Too many sections

Please also provide the following information in addition to your question:

  • Operating System: win10
  • brms Version: 2.5.0

I have some problems with the package brms. It keep complaining that there are too many sections and the file is too big. I have 8GB RAM and ~100GB disk space and the model only takes a few computational resources. I should have space problem. For example,

fit2 <- brm(rating ~ period + carry + cs(treat), data = inhaler, family = sratio(“logit”), prior = set_prior(“normal(0,5)”), chains = 2)

DIAGNOSTIC(S) FROM PARSER:

Info: left-hand side variable (name=p) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

Info: left-hand side variable (name=p) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

Compiling the C++ model

DIAGNOSTIC(S) FROM PARSER:

Info: left-hand side variable (name=p) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

Info: left-hand side variable (name=p) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

Error in compileCode(f, code, language = language, verbose = verbose) :

Compilation ERROR, function(s)/method(s) not created! C:/Rtools/mingw_64/bin/…/lib/gcc/x86_64-w64-mingw32/4.9.3/…/…/…/…/x86_64-w64-mingw32/bin/as.exe: file15e8237e12ae.o: too many sections (37437)

C:\Users\CHARLE~1\AppData\Local\Temp\ccUqegdB.s: Assembler messages:

C:\Users\CHARLE~1\AppData\Local\Temp\ccUqegdB.s: Fatal error: can’t write file15e8237e12ae.o: File too big

C:/Rtools/mingw_64/bin/…/lib/gcc/x86_64-w64-mingw32/4.9.3/…/…/…/…/x86_64-w64-mingw32/bin/as.exe: file15e8237e12ae.o: too many sections (37437)

C:\Users\CHARLE~1\AppData\Local\Temp\ccUqegdB.s: Fatal error: can’t close file15e8237e12ae.o: File too big

make: *** [C:/PROGRA~1/R/R-35~1.1/etc/x64/Makeconf:215: file15e8237e12ae.o] Error 1

In addition: Warning message:

In FUN(X[[i]], …) : restarting interrupted promise evaluation

I think I have installed the compiler and rstan properly because the following c++ and rstan commands work for me.

src <- ’

  • std::vector < std::string> s;

  • s.push_back(“hello”);

  • s.push_back(“world”);

  • return Rcpp::wrap(s);

hellofun <- cxxfunction(body = src, includes = ‘’, plugin = ‘Rcpp’, verbose = FALSE)

cat(hellofun(), ‘\n’)

hello world

and

fx <- inline::cxxfunction( signature(x = “integer”;, y = “numeric” ) , ’ return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;’ ) fx( 2L, 5 ) # 10

Additional information, here are my sessionInfo
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] brms_2.5.0 Rcpp_0.12.19 rstan_2.18.1 StanHeaders_2.18.0 ggplot2_3.0.0

loaded via a namespace (and not attached):
[1] Brobdingnag_1.2-6 gtools_3.8.1 threejs_0.3.1 shiny_1.1.0
[5] assertthat_0.2.0 stats4_3.5.1 yaml_2.2.0 backports_1.1.2
[9] pillar_1.3.0 lattice_0.20-35 glue_1.3.0 digest_0.6.17
[13] promises_1.0.1 colorspace_1.3-2 htmltools_0.3.6 httpuv_1.4.5
[17] Matrix_1.2-14 plyr_1.8.4 dygraphs_1.1.1.6 pkgconfig_2.0.2
[21] purrr_0.2.5 xtable_1.8-3 mvtnorm_1.0-8 scales_1.0.0
[25] processx_3.2.0 later_0.7.5 tibble_1.4.2 bayesplot_1.6.0
[29] DT_0.4 shinyjs_1.0 withr_2.1.2 lazyeval_0.2.1
[33] cli_1.0.1 magrittr_1.5 crayon_1.3.4 mime_0.5
[37] ps_1.2.0 nlme_3.1-137 xts_0.11-1 pkgbuild_1.0.2
[41] colourpicker_1.0 rsconnect_0.8.8 tools_3.5.1 loo_2.0.0
[45] prettyunits_1.0.2 matrixStats_0.54.0 stringr_1.3.1 munsell_0.5.0
[49] bindrcpp_0.2.2 callr_3.0.0 compiler_3.5.1 rlang_0.2.2
[53] grid_3.5.1 ggridges_0.5.1 rstudioapi_0.7 htmlwidgets_1.3
[57] crosstalk_1.0.0 igraph_1.2.2 miniUI_0.1.1.1 base64enc_0.1-3
[61] gtable_0.2.0 inline_0.3.15 abind_1.4-5 markdown_0.8
[65] reshape2_1.4.3 R6_2.2.2 gridExtra_2.3 rstantools_1.5.1
[69] zoo_1.8-4 bridgesampling_0.5-2 dplyr_0.7.6 shinythemes_1.1.1
[73] bindr_0.1.1 shinystan_2.5.0 stringi_1.1.7 parallel_3.5.1
[77] tidyselect_0.2.4 coda_0.19-1

Here is my Path

Sys.getenv()[“PATH”]
PATH C:\Program
Files\R\R-3.5.1\bin\x64;C:\Rtools\bin;C:\Rtools\mingw_64\bin;C:\Perl\site\bin;C:\Perl\bin;C:\ProgramData\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\Program
Files (x86)\QuickTime\QTSystem;C:\Program Files
(x86)\Skype\Phone;C:\Program
Files\PuTTY;C:\WINDOWS\System32\OpenSSH;C:\Program Files
(x86)\SSH Communications Security\SSH Secure
Shell;C:\Users\Charley
Work\AppData\Local\Microsoft\WindowsApps;C:\texlive\2017\bin\win3

And here is a part of my R makeconf

CXX14 = g++ -m$(WIN) -std=c++1y
CXX14FLAGS = Wa, -mbig-obj
CXX14PICFLAGS =
CXX14STD =

Can anyone help me with this?
Many thanks

In my experience, this is usually caused by not having -O3 in CXX14FLAGS of the ~/.R/Makevars file. You might as well put it in CXX11FLAGS as well.

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Thanks. It works now. I have deleted R, Rtools and R libraries completely from the windows system and then re-installed everything in the following order R, Rtools and then rstan. Finally, I have added O3 in the makevars file (by default it was O2, i changed it to O3) for both Cxx11 and Cxx14 flags, it’s now working.

Was the all that reinstalling actually necessary? Or can you make it compile or not just by switching the optimiziation level back and forth?

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