Too many sections

Interfaces brms
1

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

2

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.

1 Like
3

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.

4

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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