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/.

The software package is available with module load ceuadmin/pspp/1.6.0.

2.0.0-pre1ge32bec

The source is https://benpfaff.org/~blp/pspp-master/20230624103130/source/pspp-2.0.0-pre1ge32bec.tar.gz.

In Makefile, we replace makeinfo with makeinfo --force --no-validate,

The binaries thus produced can be merged into GNU binary build (with errors from GLIBCXX on its own):

https://benpfaff.org/~blp/pspp-master/20230624103130/x86_64/pspp-2.0.0-pre1ge32bec-x86_64-build20230624103419.tar.gz

We proceed with module load ceuadmin/pspp/2.0.0-pre1ge32bec.

Direct use of binary distribution is implicit with these modules,

module load ceuadmin/gettext/0.21 ceuadmin/readline/8.0
module load automake-1.15.1-gcc-5.4.0-kqipzs7 cairo/1.16.0
module load gcc/6 gtkplus-2.24.31-gcc-5.4.0-2a7zfti
module load libtool-2.4.6-gcc-6.2.0-sqmr7cn
module load pango-1.40.3-gcc-5.4.0-32phpcz

provided that GLIBCxx could be sorted out, i.e.,

bin/pspp: /usr/lib64/libc.so.6: version `GLIBC_2.34' not found (required by bin/pspp)
bin/pspp: /usr/lib64/libc.so.6: version `GLIBC_2.33' not found (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-2.0.0-pre1ge32bec.so)
bin/pspp: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-2.0.0-pre1ge32bec.so)
bin/pspp: /usr/lib64/libc.so.6: version `GLIBC_2.25' not found (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-core-2.0.0-pre1ge32bec.so)
bin/pspp: /usr/lib64/libc.so.6: version `GLIBC_2.26' not found (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-core-2.0.0-pre1ge32bec.so)
bin/pspp: /usr/lib64/libc.so.6: version `GLIBC_2.32' not found (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-core-2.0.0-pre1ge32bec.so)
bin/pspp: /usr/lib64/libc.so.6: version `GLIBC_2.33' not found (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-core-2.0.0-pre1ge32bec.so)
bin/pspp: /usr/lib64/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-core-2.0.0-pre1ge32bec.so)
bin/pspp: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-core-2.0.0-pre1ge32bec.so)
bin/pspp: /usr/lib64/libpq.so.5: no version information available (required by /usr/local/Cluster-Apps/ceuadmin/pspp/2.0.0-pre1ge32bec/lib/pspp/libpspp-core-2.0.0-pre1ge32bec.so)

flatpak

The use of flatpak is possible with these operations,

# root privilege is required
# echo 20000 > /proc/sys/user/max_user_namespaces
# https://wiki.archlinux.org/title/Bubblewrap

flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo --user
flatpak install flathub org.gnu.pspp
flatpak list
flatpak run org.gnu.pspp