First Time Trying To Use RStan and can't get past error

Interfaces RStan
1

Followed the install instruction and everything was working fine (checked rtool was working using R terminal and it worked, but its in a different folder than the rest of the files so that may be part of the problem). But when I went to use it VScodes R Terminal, it downloads something then gives me these errors.

Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
sh: line 1: c:/rtools40/mingw64/bin/g++: No such file or directorymake: *** [C:/PROGRA~1/R/R-41~1.1/etc/x64/Makeconf:245: file6486c7c312d.o] Error 127
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
‘-E’ not found

There is a thread on the topic but its hard to make heads or tails of it because it unorganized, and I can’t tell who’s who or which one is the right answer.

2

Just to check some configurations, can you post the output from running these in the VScode R terminal:

readLines('~./Renviron')
Sys.getenv('PATH')
Sys.which('make')
3

Here’s what printed out

readLines(’~./Renviron’)
Error in file(con, “r”) : cannot open the connection
In addition: Warning message:
In file(con, “r”) :
cannot open file ‘C:\Users\MAKE\Documents./Renviron’: No such file or directory

r$> Sys.getenv(‘PATH’)
[1] “C:\Users\MAKE\Documents\R\rtools40\usr\bin;C:\Users\MAKE\Documents\R\rtools40\usr\bin;C:\PROGRA~1\R\R-41~1.1\bin\x64;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\iCLS\;C:\Program Files\Intel\Intel(R) Management Engine Components\iCLS\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;%SYSTEMROOT%\System32\OpenSSH\;C:\Users\MAKE\AppData\Local\Microsoft\WindowsApps;C:\Users\MAKE\AppData\Local\Programs\Microsoft VS Code\bin;C:\Users\MAKE\AppData\Local\GitHubDesktop\bin”

r$> Sys.which(‘make’)
make
“C:\Users\MAKE\DOCUME~1\R\rtools40\usr\bin\make.exe”

4

Also, I used this command to make that folder but I think I installed it somewhere else.

writeLines(‘PATH="{RTOOLS40_HOME}\\usr\\bin;{PATH}"’, con = “~/.Renviron”)

5

And what do you get if you try to install a package from source:

install.packages("jsonlite",type="source")
6

Installing package into ‘C:/Users/MAKE/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)

— Please select a CRAN mirror for use in this session —
Secure CRAN mirrors

1: 0-Cloud [https] 2: Australia (Canberra) [https] 3: Australia (Melbourne 1) [https] 4: Australia (Melbourne 2) [https]
5: Australia (Perth) [https] 6: Austria [https] 7: Belgium (Brussels) [https] 8: Brazil (BA) [https]
9: Brazil (PR) [https] 10: Brazil (RJ) [https] 11: Brazil (SP 1) [https] 12: Brazil (SP 2) [https]
13: Bulgaria [https] 14: Canada (MB) [https] 15: Canada (ON 2) [https] 16: Canada (ON 3) [https]
17: Chile (Santiago) [https] 18: China (Beijing 2) [https] 19: China (Hefei) [https] 20: China (Hong Kong) [https]
21: China (Guangzhou) [https] 22: China (Lanzhou) [https] 23: China (Nanjing) [https] 24: China (Shanghai 1) [https]
25: China (Shanghai 2) [https] 26: China (Shenzhen) [https] 27: Costa Rica [https] 28: Cyprus [https]
29: Czech Republic [https] 30: Denmark [https] 31: East Asia [https] 32: Ecuador (Cuenca) [https]
33: Ecuador (Quito) [https] 34: Estonia [https] 35: France (Lyon 1) [https] 36: France (Lyon 2) [https]
37: France (Marseille) [https] 38: France (Montpellier) [https] 39: France (Paris 1) [https] 40: Germany (Erlangen) [https]
41: Germany (Leipzig) [https] 42: Germany (Göttingen) [https] 43: Germany (Münster) [https] 44: Germany (Regensburg) [https]
45: Greece [https] 46: Hungary [https] 47: Iceland [https] 48: India [https]
49: Indonesia (Jakarta) [https] 50: Iran [https] 51: Italy (Milano) [https] 52: Italy (Padua) [https]
53: Japan (Tokyo) [https] 54: Korea (Gyeongsan-si) [https] 55: Korea (Seoul 1) [https] 56: Korea (Ulsan) [https]
57: Malaysia [https] 58: Mexico (Mexico City) [https] 59: Mexico (Texcoco) [https] 60: Morocco [https]
61: Netherlands [https] 62: New Zealand [https] 63: Norway [https] 64: Russia (Moscow) [https]
65: South Africa (Johannesburg) [https] 66: Spain (A Coruña) [https] 67: Spain (Madrid) [https] 68: Sweden (Borås) [https]
69: Sweden (Umeå) [https] 70: Switzerland [https] 71: Taiwan (Taipei) [https] 72: Turkey (Denizli) [https]
73: Turkey (Istanbul) [https] 74: Turkey (Mersin) [https] 75: UK (Bristol) [https] 76: UK (London 1) [https]
77: USA (IA) [https] 78: USA (KS) [https] 79: USA (MI) [https] 80: USA (OH) [https]
81: USA (OR) [https] 82: USA (TN) [https] 83: USA (TX 1) [https] 84: Uruguay [https]
85: (other mirrors)

Selection: 82
trying URL ‘https://mirrors.nics.utk.edu/cran/src/contrib/jsonlite_1.7.2.tar.gz’
Content type ‘application/x-gzip’ length 421716 bytes (411 KB)
downloaded 411 KB

  • installing source package ‘jsonlite’ …
    ** package ‘jsonlite’ successfully unpacked and MD5 sums checked
    ERROR: cannot remove earlier installation, is it in use?
  • removing ‘C:/Users/MAKE/Documents/R/win-library/4.1/jsonlite’
  • restoring previous ‘C:/Users/MAKE/Documents/R/win-library/4.1/jsonlite’
    Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
    problem copying C:\Users\MAKE\Documents\R\win-library\4.1\00LOCK-jsonlite\jsonlite\libs\x64\jsonlite.dll to C:\Users\MAKE\Documents\R\win-library\4.1\jsonlite\libs\x64\jsonlite.dll: Permission denied

The downloaded source packages are in
‘C:\Users\MAKE\AppData\Local\Temp\RtmpkV2lKr\downloaded_packages’
Warning message:
In install.packages(“jsonlite”, type = “source”) :
installation of package ‘jsonlite’ had non-zero exit status

7

Hmm, it looks you can’t install R packages at all at the moment. Can you try restarting Vscode and making sure that the folder: C:\Users\MAKE\Documents\R\win-library\4.1\00LOCK-jsonlite has been deleted, and then try the install again?

8

That folder doesn’t exist

Just this one C:\Users\MAKE\Documents\R\win-library\4.1\jsonlite , so I deleted that once, restarted VScode to try the code again and got this:

r$> install.packages(“jsonlite”,type=“source”)
Installing package into ‘C:/Users/MAKE/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
— Please select a CRAN mirror for use in this session —
Secure CRAN mirrors

1: 0-Cloud [https] 2: Australia (Canberra) [https] 3: Australia (Melbourne 1) [https] 4: Australia (Melbourne 2) [https]
5: Australia (Perth) [https] 6: Austria [https] 7: Belgium (Brussels) [https] 8: Brazil (BA) [https]
9: Brazil (PR) [https] 10: Brazil (RJ) [https] 11: Brazil (SP 1) [https] 12: Brazil (SP 2) [https]
13: Bulgaria [https] 14: Canada (MB) [https] 15: Canada (ON 2) [https] 16: Canada (ON 3) [https]
17: Chile (Santiago) [https] 18: China (Beijing 2) [https] 19: China (Hefei) [https] 20: China (Hong Kong) [https]
21: China (Guangzhou) [https] 22: China (Lanzhou) [https] 23: China (Nanjing) [https] 24: China (Shanghai 1) [https]
25: China (Shanghai 2) [https] 26: China (Shenzhen) [https] 27: Costa Rica [https] 28: Cyprus [https]
29: Czech Republic [https] 30: Denmark [https] 31: East Asia [https] 32: Ecuador (Cuenca) [https]
33: Ecuador (Quito) [https] 34: Estonia [https] 35: France (Lyon 1) [https] 36: France (Lyon 2) [https]
37: France (Marseille) [https] 38: France (Montpellier) [https] 39: France (Paris 1) [https] 40: Germany (Erlangen) [https]
41: Germany (Leipzig) [https] 42: Germany (Göttingen) [https] 43: Germany (Münster) [https] 44: Germany (Regensburg) [https]
45: Greece [https] 46: Hungary [https] 47: Iceland [https] 48: India [https]
49: Indonesia (Jakarta) [https] 50: Iran [https] 51: Italy (Milano) [https] 52: Italy (Padua) [https]
53: Japan (Tokyo) [https] 54: Korea (Gyeongsan-si) [https] 55: Korea (Seoul 1) [https] 56: Korea (Ulsan) [https]
57: Malaysia [https] 58: Mexico (Mexico City) [https] 59: Mexico (Texcoco) [https] 60: Morocco [https]
61: Netherlands [https] 62: New Zealand [https] 63: Norway [https] 64: Russia (Moscow) [https]
65: South Africa (Johannesburg) [https] 66: Spain (A Coruña) [https] 67: Spain (Madrid) [https] 68: Sweden (Borås) [https]
69: Sweden (Umeå) [https] 70: Switzerland [https] 71: Taiwan (Taipei) [https] 72: Turkey (Denizli) [https]
73: Turkey (Istanbul) [https] 74: Turkey (Mersin) [https] 75: UK (Bristol) [https] 76: UK (London 1) [https]
77: USA (IA) [https] 78: USA (KS) [https] 79: USA (MI) [https] 80: USA (OH) [https]
81: USA (OR) [https] 82: USA (TN) [https] 83: USA (TX 1) [https] 84: Uruguay [https]
85: (other mirrors)

Selection: 82
trying URL ‘https://mirrors.nics.utk.edu/cran/src/contrib/jsonlite_1.7.2.tar.gz’
Content type ‘application/x-gzip’ length 421716 bytes (411 KB)
downloaded 411 KB

  • installing source package ‘jsonlite’ …
    ** package ‘jsonlite’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs

*** arch - i386
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base64.c -o base64.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c collapse_array.c -o collapse_array.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c collapse_object.c -o collapse_object.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c collapse_pretty.c -o collapse_pretty.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c escape_chars.c -o escape_chars.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c integer64_to_na.c -o integer64_to_na.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c is_datelist.c -o is_datelist.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c is_recordlist.c -o is_recordlist.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c is_scalarlist.c -o is_scalarlist.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c modp_numtoa.c -o modp_numtoa.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c null_to_na.c -o null_to_na.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c num_to_char.c -o num_to_char.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c parse.c -o parse.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c prettify.c -o prettify.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c push_parser.c -o push_parser.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c r-base64.c -o r-base64.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c row_collapse.c -o row_collapse.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transpose_list.c -o transpose_list.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c validate.c -o validate.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl.c -o yajl/yajl.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_buf.c -o yajl/yajl_buf.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_encode.c -o yajl/yajl_encode.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_gen.c -o yajl/yajl_gen.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_lex.c -o yajl/yajl_lex.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_parser.c -o yajl/yajl_parser.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_tree.c -o yajl/yajl_tree.o
"C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/"ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
C:/Users/MAKE/Documents/R/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o jsonlite.dll tmp.def base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -LC:/PROGRA~1/R/R-41~1.1/bin/i386 -lR
installing to C:/Users/MAKE/Documents/R/win-library/4.1/00LOCK-jsonlite/00new/jsonlite/libs/i386

*** arch - x64
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base64.c -o base64.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c collapse_array.c -o collapse_array.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c collapse_object.c -o collapse_object.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c collapse_pretty.c -o collapse_pretty.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c escape_chars.c -o escape_chars.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c integer64_to_na.c -o integer64_to_na.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c is_datelist.c -o is_datelist.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c is_recordlist.c -o is_recordlist.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c is_scalarlist.c -o is_scalarlist.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c modp_numtoa.c -o modp_numtoa.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c null_to_na.c -o null_to_na.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c num_to_char.c -o num_to_char.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c parse.c -o parse.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c prettify.c -o prettify.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c push_parser.c -o push_parser.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c r-base64.c -o r-base64.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c row_collapse.c -o row_collapse.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transpose_list.c -o transpose_list.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c validate.c -o validate.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl.c -o yajl/yajl.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_buf.c -o yajl/yajl_buf.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_encode.c -o yajl/yajl_encode.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_gen.c -o yajl/yajl_gen.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_lex.c -o yajl/yajl_lex.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_parser.c -o yajl/yajl_parser.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/“gcc -I"C:/PROGRA~1/R/R-41~1.1/include” -DNDEBUG -Iyajl/api -D__USE_MINGW_ANSI_STDIO -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c yajl/yajl_tree.c -o yajl/yajl_tree.o
"C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/"ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
C:/Users/MAKE/Documents/R/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o jsonlite.dll tmp.def base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -LC:/PROGRA~1/R/R-41~1.1/bin/x64 -lR
installing to C:/Users/MAKE/Documents/R/win-library/4.1/00LOCK-jsonlite/00new/jsonlite/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘asJSON’ with signature ‘“blob”’: no definition for class “blob”
** help
*** installing help indices
converting help for package ‘jsonlite’
finding HTML links … done
base64 html
flatten html
fromJSON html
prettify html
rbind_pages html
read_json html
serializeJSON html
stream_in html
unbox html
validate html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path

  • DONE (jsonlite)

The downloaded source packages are in
‘C:\Users\MAKE\AppData\Local\Temp\Rtmp4C1Ukr\downloaded_packages’

9

Great, that’s a good sign. It’s finding the toolchain and compiling the package. Can you try the rstan install again next:

# Compile packages using all cores
Sys.setenv(MAKEFLAGS = paste0("-j",parallel::detectCores()))

install.packages(c("StanHeaders","rstan"),type="source")
10

Looks Like It Worked!

Way too much to post all of it but the last pert said installing help indicies and a few more lines before

The downloaded source packages are in
‘C:\Users\MAKE\AppData\Local\Temp\Rtmp4C1Ukr\downloaded_packages’

11

I also did the example model script and it worked perfectly!

Thank you!

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