic_proxy::operator U() const [with U = double, int RTYPE = 19, StoragePolicy = Rcpp::PreserveStorage]
make: *** [encode.o] Error 1
ERROR: compilation failed for package ‘googlePolylines’
removing ‘/home/arubio/R/x86_64-redhat-linux-gnu-library/3.4/googlePolylines’
Warning in install.packages :
installation of package ‘googlePolylines’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpwwAJSv/downloaded_packages’
I haven't found almost any information about these two packages, so I would appreciate if anyone could help me, thank you.

Error when installing TDA package on R: recipe for target 'diag.o' failed

Using Ubuntu 16.04 and R 3.4.1. I get an error message when installing R package TDA. It appears to be something with making CGAL, diag.cpp, and/or diag.o (full error printout at end).
I looked closely at this:
Error when installing TDA package on R
but I have libgmp3-dev and libmpfr-dev installed (I tried removing them and then I did get that error message). I also tried removing and manually installing the Imports and LinkingTo packages for TDA (https://cran.r-project.org/web/packages/TDA/index.html), but no luck. Also tried
running R with sudo and install.packages
downloading the binaries and installing with sudo R CMD INSTALL TDA
installing CGAL
Any help appreciated.
install.packages("TDA")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.revolutionanalytics.com/src/contrib/TDA_1.5.1.tar.gz'
Content type 'application/octet-stream' length 2008762 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
* installing *source* package ‘TDA’ ...
** package ‘TDA’ successfully unpacked and MD5 sums checked
** libs
g++ -std=gnu++11 -I/usr/share/R/include -I. -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/BH/include" -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/usr/share/R/include -I. -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/BH/include" -DBOOST_DISABLE_THREADS -DCGAL_EIGEN3_ENABLED -DCGAL_HEADER_ONLY -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c diag.cpp -o diag.o
In file included from ./CGAL/Triangulation_ds_cell_base_3.h:27:0,
from ./CGAL/Triangulation_data_structure_3.h:47,
from ./CGAL/Triangulation_3.h:43,
from ./CGAL/Delaunay_triangulation_3.h:37,
from ./tdautils/cgalUtils.h:5,
from diag.cpp:25:
./CGAL/Triangulation_ds_cell_base_3.h: In instantiation of ‘void CGAL::Triangulation_ds_cell_base_3<TDS>::set_neighbor(int, CGAL::Triangulation_ds_cell_base_3<TDS>::Cell_handle) [with TDS = CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> >; CGAL::Triangulation_ds_cell_base_3<TDS>::Cell_handle = CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Triangulation_cell_base_3<CGAL::Epick, CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > > >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Default, CGAL::Default, CGAL::Default>, false>]’:
./CGAL/Triangulation_data_structure_3.h:2782:7: required from ‘CGAL::Triangulation_data_structure_3<Vb, Cb, Concurrency_tag_>::Vertex_handle CGAL::Triangulation_data_structure_3<Vb, Cb, Concurrency_tag_>::insert_increase_dimension(CGAL::Triangulation_data_structure_3<Vb, Cb, Concurrency_tag_>::Vertex_handle) [with Vb = CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>; Cb = CGAL::Alpha_shape_cell_base_3<CGAL::Epick>; Concurrency_tag_ = CGAL::Sequential_tag; CGAL::Triangulation_data_structure_3<Vb, Cb, Concurrency_tag_>::Vertex_handle = CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick, CGAL::Triangulation_vertex_base_3<CGAL::Epick, CGAL::Triangulation_ds_vertex_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > > >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >, CGAL::Default, CGAL::Default, CGAL::Default>, false>]’
./CGAL/Triangulation_3.h:623:16: required from ‘void CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::init_tds() [with GT = CGAL::Epick; Tds_ = CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> >; Lock_data_structure_ = CGAL::Default]’
./CGAL/Triangulation_3.h:655:15: required from ‘CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Triangulation_3(const GT&, CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Lock_data_structure*) [with GT = CGAL::Epick; Tds_ = CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> >; Lock_data_structure_ = CGAL::Default; CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Lock_data_structure = void]’
./CGAL/Delaunay_triangulation_3.h:229:26: required from ‘CGAL::Delaunay_triangulation_3<Gt, Tds_, CGAL::Default, Lock_data_structure_>::Delaunay_triangulation_3(const Gt&, CGAL::Delaunay_triangulation_3<Gt, Tds_, CGAL::Default, Lock_data_structure_>::Lock_data_structure*) [with Gt = CGAL::Epick; Tds_ = CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> >; Lock_data_structure_ = CGAL::Default; CGAL::Delaunay_triangulation_3<Gt, Tds_, CGAL::Default, Lock_data_structure_>::Lock_data_structure = void]’
./CGAL/Alpha_shape_3.h:263:51: required from ‘CGAL::Alpha_shape_3<Dt, ExactAlphaComparisonTag>::Alpha_shape_3(const InputIterator&, const InputIterator&, const NT&, CGAL::Alpha_shape_3<Dt, ExactAlphaComparisonTag>::Mode) [with InputIterator = std::_List_iterator<CGAL::Point_3<CGAL::Epick> >; Dt = CGAL::Delaunay_triangulation_3<CGAL::Epick, CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > >; ExactAlphaComparisonTag = CGAL::Boolean_tag<false>; CGAL::Alpha_shape_3<Dt, ExactAlphaComparisonTag>::NT = double]’
diag.cpp:680:65: required from here
./CGAL/Triangulation_ds_cell_base_3.h:166:39: error: ‘class CGAL::Alpha_shape_cell_base_3<CGAL::Epick, CGAL::Triangulation_cell_base_3<CGAL::Epick, CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick>, CGAL::Alpha_shape_cell_base_3<CGAL::Epick> > > >, CGAL::Boolean_tag<false>, CGAL::Boolean_tag<false> >’ has no member named ‘operator()’
CGAL_triangulation_precondition(this != n->operator());
^
./CGAL/triangulation_assertions.h:130:20: note: in definition of macro ‘CGAL_triangulation_precondition’
(CGAL::possibly(EX)?(static_cast<void>(0)): ::CGAL::precondition_fail( # EX
^
/usr/lib/R/etc/Makeconf:168: recipe for target 'diag.o' failed
make: *** [diag.o] Error 1
ERROR: compilation failed for package ‘TDA’
* removing ‘/usr/local/lib/R/site-library/TDA’
The downloaded source packages are in
‘/tmp/RtmpFqA1Fu/downloaded_packages’
Warning message:
In install.packages("TDA") :
installation of package ‘TDA’ had non-zero exit status
>
TDA v1.5.1 has the same issue on my Linux servers. Try install a previous version:
install.packages("devtools")
require(devtools);
install_version('TDA', version='1.4.1')

Can not make qmqtt

I had previously installed qt4. Now, I have installed QT5.7. I am trying to compile the qmqtt project to generate the libqmqtt file. Qmake is fine. But make gives the following error.
Link:
https://github.com/emqtt/qmqtt
g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O2 -fvisibility=hidden -fvisibility-inlines-hidden -std=c++0x -fno-exceptions -Wall -W -D_REENTRANT -fPIC -DQT_NO_MTDEV -DQT_NO_CAST_TO_ASCII -DQT_NO_CAST_FROM_ASCII -DQT_BUILD_MQTT_LIB -DQT_BUILDING_QT -DQT_ASCII_CAST_WARNINGS -DQT_MOC_COMPAT -DQT_USE_QSTRINGBUILDER -DQT_DEPRECATED_WARNINGS -DQT_DISABLE_DEPRECATED_BEFORE=0x050000 -DQT_NO_EXCEPTIONS -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -DQT_NO_DEBUG -DQT_NETWORK_LIB -DQT_CORE_LIB -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++-64 -I/home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt -I/home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt -I/home/sm/qt_applications/qmqtt/qmqtt-master/include -I/home/sm/qt_applications/qmqtt/qmqtt-master/include/qmqtt -I../../include -I../../include/qmqtt -I/home/sm/qt_applications/qmqtt/qmqtt-master/include/qmqtt/1.0.0 -I/home/sm/qt_applications/qmqtt/qmqtt-master/include/qmqtt/1.0.0/qmqtt -I/usr/include/qt5 -I/usr/include/qt5/QtNetwork -I/usr/include/qt5/QtCore -I.moc -I. -o .obj/qmqtt_routedmessage.o /home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_routedmessage.cpp
g++ -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O2 -fvisibility=hidden -fvisibility-inlines-hidden -std=c++0x -fno-exceptions -Wall -W -D_REENTRANT -fPIC -DQT_NO_MTDEV -DQT_NO_CAST_TO_ASCII -DQT_NO_CAST_FROM_ASCII -DQT_BUILD_MQTT_LIB -DQT_BUILDING_QT -DQT_ASCII_CAST_WARNINGS -DQT_MOC_COMPAT -DQT_USE_QSTRINGBUILDER -DQT_DEPRECATED_WARNINGS -DQT_DISABLE_DEPRECATED_BEFORE=0x050000 -DQT_NO_EXCEPTIONS -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -DQT_NO_DEBUG -DQT_NETWORK_LIB -DQT_CORE_LIB -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++-64 -I/home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt -I/home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt -I/home/sm/qt_applications/qmqtt/qmqtt-master/include -I/home/sm/qt_applications/qmqtt/qmqtt-master/include/qmqtt -I../../include -I../../include/qmqtt -I/home/sm/qt_applications/qmqtt/qmqtt-master/include/qmqtt/1.0.0 -I/home/sm/qt_applications/qmqtt/qmqtt-master/include/qmqtt/1.0.0/qmqtt -I/usr/include/qt5 -I/usr/include/qt5/QtNetwork -I/usr/include/qt5/QtCore -I.moc -I. -o .obj/qmqtt_router.o /home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_router.cpp
In file included from /usr/include/qt5/QtCore/qobjectdefs.h:47:0,
from /usr/include/qt5/QtCore/qobject.h:48,
from /usr/include/qt5/QtCore/QObject:1,
from /home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_router.h:38,
from /home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_router.cpp:33:
/usr/include/qt5/QtCore/qobjectdefs_impl.h: In instantiation of ‘struct QtPrivate::AreArgumentsCompatible<QMQTT::Message, QMQTT::Message>’:
/usr/include/qt5/QtCore/qobjectdefs_impl.h:599:21: required from ‘struct QtPrivate::CheckCompatibleArguments<QtPrivate::List<const QMQTT::Message&>, QtPrivate::List<const QMQTT::Message&> >’
/usr/include/qt5/QtCore/qobject.h:241:80: required from ‘static QMetaObject::Connection QObject::connect(const typename QtPrivate::FunctionPointer<Func>::Object*, Func1, const typename QtPrivate::FunctionPointer<Func2>::Object*, Func2, Qt::ConnectionType) [with Func1 = void (QMQTT::Client::*)(const QMQTT::Message&); Func2 = void (QMQTT::RouteSubscription::*)(const QMQTT::Message&); typename QtPrivate::FunctionPointer<Func>::Object = QMQTT::Client; typename QtPrivate::FunctionPointer<Func2>::Object = QMQTT::RouteSubscription]’
/home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_router.cpp:52:87: required from here
/usr/include/qt5/QtCore/qobjectdefs_impl.h:573:42: error: invalid use of incomplete type ‘class QMQTT::Message’
enum { value = sizeof(test(dummy())) == sizeof(int) };
^
In file included from /home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_router.cpp:35:0:
/home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_client.h:95:7: error: forward declaration of ‘class QMQTT::Message’
class Message;
^
In file included from /home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_global.h:35:0,
from /home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_router.h:36,
from /home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_router.cpp:33:
/usr/include/qt5/QtCore/qobject.h: In instantiation of ‘static QMetaObject::Connection QObject::connect(const typename QtPrivate::FunctionPointer<Func>::Object*, Func1, const typename QtPrivate::FunctionPointer<Func2>::Object*, Func2, Qt::ConnectionType) [with Func1 = void (QMQTT::Client::*)(const QMQTT::Message&); Func2 = void (QMQTT::RouteSubscription::*)(const QMQTT::Message&); typename QtPrivate::FunctionPointer<Func>::Object = QMQTT::Client; typename QtPrivate::FunctionPointer<Func2>::Object = QMQTT::RouteSubscription]’:
/home/sm/qt_applications/qmqtt/qmqtt-master/src/mqtt/qmqtt_router.cpp:52:87: required from here
/usr/include/qt5/QtCore/qglobal.h:669:47: error: static assertion failed: Signal and slot arguments are not compatible.
#define Q_STATIC_ASSERT_X(Condition, Message) static_assert(bool(Condition), Message)
^
/usr/include/qt5/QtCore/qobject.h:228:9: note: in expansion of macro ‘Q_STATIC_ASSERT_X’
Q_STATIC_ASSERT_X((QtPrivate::CheckCompatibleArguments<typename SignalType::Arguments, typename SlotType::Arguments>::value),
^
make[2]: *** [.obj/qmqtt_router.o] Error 1
make[2]: Leaving directory `/home/sm/qt_applications/qmqtt/qmqtt-master/build/src/mqtt'
make[1]: *** [sub-mqtt-make_first] Error 2
make[1]: Leaving directory `/home/sm/qt_applications/qmqtt/qmqtt-master/build/src'
make: *** [sub-src-make_first] Error 2
Spent a lot of time. After compiling by Qt 5.7.0, there was no Dll-files in the folder "release". I looking at the compilation log and I saw that there was created the folder "lib" in the root of the disk with the project, there I found Dll. But work with DLL allows you to work on Windows. I need on Android.
In github someone suggests just use it as plain code.
I rewrite it to "plain code" and made example-project. It is here. There is two folders: project and mosquitto for using mqtt on localhost

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