malloc error with fixef() #630
Description
Hi
Sorry the dumb issue but I keep getting this while comparing the slopes with base R, alpaca and capybara.
library(dplyr)
library(tidyr)
library(janitor)
library(haven)
library(fixest)
url <- "https://prod-dcd-datasets-cache-zipfiles.s3.eu-west-1.amazonaws.com/n67gft8fvm-1.zip"
zip <- "~/Documents/phd-thesis/capybara-benchmarks/The Tails of Gravity.zip"
dir <- "~/Documents/phd-thesis/capybara-benchmarks/The Tails of Gravity"
if (!file.exists(zip)) {
download.file(url, destfile = zip, mode = "wb")
}
if (!file.exists(dir)) {
unzip(zip, exdir = "~/Documents/phd-thesis/capybara-benchmarks/")
zip2 <- "~/Documents/phd-thesis/capybara-benchmarks/The Tails of Gravity/Tails of Gravity data.zip"
unzip(
zip2,
exdir = "~/Documents/phd-thesis/capybara-benchmarks/The Tails of Gravity"
)
}
zip <- file.path(Sys.getenv("HOME"), "Documents/phd-thesis/capybara-benchmarks/The Tails of Gravity.zip")
exdir <- file.path(Sys.getenv("HOME"), "Documents/phd-thesis/capybara-benchmarks")
data_dta <- file.path(exdir, "The Tails of Gravity", "Tails of Gravity data.dta")
data_table4 <- haven::read_dta(data_dta)
# replicate the minimal preprocessing from the original script
data_table4 <- data_table4 %>%
clean_names() %>%
select(year, iso_o, iso_d, dist, contig, fta, trade = trade_x) %>%
mutate(
etfe = paste0(iso_o, year),
itfe = paste0(iso_d, year),
pair = paste0(iso_o, "_", iso_d)
) %>%
filter(year %in% seq(min(year), max(year), 5)) %>%
select(-c(iso_o, iso_d)) %>%
drop_na() %>%
filter(year <= quantile(data_table4$year, 0.75))
fit <- feglm(
trade ~ log(dist) + contig + fta | etfe + itfe,
data = data_table4,
cluster = ~pair,
family = "poisson"
)
fit$fixed_effects <- fixef(fit)
=> result malloc(): unsorted double linked list corrupted
I made sure I have sufficient free memory (it is not a quite large dataset)
here is my session info:
> sessionInfo()
R version 4.5.2 (2025-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Manjaro Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.12.0.backup
LAPACK: /usr/lib/libopenblas.so.0.3; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fixest_0.13.2 haven_2.5.5 janitor_2.2.1 tidyr_1.3.1 dplyr_1.1.4
[6] devtools_2.4.6 usethis_3.2.1
loaded via a namespace (and not attached):
[1] compiler_4.5.2 Rcpp_1.1.0 tidyselect_1.2.1
[4] stringr_1.6.0 snakecase_0.11.1 fastmap_1.2.0
[7] lattice_0.22-7 R6_2.6.1 generics_0.1.4
[10] Formula_1.2-5 forcats_1.0.1 tibble_3.3.0
[13] lubridate_1.9.4 pillar_1.11.1 rlang_1.1.6
[16] cachem_1.1.0 stringi_1.8.7 fs_1.6.6
[19] stringmagic_1.2.0 pkgload_1.4.1 timechange_0.3.0
[22] memoise_2.0.1 cli_3.6.5 magrittr_2.0.4
[25] grid_4.5.2 remotes_2.5.0 hms_1.1.4
[28] sandwich_3.1-1 nlme_3.1-168 lifecycle_1.0.4
[31] vctrs_0.6.5 glue_1.8.0 numDeriv_2016.8-1.1
[34] zoo_1.8-14 sessioninfo_1.2.3 pkgbuild_1.4.8
[37] dreamerr_1.5.0 purrr_1.2.0 tools_4.5.2
[40] pkgconfig_2.0.3 ellipsis_0.3.2