#!/bin/csh
source /data/gannet/ripley/R/packages/common.csh
## needed by KFAS NPRED SynchWave TSSS calcWOI sequoia
limit stacksize 50M

setenv _R_CHECK_SUGGESTS_ONLY_ true

setenv _R_CHECK_PKG_SIZES_ true
unsetenv _R_CHECK_COMPILATION_FLAGS_KNOWN_
setenv _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_ true
setenv _R_CHECK_CODE_DATA_INTO_GLOBALENV_ true

## orphaned check may need CRAN_package_db()
#setenv R_CRAN_WEB http://cran.r-project.org
setenv _R_CHECK_ORPHANED_ true
setenv _R_CHECK_EXCESSIVE_IMPORTS_ 20
setenv _R_CHECK_XREFS_PKGS_ARE_DECLARED_ true
setenv _R_CHECK_BASHISMS_ true
##setenv _R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_ true
setenv _R_CHECK_SRC_MINUS_W_IMPLICIT_ true

setenv _R_CHECK_COMPILATION_FLAGS_KNOWN_ "-Werror=implicit-function-declaration -Wno-error=enum-constexpr-conversion -Wp,-D_FORTIFY_SOURCE=3"

setenv JAGS_LIB /usr/local/clang/lib64
setenv PKG_CONFIG_PATH /usr/local/clang/lib64/pkgconfig:/usr/local/lib64/pkgconfig:/usr/lib64/pkgconfig
set path=(/usr/local/clang/bin $path)

nohup make -j30 -k check >&! check_log