pspp
Official page: https://www.gnu.org/software/pspp/ (News).
1.2.0
module load pspp/1.2.0
pspp example.sps
where example.sps is the documentation example. Nevertheless psppire
is not yet functioning.
However, it is possible to compile it directly by using
-
gtksourceview1 4.0.3 (4.4.0 is more demanding with Python 3.5, meson, Vala, etc.) and use PKG_CONFIG_PATH when appropriate
./configure --prefix=$HPC_WORK CFLAGS=-I$HPC_work/include LDFLAGS=-L$HPC_WORK/lib LIBS=-lintl --enable-static make make install
See https://www.gnu.org/software/gettext/FAQ.html for any error messages.
- spread-sheet-widget-0.3
- fribidi-1.0.8
- GTKSOURVIEW_CFLAGS and GTKSOURVIEW_LIBS in the configuration.
export PREFIX=/rds/user/$USER/hpc-work
export GTKSOURCEVIEW_CFLAGS=-I${PREFIX}/include/gtksourceview-4
export GTKSOURCEVIEW_LIBS="-L${PREFIX}/lib -lgtksourceview-4"
./configure --prefix=${PREFIX}
make
make install
note that it is necessary to comment on the statement kludge = gtk_source_view_get_type ();
from src/ui/gui/widgets.c
and to remove the PREFIX=
specification in the Perl part of compiling, i.e,
cd perl-module
/usr/bin/perl Makefile.PL PREFIX=/rds/user/$USER/hpc-work OPTIMIZE="-g -O2 -I/rds-d4/user/$USER/hpc-work/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng15 -I/usr/include/uuid -I/usr/include/libdrm -I/usr/include/pango-1.0 -I/usr/include/harfbuzz "
Now we can execute plot.sps
psppire plot.ps &
More documentation examples are in the examples directory.
1.4.1
Version 1.4.1 requires spread-sheet-widget 0.6 and we follow the following steps,
wget http://alpha.gnu.org/gnu/ssw/spread-sheet-widget-0.7.tar.gz
tar xvfz spread-sheet-widget-0.7.tar.gz
cd spread-sheet-widget-0.7
./configure --prefix=$HPC_WORK
make
make install
export PREFIX=/rds/user/$USER/hpc-work
export GTKSOURCEVIEW_CFLAGS=-I${PREFIX}/include/gtksourceview-4
export GTKSOURCEVIEW_LIBS="-L${PREFIX}/lib -lgtksourceview-4"
wget http://mirror.lyrahosting.com/gnu/pspp/pspp-1.4.1.tar.gz
tar xvfz pspp-1.4.1.tar.gz
cd pspp-1.4.1
./configure --prefix=${PREFIX}
Again we removed PREFIX= in call to perl-module/Makefile.PL.
Finally, the LD = flag was not set in perl-module/Makefile and we use LD = ‘gcc'.
The package seems really attractive with its support for over 1 billion cases and 1 billion variables, while giving the appeal of data visualisation in SPSS. The following is an example code generated by the package to read/list GREAT annotation.
GET DATA
/TYPE=TXT
/FILE="IL12B-all.tsv"
/ARRANGEMENT=DELIMITED
/DELCASE=LINE
/FIRSTCASE=2
/DELIMITERS="\t"
/VARIABLES=
Ontology A21
ID A10
Desc A158
BinomRank F3.0
BinomP F12.7
BinomBonfP F9.0
BinomFdrQ F10.2
RegionFoldEnrich F9.5
ExpRegions F12.7
ObsRegions F1.0
GenomeFrac F12.8
SetCov F5.2
HyperRank F3.0
HyperP F12.7
HyperBonfP F9.0
HyperFdrQ F9.2
GeneFoldEnrich F9.5
ExpGenes F12.7
ObsGenes F2.0
TotalGenes F5.0
GeneSetCov F6.3
TermCov F12.7
Regions A193
Genes A98.
VARIABLE LEVEL Ontology (SCALE).
VARIABLE ALIGNMENT Ontology (RIGHT).
VARIABLE WIDTH Ontology (8).
VARIABLE LEVEL ID (SCALE).
VARIABLE ALIGNMENT ID (RIGHT).
VARIABLE WIDTH ID (8).
VARIABLE LEVEL Desc (SCALE).
VARIABLE ALIGNMENT Desc (RIGHT).
VARIABLE WIDTH Desc (8).
VARIABLE LEVEL Regions (SCALE).
VARIABLE ALIGNMENT Regions (RIGHT).
VARIABLE WIDTH Regions (8).
VARIABLE LEVEL Genes (SCALE).
VARIABLE ALIGNMENT Genes (RIGHT).
VARIABLE WIDTH Genes (8).
list.
1.6.0
A couple of Perl modules are required and can be made available as follows,
perl -MCPAN -e shell
install Config::Perl::V
install Memory::Usage
Assuming libreadline
is installed from https://ftp.gnu.org/gnu/readline/, the installation then proceeds with
module load libiconv-1.15-gcc-5.4.0-ymwv5vs
module load gettext-0.19.8.1-gcc-5.4.0-zaldouz
module load texinfo-6.3-gcc-5.4.0-gszsfum
wget -qO- https://ftp.nluug.nl/pub/gnu/pspp/pspp-1.6.0.tar.gz | \
tar xvfz -
cd pspp-1.6.0
configure --prefix=$HPC_WORK LDFLAGS="-lreadline -ltinfo" --with-gnu-ld
make
Near the end we see complaints about Perl module and we specifically run the following code
cd perl-module && /usr/bin/perl Makefile.PL \
OPTIMIZE="-g -O2 -DGCC_LINT \
-I/usr/local/software/archive/linux-scientific7-x86_64/gcc-9/zlib-1.2.11-lnf7bswyozdhprbg7jo6n5ha5633ftj2/include \
-I/rds/user/jhz22/hpc-work/include/libpng15 -I/rds/user/jhz22/hpc-work/include \
-I/rds-d4/user/jhz22/hpc-work/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0 \
-I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/uuid -I/usr/include/libdrm \
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -Wno-error" \
LD="`/usr/bin/perl -e 'use Config::Perl::V;print Config::Perl::V::myconfig()->{config}{ld};'` -lreadline -ltinfo"
cd -
make
make install
where we drop PREFIX=/rds/user/jhz22/hpc-work
after Makefile.PL
and furnish the installation with another make/make install
.
Note that the Windows version is available from https://caeis.etech.fh-augsburg.de/downloads/windows/pspp-win-daily/1.6.0-ge6b96c/.
-
gtksourceview 4.6.0 installation
source py37/bin/activate python -m pip install meson==0.63.3 python -m pip install --force-reinstall ninja==1.10.0 wget -qO- https://github.com/GNOME/gtksourceview/archive/refs/tags/4.6.0.tar.gz | tar xfz - cd gtksourceview-4.6.0 mkdir build meson configure --prefix=$CEUADMIN/gtksourcereview/4.6.0 --default-library=both meson build cd build ninja install
where ninja releases are seen from https://github.com/ninja-build/ninja/releases. One may need to insert -L$HPC_WORK/lib -I$HPC_WORK/include to the command manually. ↩