I was trying to update my package eggCounts, but when I tried to do R CMD check --as-cran there was this warning:
> checking compiled code ... WARNING
> File ‘eggCounts/libs/eggCounts.so’:
> Found ‘abort’, possibly from ‘abort’ (C)
> Object: ‘Modules.o’
I did a search and it found this:
> grep -rnw '/home/b/crwang/PhD/Git/eggCount/eggCounts_dev/' -e 'assert' > Binary file /home/b/crwang/PhD/Git/eggCount/eggCounts_dev/src/Modules.o matches > Binary file /home/b/crwang/PhD/Git/eggCount/eggCounts_dev/src/eggCounts.so matches
I did not modify my Makevars or any of my stan models, the only difference I see is that the models.hpp code is now generated with Stan version 2.17.0 instead of 2.16.0 in the previous version of my package. Here is my session info:
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /usr/lib/atlas-base/libf77blas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=C LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_CH.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BH_1.66.0-1 eggCounts_2.1 rstan_2.17.3 StanHeaders_2.17.2 ggplot2_3.0.0 Rcpp_0.12.18