g++: command not found & make: Error 127

[Blevy2]

Hi everyone,

I think I may be having a dependency issue, but I am at a loss about what it is and how to correct it. It started last week when an error made me believe I needed to reinstall INLA. Along the way I have removed and reinstalled a number of packages including VAST, INLA, sp, and TMB. I have tried to align my packages with what was working for me before and currently have the following versions installed:

VAST 3.9.1
TMB 1.7.22
sp 1.4.7
FishStatsUtils 2.11.0

The above package combination previously worked for me with VAST 3.8.0 so I tried rolling back to VAST 3.8.0 but am still coming up with the below error. I cannot find any information online related to this error so any help you could provide is very much welcomed.

Thank you,

Ben Levy

Edit 1: I should also mention that I recently updated to R 4.2.1 as part of reinstalling INLA. Might that be the problem?

Edit 2: I will also add that I am working on a government issued Windows machine.

[Blevy2]

I may have resolved this problem. It looks like rolling back to R version 4.1.3 worked.

I was able to successfully move past "Making TMB object" with the following R and package versions:

R version 4.1.3
VAST 3.9.0
TMB 1.8.1
sp 1.5.0
FishStatsUtils 2.11.0

Ben

[jlmorano]

I am having the same problem, but I haven't been able to work around it no matter what version combos of R, VAST, and INLA I do. I think INLA is the source because I haven't been able to figure out which previous version of INLA I had been using without trouble. INLA 22.05.03 and 22.05.07 are not it.

[Blevy2]

I recently had a few nasty compatibility issues that were tough to move past. I thought they were related to INLA and the version of R I was using. What is currently working for me are the versions I listed above along with INLA 22.05.07. A colleague of mine who has been digging deep with VAST also recently struggled with INLA dependencies and specifically recommended 22.05.07 to me.

[slarge]

I'll add my experience to this thread. I updated to R 4.2.2 and got the same "Error 127" as @Blevy2 (see SessionInfo() at the bottom for package versions). Running the simple univariate EBS_pollock model with different VAST versions, I am able to compile and run the model with VAST version "VAST_v13_0_0". However, the following VAST versions result in the same "Error 127" ( "VAST_v13_1_0", "VAST_V14_0_0", and "VAST_v14_1_0"). @James-Thorson-NOAA , have you seen this before? I didn't see any other issues where R4.2.2 and VAST >13_0_0 don't get along.

`

Load package

library(VAST)

load data set

example = load_example( data_set="EBS_pollock" )

Make settings (turning off bias.correct to save time for example)

settings = make_settings( n_x = 100,
Region = example$Region,
purpose = "index2",
bias.correct = FALSE )

For some reason I need to make sure Rtools has path properly set, else TMB won't compile

Sys.setenv(PATH = paste("C:/Rtools/bin", Sys.getenv("PATH"), sep=";"))
Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")

Run model

fit = fit_model( settings = settings,
Lat_i = example$sampling_data[,'Lat'],
Lon_i = example$sampling_data[,'Lon'],
t_i = example$sampling_data[,'Year'],
b_i = example$sampling_data[,'Catch_KG'],
Version = "VAST_v14_0_1",
a_i = example$sampling_data[,'AreaSwept_km2'] )
`

Writing output from fit_model in directory: C:/Users/scott.large/Documents/projects/zoopDFA/

Making extrapolation-grid

Using strata All_areas
For the UTM conversion, automatically detected zone 2.

Reducing extrapolation-grid from 38284 to 2000 cells for Region(s): eastern_bering_sea

Loaded from C:/Users/scott.large/Documents/projects/zoopDFA//Kmeans_extrapolation-2000.RData

Making spatial information

Loaded from C:/Users/scott.large/Documents/projects/zoopDFA//Kmeans_knots-100.RData

Making data object

Coercing b_i to have units kg; I recommend using explicit units, e.g., as_units(b_i,'kg'), as_units(b_i,'count') or as_units(b_i,unitless)Coercinga_ito have unitskm^2; I recommend using explicit units, e.g., as_units(a_i,'km^2')oras_units(a_i,unitless)`
FieldConfig_input is:
Component_1 Component_2
Omega -2 -2
Epsilon -2 -2
Beta -2 -2
Epsilon_time -3 -3
OverdispersionConfig_input is:
Eta1 Eta2
-1 -1
Calculating range shift for stratum #1:

Making TMB object

C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/scott.large/AppData/Local/Programs/R/R-4.2.2/include" -DNDEBUG -I"C:/Users/SCOTT1.LAR/AppData/Local/Programs/R/R-421.2/library/TMB/include" -I"C:/Users/SCOTT1.LAR/AppData/Local/Programs/R/R-421.2/library/RCPPEI~1/include" -DTMB_SAFEBOUNDS -DTMB_EIGEN_DISABLE_WARNINGS -DLIB_UNLOAD=R_unload_VAST_v14_0_1_TMBad -DTMB_LIB_INIT=R_init_VAST_v14_0_1_TMBad -DTMBAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -Wno-ignored-attributes -O2 -mfpmath=sse -msse2 -mstackrealign -c VAST_v14_0_1_TMBad.cpp -o VAST_v14_0_1_TMBad.o
/bin/sh: line 1: C:/Rtools/mingw_64/bin/g++: No such file or directory
make: *** [C:/Users/scott.large/AppData/Local/Programs/R/R-4.2.2/etc/x64/Makeconf:260: VAST_v14_0_1_TMBad.o] Error 127

sessionInfo()

sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

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

other attached packages:
[1] VAST_3.10.0 FishStatsUtils_2.12.0 units_0.8-1 TMB_1.9.1

loaded via a namespace (and not attached):
[1] rnaturalearth_0.1.0 Rcpp_1.0.9 here_1.0.1 lattice_0.20-45 class_7.3-20 rprojroot_2.0.3 utf8_1.2.2
[8] R6_2.5.1 cellranger_1.1.0 plyr_1.8.8 rnaturalearthdata_0.1.0 RSQLite_2.2.20 e1071_1.7-12 ggplot2_3.4.0
[15] pillar_1.8.1 ThorsonUtilities_1.0 rlang_1.0.6 googlesheets4_1.0.1 rstudioapi_0.14 raster_3.6-13 blob_1.2.3
[22] Matrix_1.5-1 splines_4.2.2 rgdal_1.6-3 googledrive_2.0.0 readr_2.1.3 stringr_1.5.0 igraph_1.3.5
[29] bit_4.0.5 munsell_0.5.0 proxy_0.4-27 compiler_4.2.2 pkgconfig_2.0.3 shape_1.4.6 marmap_1.0.9
[36] tidyselect_1.2.0 tibble_3.1.8 RANN_2.6.1 codetools_0.2-18 fansi_1.0.3 TMBhelper_1.4.0 dplyr_1.0.10
[43] tzdb_0.3.0 sf_1.0-9 grid_4.2.2 gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3 adehabitatMA_0.3.15
[50] magrittr_2.0.3 scales_1.2.1 ncdf4_1.21 KernSmooth_2.23-20 cli_3.5.0 stringi_1.7.8 cachem_1.0.6
[57] INLA_22.12.16 reshape2_1.4.4 fs_1.5.2 sp_1.5-1 ellipsis_0.3.2 generics_0.1.3 vctrs_0.5.1
[64] tools_4.2.2 bit64_4.0.5 glue_1.6.2 purrr_1.0.0 splancs_2.01-43 hms_1.1.2 abind_1.4-5
[71] parallel_4.2.2 fastmap_1.1.0 colorspace_2.0-3 gargle_1.2.1 gdistance_1.6 terra_1.6-47 classInt_0.4-8
[78] memoise_2.0.1 usethis_2.1.6

[James-Thorson-NOAA]

There might be two issues here, I can't really tell.

@Blevy2 it sounds like you're having some RINLA install issues, and consider trying the steps here

@slarge it seems like you're having some TMB compilation issues (that's what Error-127 means). I can't replicate the problem on my machine, but will try to look around a bit.