jqr

1.2.3

Under R 4.3.0, we see error as follows,

* installing *source* package ‘jqr' ...
** package ‘jqr' successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
Using PKG_LIBS=-ljq
--------------------------- [ANTICONF] --------------------------------
Configuration failed because libjq was not found. Try installing:
 * deb: libjq-dev (Debian, Ubuntu).
 * rpm: jq-devel (Fedora, EPEL)
 * csw: libjq_dev (Solaris)
 * brew: jq (OSX)
If  is already installed set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
-------------------------- [ERROR MESSAGE] ---------------------------
<stdin>:1:16: fatal error: jq.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘jqr'
* removing ‘/rds/user/jhz22/hpc-work/R/jqr'
* restoring previous ‘/rds/user/jhz22/hpc-work/R/jqr'

The downloaded source packages are in
        ‘/rds/user/jhz22/hpc-work/work/RtmpRfkrxq/downloaded_packages'
Warning message:
In install.packages("jqr") :
  installation of package ‘jqr' had non-zero exit status

 

Since we have already had libjq.so installed at /rds/user/jhz22/hpc-work/lib, see https://cambridge-ceu.github.io/csd3/applications/DNAnexus.html; we would need change the default configuration,

Rscript -e 'download.packages("jqr",".")'
tar xvfz jqr_1.2.3.tar.gz
cd jqr
mv configure configure.save
cat <(
cat <<'EOL'
PKG_CPPFLAGS=-I/rds/user/jhz22/hpc-work/include
PKG_LIBS=-L/rds/user/jhz22/hpc-work/lib -ljq
EOL
) <(awk 'NR>2' src/Makevars.in) > src/Makevars
cd -
R CMD INSTALL jqr
 

where the body of Makevars is duplicated from Makevars.in adding location of jq.h and jq.so.

1.3.0

The error message is simiar, but we proceed with a relatively simpler syntax,

Rscript -e 'download.packages("jqr",".")'
R CMD INSTALL --configure-vars='INCLUDE_DIR=/rds/user/jhz22/hpc-work/include LIB_DIR=/rds/user/jhz22/hpc-work/lib' jqr_1.3.0.tar.gz
rm jqr_*
 

1.3.3

This mirrors efforts above.

# Rscript -e 'download.packages("jqr",".")'
tar xvfz jqr_1.3.3.tar.gz
cd jqr
mv configure configure.sav
cd -
 

but with src/Makevars as follows,

# Use C++17 standard
CXX_STD = CXX17

# Compiler flags
CXXFLAGS = -Wall -O3

# Linker flags
LDFLAGS = -shared

# Include directories
PKG_CPPFLAGS = -I/usr/local/Cluster-Apps/ceuadmin/jq/1.6/include

# Libraries to link against
PKG_LIBS = -L/usr/local/Cluster-Apps/ceuadmin/jq/1.6/lib -ljq
 

followd by R CMD INSTALL jqr.