aboutsummaryrefslogtreecommitdiff
path: root/reproduce
diff options
context:
space:
mode:
authorMohammad Akhlaghi <mohammad@akhlaghi.org>2020-09-03 21:18:11 +0100
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2020-09-03 21:18:11 +0100
commit3239fc6037199e28b54fbe104b082a9bd13b6ad9 (patch)
tree9b54fa586bead68bf2c0d38f5e21adbb84eb451b /reproduce
parent621d71e03bc66b89e9dc5d6acc8c37b403adc8a2 (diff)
parent6d18576568da8298295c82c0853057d7ea5e8b61 (diff)
Imported recent work in Maneage, minor conflicts fixed
Only two small conflicts came up: * The addition of the hardware architecture macro in 'paper.tex' (which was removed for now, but will be added as the referee has requested within the text). * The usage of "" around directory variables in 'paper.mk'.
Diffstat (limited to 'reproduce')
-rw-r--r--reproduce/analysis/make/paper.mk11
-rw-r--r--reproduce/software/config/checksums.conf3
-rw-r--r--reproduce/software/config/urls.conf3
-rw-r--r--reproduce/software/config/versions.conf3
-rw-r--r--reproduce/software/make/basic.mk25
-rw-r--r--reproduce/software/make/high-level.mk53
-rwxr-xr-xreproduce/software/shell/configure.sh258
-rwxr-xr-xreproduce/software/shell/pre-make-build.sh86
8 files changed, 306 insertions, 136 deletions
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 2c08847..f363b6f 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -47,8 +47,9 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
@if [ -f .local/bin/latex ] && [ x"$(pdf-build-final)" != x ]; then
# Put a LaTeX input command for all the necessary macro files.
+ # 'hardware-parameters.tex' is created in 'configure.sh'.
rm -f $(mtexdir)/project.tex
- for t in $(subst paper,,$(makesrc)); do
+ for t in $(subst paper,,$(makesrc)) hardware-parameters; do
echo "\input{tex/build/macros/$$t.tex}" >> $(mtexdir)/project.tex
done
else
@@ -127,7 +128,7 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
# do not use PGFPlots, then you should remove the `-shell-escape'
# option for better security. See
# https://savannah.nongnu.org/task/?15694 for details.
- latex -shell-escape -halt-on-error $$p/paper.tex
+ latex -shell-escape -halt-on-error "$$p"/paper.tex
bibtex paper
# Hack: tidy up eprint+doi style that didn't work in .bst file.
@@ -143,7 +144,7 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
| sed -e 's/EOLINE/\n/g' > paper.bbl
# The pre-final run of LaTeX after 'paper.bbl' was created.
- latex -shell-escape -halt-on-error $$p/paper.tex
+ latex -shell-escape -halt-on-error "$$p"/paper.tex
fi
@@ -171,7 +172,7 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
# See above for a warning and brief discussion on the the
# pdflatex option `-shell-escape'.
- latex -shell-escape -halt-on-error $$p/paper.tex
+ latex -shell-escape -halt-on-error "$$p"/paper.tex
# Convert the DVI to PostScript, and the PostScript to PDF. The
# `-dNOSAFER' option to GhostScript allows transparencies in the
@@ -182,6 +183,6 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
# Come back to the top project directory and copy the built PDF
# file here.
- cd $$p
+ cd "$$p"
cp $(texbdir)/$@ $(final-paper)
fi
diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index b516a61..e7a0e63 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -44,6 +44,7 @@ make-checksum = ddf0fdcb9ee1b182ef294c5da70c1275288c99bef60e63a25c0abed2ddd44aba
metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a
mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628
mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88
+nano-checksum = d101e7f4802c079254e79340b433749dcd699fa9adec3f96e4218ec12f066a1f6b0954c27254bb6f019bc370ee2116817717870f4e2bc782c552442f2cc75195
ncurses-checksum = 4c1333dcc30e858e8a9525d4b9aefb60000cfc727bc4a1062bace06ffc4639ad9f6e54f6bdda0e3a0e5ea14de995f96b52b3327d9ec633608792c99a1e8d840d
openssl-checksum = 1523985ba90f38aa91aa6c2d57652f4e243cb2a095ce6336bf34b39b5a9b5b876804299a6825c758b65990e57948da532cca761aa12b10958c97478d04dd6d34
patchelf-checksum = 39745662651cf0a9915685b2767a611ceab4286f8fa57eace342b3f44248431616e8563d4ac6709c97d8534229c73c05470239e462b7e74b36bf629a876dfbad
@@ -86,6 +87,7 @@ cdsclient-checksum = 2d7abf0079189b9dd19cb8919061445fd19ea9f7dfd54e8ceee26b74321
cfitsio-checksum = 08a13931726b0ee15bd4e2ad6dd4debb8268f3b0bc33adadec5c6a29295dd536bcccb3cc949721c6cebac6f43b6118e5e38332ac0ba8a07a43553416d8debae5
cmake-checksum = e0591d5fb234f3e7b74d6d2aad44fbf3e19e69547bd428681ba6ad0461d4f3d2a154605808b4733531d2c66f0e91eb39a179ae0d89a37e92a3f20e9cae691468
eigen-checksum = 34cf600914cce719d61511577ef9cd26fbdcb7a6fad1d0ab8396f98b887fac6a5577d3967e84a8f56225cc50de38f3b91f34f447d14312028383e32b34ea1972
+emacs-checksum = dfb26531d2c19cf9fb56505f03d799654b45e5f9528e777900e8280ed2c1d21e04c52f510528e31e015977c471ae63164cedee6174b7439ebcf479a21fc18064
expat-checksum = 514ff2ef3c93af0b1715b7a08732db33c13a113c4c72422716a22ee26c09235deed71ec55510cee24c33bcd6b2347602bd71ce70a432d5583fb63765ff9e0e09
fftw-checksum = ab918b742a7c7dcb56390a0a0014f517a6dff9a2e4b4591060deeb2c652bf3c6868aa74559a422a276b853289b4b701bdcbd3d4d8c08943acf29167a7be81a38
flex-checksum = b4ef58d4a1d66b213e2f59df06959decf46d26b253cdc3f51cd26e2e2b505461ef23dafa974dd2005b1f0cafa5a83fe9258baf78004b2fdae6dfc299bc17bfd1
@@ -130,6 +132,7 @@ swarp-checksum = 80f4ade59738df3d4c9b47bda04148b53c6ba995d523fa8d1e02fb5d952b607
swig-checksum = 5eaa2e06d8e4197fd02194051db1e518325dbb074a4c55a91099ad9c55193874f577764afc9029409a41bd520a95154095f26e33ef5add5c102bb2c1d98d33eb
tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108
util-linux-checksum = c95d26b9037d6b877a247e6aeb58d17aa80f7e1bd6b523a4e0fde559fe07b3d924ece6d373300fefb65d1f206b3f990aeddb3a03605040e72ce6d6ee88591021
+vim-checksum = 06ba43386fcf308520d88d7a68e9bc1fabd824b05078b8f9112500a2ad4e50a91f1a1c2925889b7c06dbce34307f12abf508e2172b05fd283f965cc06552eb6d
wcslib-checksum = 8c98c4b575056e2d966b77a4bc951256d02ecee3a11847e140fd38d93afd0f76b3e906d590c952dc9fc58ceeb1ba062b19d8e1e676ee0032f5b7ed13a9dfa892
xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c
yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02
diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf
index 34c4d89..417f5ed 100644
--- a/reproduce/software/config/urls.conf
+++ b/reproduce/software/config/urls.conf
@@ -47,6 +47,7 @@
#metastore-url = http://akhlaghi.org/maneage-software
#mpc-url = http://ftp.gnu.org/gnu/mpc
#mpfr-url = http://www.mpfr.org/mpfr-current
+#nano-url = https://www.nano-editor.org/dist/v$(word 1, $(subst ., ,$(nano-version)))
#ncurses-url = http://ftp.gnu.org/gnu/ncurses
#openssl-url = http://www.openssl.org/source
#patchelf-url = http://nixos.org/releases/patchelf/patchelf-$(patchelf-version)
@@ -88,6 +89,7 @@
#cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c
#cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv)
#eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz
+#emacs-url = http://ftp.gnu.org/gnu/emacs
#expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz)
#fftw-url = ftp://ftp.fftw.org/pub/fftw
#flex-url = https://github.com/westes/flex/files/981163
@@ -133,6 +135,7 @@
#tides-url = http://akhlaghi.org/maneage-software
#util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.35/
#valgrind-url = https://sourceware.org/pub/valgrind
+#vim-url = ftp://ftp.vim.org/pub/vim/unix
#wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib
#xlsxio-url = https://github.com/brechtsanders/xlsxio/archive
#yaml-url = pyyaml.org/download/libyaml
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 0a9e21e..0b3a4d2 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -44,6 +44,7 @@ make-version = 4.3
metastore-version = 1.1.2-23-fa9170b
mpc-version = 1.1.0
mpfr-version = 4.0.2
+nano-version = 5.2
ncurses-version = 6.2
patchelf-version = 0.10
perl-version = 5.32.0
@@ -94,6 +95,7 @@ cdsclient-version = 3.84
cfitsio-version = 3.48
cmake-version = 3.18.1
eigen-version = 3.3.7
+emacs-version = 27.1
expat-version = 2.2.9
fftw-version = 3.3.8
flex-version = 2.6.4-91-ga631f5d
@@ -134,6 +136,7 @@ swarp-version = 2.38.0
swig-version = 3.0.12
tides-version = 2.0
util-linux-version = 2.35
+vim-version = 8.2
xlsxio-version = 0.2.21
yaml-version = 0.2.5
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 0b672d8..934580a 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -56,8 +56,13 @@ ibdir = $(BDIR)/software/installed/bin
ildir = $(BDIR)/software/installed/lib
ibidir = $(BDIR)/software/installed/version-info/proglib
-# Ultimate Makefile target.
-targets-proglib = low-level-links gcc-$(gcc-version)
+# Ultimate Makefile target. GNU Nano (a simple and very light-weight text
+# editor) is installed by default, it is recommended to have it in the
+# 'basic.mk', so Maneaged projects can be edited on any system (even when
+# there is no command-line text editor is available).
+targets-proglib = low-level-links \
+ gcc-$(gcc-version) \
+ nano-$(nano-version)
all: $(foreach p, $(targets-proglib), $(ibidir)/$(p))
# Define the shell environment
@@ -852,7 +857,8 @@ $(ibidir)/diffutils-$(diffutils-version): \
$(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version)
tarball=file-$(file-version).tar.gz
$(call import-source, $(file-url), $(file-checksum))
- $(call gbuild, file-$(file-version), static,,V=1)
+ $(call gbuild, file-$(file-version), static, \
+ --disable-libseccomp, V=1)
echo "File $(file-version)" > $@
$(ibidir)/findutils-$(findutils-version): \
@@ -1145,11 +1151,22 @@ $(ibidir)/texinfo-$(texinfo-version): \
echo "GNU Texinfo $(texinfo-version)" > $@
$(ibidir)/which-$(which-version): $(ibidir)/coreutils-$(coreutils-version)
- tarball=/which-$(which-version).tar.gz
+ tarball=which-$(which-version).tar.gz
$(call import-source, $(which-url), $(which-checksum))
$(call gbuild, which-$(which-version), static)
echo "GNU Which $(which-version)" > $@
+# GNU Nano is a very light-weight and small, command-line text editor (in
+# total around 3.5 Mb after installation!). It is top-level target in the
+# basic tools (nothing depends on it, it just depends on GCC). This is
+# because some projects may choose to not have it by manually removing it
+# from 'targets-proglib' above (it has no effect on processing after all!).
+$(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version)
+ tarball=nano-$(nano-version).tar.xz
+ $(call import-source, $(nano-url), $(nano-checksum))
+ $(call gbuild, nano-$(nano-version), static)
+ echo "GNU Nano $(nano-version)" > $@
+
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 9f434bc..3c5e518 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -54,9 +54,9 @@ ibidir = $(BDIR)/software/installed/version-info/proglib
# Basic directories (specific to this Makefile).
il64dir = $(BDIR)/software/installed/lib64
iidir = $(BDIR)/software/installed/include
-shsrcdir = $(shell pwd)/reproduce/software/shell
-dtexdir = $(shell pwd)/reproduce/software/bibtex
-patchdir = $(shell pwd)/reproduce/software/patches
+shsrcdir = "$(shell pwd)"/reproduce/software/shell
+dtexdir = "$(shell pwd)"/reproduce/software/bibtex
+patchdir = "$(shell pwd)"/reproduce/software/patches
itidir = $(BDIR)/software/installed/version-info/tex
ictdir = $(BDIR)/software/installed/version-info/cite
ipydir = $(BDIR)/software/installed/version-info/python
@@ -449,6 +449,25 @@ $(ibidir)/eigen-$(eigen-version):
rm -rf $(ddir)/eigen-eigen-*
echo "Eigen $(eigen-version)" > $@
+# GNU Emacs is an advanced text editor (among many other things!), so it
+# isn't directly related to the analysis phase of a project. However, it
+# can be useful during the development of a project on systems that don't
+# have it natively. So probably after the project is finished and is ready
+# for publication, you can remove it from 'TARGETS.conf'.
+#
+# However, the full Emacs build has a very large number of dependencies
+# which aren't necessary in many scenarios so we are disabling everything
+# except the core Emacs functionality (using '--without-all') and we are
+# also disabling all graphic user interface features (using '--without-x').
+$(ibidir)/emacs-$(emacs-version):
+ tarball=emacs-$(emacs-version).tar.xz
+ $(call import-source, $(emacs-url), $(emacs-checksum))
+ $(call gbuild, emacs-$(emacs-version), static, \
+ --without-all --without-x \
+ --without-gnutls --with-ns=no, \
+ -j$(numthreads) V=1)
+ echo "GNU Emacs $(emacs-version)" > $@
+
$(ibidir)/expat-$(expat-version):
tarball=expat-$(expat-version).tar.lz
$(call import-source, $(expat-url), $(expat-checksum))
@@ -1374,8 +1393,30 @@ $(ibidir)/xlsxio-$(xlsxio-version): \
rm $(ibdir)/example_xlsxio_*
echo "XLSX I/O $(xlsxio-version)" > $@
-
-
+# VIM is a text editor which doesn't directly affect processing but can be
+# useful in projects during its development, for more see the comment above
+# GNU Emacs.
+$(ibidir)/vim-$(vim-version):
+ tarball=vim-$(vim-version).tar.bz2
+ $(call import-source, $(vim-url), $(vim-checksum))
+ cd $(ddir)
+ tar xf $(tdir)/$$tarball
+ n=$$(echo $(vim-version) | sed -e's|\.||')
+ cd $(ddir)/vim$$n
+ ./configure --prefix=$(idir) \
+ --disable-canberra \
+ --enable-multibyte \
+ --disable-netbeans \
+ --disable-fontset \
+ --disable-gpm \
+ --disable-acl \
+ --disable-gui \
+ --with-x=no
+ make -j$(numthreads)
+ make install
+ cd ..
+ rm -rf vim$$n
+ echo "VIM $(vim-version)" > $@
@@ -1411,7 +1452,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
tar xf $(tdir)/install-tl-unx.tar.gz
cd install-tl-*
sed -e's|@installdir[@]|$(idir)|g' \
- $$topdir/reproduce/software/config/texlive.conf \
+ "$$topdir"/reproduce/software/config/texlive.conf \
> texlive.conf
# TeX Live's installation may fail due to any reason. But TeX Live
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 6ffb4ff..0d22dcc 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -48,7 +48,7 @@ need_gfortran=0
# --------------------
#
# These are defined to help make this script more readable.
-topdir=$(pwd)
+topdir="$(pwd)"
optionaldir="/optional/path"
adir=reproduce/analysis/config
cdir=reproduce/software/config
@@ -96,7 +96,8 @@ create_file_with_notice ()
# an absolute address. With this function we can make sure of that.
absolute_dir ()
{
- if stat "$1" 1> /dev/null; then
+ address="$1"
+ if stat "$address" 1> /dev/null; then
echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
else
exit 1;
@@ -136,18 +137,18 @@ check_permission ()
{
# Make a `junk' file, activate its executable flag and record its
# permissions generally.
- local junkfile=$1/check_permission_tmp_file
- rm -f $junkfile
- echo "Don't let my short life go to waste" > $junkfile
- chmod +x $junkfile
- local perm_before=$(ls -l $junkfile | awk '{print $1}')
+ local junkfile="$1"/check_permission_tmp_file
+ rm -f "$junkfile"
+ echo "Don't let my short life go to waste" > "$junkfile"
+ chmod +x "$junkfile"
+ local perm_before=$(ls -l "$junkfile" | awk '{print $1}')
# Now, remove the executable flag and record the permissions.
- chmod -x $junkfile
- local perm_after=$(ls -l $junkfile | awk '{print $1}')
+ chmod -x "$junkfile"
+ local perm_after=$(ls -l "$junkfile" | awk '{print $1}')
# Clean up before leaving the function
- rm -f $junkfile
+ rm -f "$junkfile"
# If the permissions are equal, the filesystem doesn't allow
# permissions.
@@ -187,8 +188,8 @@ check_permission ()
free_space_warning()
{
fs_threshold=$1
- fs_destpath=$2
- return $(df $fs_destpath \
+ IFS='"' fs_destpath="$2"
+ return $(df "$fs_destpath" \
| awk 'FNR==2 {if($4>'$fs_threshold') print 1; \
else print 0; }')
}
@@ -224,6 +225,62 @@ fi
+# Collect CPU information
+# -----------------------
+#
+# When the project is built, the type of a machine that built it also has
+# to to be documented. This way, if different results or behaviors are
+# observed in software-related or analysis-related phases of the project,
+# it would be easier to track down the root cause. So far this is just
+# later recorded as a LaTeX macro to be put in the final paper, but it
+# could be used in a more systematic way to optimize/revise project
+# workflow and build.
+hw_class=$(uname -m)
+if [ x$kernelname = xLinux ]; then
+ byte_order=$(lscpu \
+ | grep 'Byte Order' \
+ | awk '{ \
+ for(i=3;i<NF;++i) \
+ printf "%s ", $i; \
+ printf "%s", $NF}')
+ address_sizes=$(lscpu \
+ | grep 'Address sizes' \
+ | awk '{ \
+ for(i=3;i<NF;++i) \
+ printf "%s ", $i; \
+ printf "%s", $NF}')
+elif [ x$on_mac_os = xyes ]; then
+ hw_byteorder=$(sysctl -n hw.byteorder)
+ if [ x$hw_byteorder = x1234 ]; then byte_order="Little Endian";
+ elif [ x$hw_byteorder = x4321 ]; then byte_order="Big Endian";
+ fi
+ address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical)
+ address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual)
+ address_sizes="$address_size_physical bits physical, "
+ address_sizes+="$address_size_virtual bits virtual"
+else
+ byte_order="unrecognized"
+ address_sizes="unrecognized"
+ cat <<EOF
+______________________________________________________
+!!!!!!! WARNING !!!!!!!
+
+Machine byte order and address sizes could not be recognized. You can add
+the necessary steps in the 'reproduce/software/shell/configure.sh' script
+(just above this error message), or contact us with this web-form:
+
+ https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ sleep 5
+fi
+
+
+
+
+
# Check for C/C++ compilers
# -------------------------
#
@@ -717,7 +774,7 @@ fi
# Build directory
# ---------------
-currentdir=$(pwd)
+currentdir="$(pwd)"
if [ $rewritepconfig = yes ]; then
cat <<EOF
@@ -746,7 +803,7 @@ directory). The build directory cannot be a subdirectory of the source.
EOF
bdir=
junkname=pure-junk-974adfkj38
- while [ x$bdir = x ]
+ while [ x"$bdir" = x ]
do
# Ask the user (if not already set on the command-line).
if [ x"$build_dir" = x ]; then
@@ -761,31 +818,31 @@ EOF
fi
# If it exists, see if we can write in it. If not, try making it.
- if [ -d $build_dir ]; then
- if mkdir $build_dir/$junkname 2> /dev/null; then
+ if [ -d "$build_dir" ]; then
+ if echo "test" > "$build_dir"/$junkname ; then
+ rm -f "$build_dir"/$junkname
instring="the already existing"
- bdir=$(absolute_dir $build_dir)
- rm -rf $build_dir/$junkname
+ bdir="$(absolute_dir "$build_dir")"
else
echo " ** Can't write in '$build_dir'";
fi
else
- if mkdir $build_dir 2> /dev/null; then
+ if mkdir "$build_dir" 2> /dev/null; then
instring="the newly created"
- bdir=$(absolute_dir $build_dir)
+ bdir="$(absolute_dir "$build_dir")"
else
echo " ** Can't create '$build_dir'";
fi
fi
- # If its given, make sure it isn't a subdirectory of the source
+ # If it is given, make sure it isn't a subdirectory of the source
# directory.
if ! [ x"$bdir" = x ]; then
if echo "$bdir/" \
- | grep '^'$currentdir 2> /dev/null > /dev/null; then
+ | grep '^'"$currentdir" 2> /dev/null > /dev/null; then
# If it was newly created, it will be empty, so delete it.
- if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
+ if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi
# Inform the user that this is not acceptable and reset `bdir'.
bdir=
@@ -793,10 +850,30 @@ EOF
fi
fi
- # If everything is fine until now, see if we're able to manipulate
- # file permissions.
+ # If things are fine so far, make sure it does not contain a space
+ # or other meta-characters which can cause problems during software
+ # building.
+ if ! [ x"$bdir" = x ]; then
+ hasmeta=0;
+ case $bdir in *['!'\@\#\$\%\^\&\*\(\)\+\;\ ]* ) hasmeta=1 ;; esac
+ if [ $hasmeta = 1 ]; then
+
+ # If it was newly created, it will be empty, so delete it.
+ if ! [ "$(ls -A "$bdir")" ]; then rm --dir "$bdir"; fi
+
+ # Inform the user and set 'bdir' to empty again.
+ bdir=
+ echo " ** Build directory should not contain meta-characters"
+ echo " ** (like SPACE, %, \$, !, ;, or parenthesis, among "
+ echo " ** others): they can interrup the build for some software."
+ fi
+ fi
+
+ # If everything is still fine so far, see if we're able to
+ # manipulate file permissions in the directory's filesystem and if
+ # so, see if there is atleast 5GB free space.
if ! [ x"$bdir" = x ]; then
- if ! $(check_permission $bdir); then
+ if ! $(IFS='"' check_permission "$bdir"); then
# Unable to handle permissions well
bdir=
echo " ** File permissions can't be modified in this directory"
@@ -804,7 +881,7 @@ EOF
# Able to handle permissions, now check for 5GB free space
# in the given partition (note that the number is in units
# of 1024 bytes). If this is not the case, print a warning.
- if $(free_space_warning 5000000 $bdir); then
+ if $(free_space_warning 5000000 "$bdir"); then
echo " !! LESS THAN 5GB FREE SPACE IN: $bdir"
echo " !! We recommend choosing another partition."
echo " !! Build will continue in 5 seconds..."
@@ -817,7 +894,7 @@ EOF
# reset `build_dir' to blank, so it continues asking for another
# directory and let the user know that they must select a new
# directory.
- if [ x$bdir = x ]; then
+ if [ x"$bdir" = x ]; then
build_dir=
echo " ** Please select another directory."
echo ""
@@ -834,9 +911,9 @@ fi
# Input directory
# ---------------
if [ x"$input_dir" = x ]; then
- indir=$optionaldir
+ indir="$optionaldir"
else
- indir=$input_dir
+ indir="$input_dir"
fi
noninteractive_sleep=2
if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
@@ -878,7 +955,7 @@ EOF
# In case an input-directory is given, write it in 'indir'.
if [ x$inindir != x ]; then
- indir=$(absolute_dir $inindir)
+ indir="$(absolute_dir "$inindir")"
echo " -- Using '$indir'"
fi
fi
@@ -922,7 +999,7 @@ EOF
# If given, write the software directory.
if [ x"$tmpddir" != x ]; then
- ddir=$(absolute_dir $tmpddir)
+ ddir="$(absolute_dir "$tmpddir")"
echo " -- Using '$ddir'"
fi
fi
@@ -946,11 +1023,18 @@ if [ $rewritepconfig = yes ]; then
-e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
$pconf.in >> $pconf
else
- # Read the values from existing configuration file.
- inbdir=$(awk '$1=="BDIR" {print $3}' $pconf)
-
- # Read the software directory.
- ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $pconf)
+ # Read the values from existing configuration file. Note that the build
+ # directory may have space characters. Even though we currently check
+ # against it, we hope to be able to remove this condition in the
+ # future.
+ inbdir=$(awk '$1=="BDIR" { for(i=3; i<NF; i++) \
+ printf "%s ", $i; \
+ printf "%s", $NF }' $pconf)
+
+ # Read the software directory (same as 'inbdir' above about space).
+ ddir=$(awk '$1=="DEPENDENCIES-DIR" { for(i=3; i<NF; i++) \
+ printf "%s ", $i; \
+ printf "%s", $NF}' $pconf)
# The downloader command may contain multiple elements, so we'll just
# change the (in memory) first and second tokens to empty space and
@@ -968,9 +1052,9 @@ else
# Make sure `bdir' is an absolute path and it exists.
berr=0
ierr=0
- bdir=$(absolute_dir $inbdir)
+ bdir="$(absolute_dir "$inbdir")"
- if ! [ -d $bdir ]; then if ! mkdir $bdir; then berr=1; err=1; fi; fi
+ if ! [ -d "$bdir" ]; then if ! mkdir "$bdir"; then berr=1; err=1; fi; fi
if [ $err = 1 ]; then
cat <<EOF
@@ -1013,10 +1097,10 @@ fi
# (without the user noticing), in the end of this script we make a file and
# we'll delete it here (at the start). Therefore if the script crashed in
# the middle that file won't exist.
-sdir=$bdir/software
-finaltarget=$sdir/configuration-done.txt
-if ! [ -d $sdir ]; then mkdir $sdir; fi
-rm -f $finaltarget
+sdir="$bdir"/software
+finaltarget="$sdir"/configuration-done.txt
+if ! [ -d "$sdir" ]; then mkdir "$sdir"; fi
+rm -f "$finaltarget"
@@ -1030,56 +1114,56 @@ rm -f $finaltarget
# analysis Makefiles (thus making them hard to read), we are just building
# them here
# Software tarballs
-tardir=$sdir/tarballs
-if ! [ -d $tardir ]; then mkdir $tardir; fi
+tardir="$sdir"/tarballs
+if ! [ -d "$tardir" ]; then mkdir "$tardir"; fi
# Installed software
-instdir=$sdir/installed
-if ! [ -d $instdir ]; then mkdir $instdir; fi
+instdir="$sdir"/installed
+if ! [ -d "$instdir" ]; then mkdir "$instdir"; fi
# To record software versions and citation.
-verdir=$instdir/version-info
-if ! [ -d $verdir ]; then mkdir $verdir; fi
+verdir="$instdir"/version-info
+if ! [ -d "$verdir" ]; then mkdir "$verdir"; fi
# Program and library versions and citation.
-ibidir=$verdir/proglib
-if ! [ -d $ibidir ]; then mkdir $ibidir; fi
+ibidir="$verdir"/proglib
+if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi
# Python module versions and citation.
-ipydir=$verdir/python
-if ! [ -d $ipydir ]; then mkdir $ipydir; fi
+ipydir="$verdir"/python
+if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi
# Used software BibTeX entries.
-ictdir=$verdir/cite
-if ! [ -d $ictdir ]; then mkdir $ictdir; fi
+ictdir="$verdir"/cite
+if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
# TeXLive versions.
-itidir=$verdir/tex
-if ! [ -d $itidir ]; then mkdir $itidir; fi
+itidir="$verdir"/tex
+if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi
# Top-level LaTeX.
-texdir=$bdir/tex
-if ! [ -d $texdir ]; then mkdir $texdir; fi
+texdir="$bdir"/tex
+if ! [ -d "$texdir" ]; then mkdir "$texdir"; fi
# LaTeX macros.
-mtexdir=$texdir/macros
-if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi
+mtexdir="$texdir"/macros
+if ! [ -d "$mtexdir" ]; then mkdir "$mtexdir"; fi
# TeX build directory. If built in a group scenario, the TeX build
# directory must be separate for each member (so they can work on their
# relevant parts of the paper without conflicting with each other).
if [ "x$reproducible_paper_group_name" = x ]; then
- texbdir=$texdir/build
+ texbdir="$texdir"/build
else
user=$(whoami)
- texbdir=$texdir/build-$user
+ texbdir="$texdir"/build-$user
fi
-if ! [ -d $texbdir ]; then mkdir $texbdir; fi
+if ! [ -d "$texbdir" ]; then mkdir "$texbdir"; fi
# TiKZ (for building figures within LaTeX).
-tikzdir=$texbdir/tikz
-if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi
+tikzdir="$texbdir"/tikz
+if ! [ -d "$tikzdir" ]; then mkdir "$tikzdir"; fi
# If 'tex/build' and 'tex/tikz' aren't symbolic links, then we are in the
# tarball (not the Git repository), so we'll give them another name and let
@@ -1120,14 +1204,14 @@ fi
# safe, we are deleting all the links on each re-configure of the project.
rm -f .build .local
-ln -s $bdir .build
-ln -s $instdir .local
-ln -s $texdir tex/build
-ln -s $tikzdir tex/tikz
+ln -s "$bdir" .build
+ln -s "$instdir" .local
+ln -s "$texdir" tex/build
+ln -s "$tikzdir" tex/tikz
# --------- Delete for no Gnuastro ---------
rm -f .gnuastro
-ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro
+ln -s "$topdir"/reproduce/analysis/config/gnuastro .gnuastro
# ------------------------------------------
@@ -1143,8 +1227,8 @@ ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro
# project names). Maybe later, we can use something like `mktemp' to add
# random characters to this name and make it unique to every run (even for
# a single user).
-tmpblddir=$sdir/build-tmp
-rm -rf $tmpblddir/* $tmpblddir # If its a link, we need to empty its
+tmpblddir="$sdir"/build-tmp
+rm -rf "$tmpblddir"/* "$tmpblddir" # If its a link, we need to empty its
# contents first, then itself.
# Set the top-level shared memory location.
@@ -1156,12 +1240,12 @@ fi
# there (in RAM), build a temporary directory for this project.
needed_space=2000000
if [ x"$shmdir" != x ]; then
- available_space=$(df $shmdir | awk 'NR==2{print $4}')
+ available_space=$(df "$shmdir" | awk 'NR==2{print $4}')
if [ $available_space -gt $needed_space ]; then
dirname=$(pwd | sed -e's/\// /g' \
| awk '{l=NF-1; printf("%s-%s",$l, $NF)}')
- tbshmdir=$shmdir/"$dirname"-$(whoami)
- if ! [ -d $tbshmdir ]; then mkdir $tbshmdir; fi
+ tbshmdir="$shmdir"/"$dirname"-$(whoami)
+ if ! [ -d "$tbshmdir" ]; then mkdir "$tbshmdir"; fi
fi
else
tbshmdir=""
@@ -1170,8 +1254,8 @@ fi
# If a shared memory directory was created set `build-tmp' to be a
# symbolic link to it. Otherwise, just build the temporary build
# directory under the project build directory.
-if [ x$tbshmdir = x ]; then mkdir $tmpblddir;
-else ln -s $tbshmdir $tmpblddir;
+if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir";
+else ln -s "$tbshmdir" "$tmpblddir";
fi
@@ -1540,6 +1624,24 @@ fi
+# Report machine architecture
+# ---------------------------
+#
+# Report hardware
+hwparam="$mtexdir/hardware-parameters.tex"
+
+# Add the text to the ${hwparam} file. Since harware class might include
+# underscore, it must be replaced with '\_', otherwise pdftex would
+# complain and break the build process when doing ./project make.
+hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')"
+.local/bin/echo "\\newcommand{\\machinearchitecture}{$hw_class_fixed}" > $hwparam
+.local/bin/echo "\\newcommand{\\machinebyteorder}{$byte_order}" >> $hwparam
+.local/bin/echo "\\newcommand{\\machineaddresssizes}{$address_sizes}" >> $hwparam
+
+
+
+
+
# Clean the temporary build directory
# ---------------------------------
#
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index 9188fc9..a18966f 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -30,32 +30,32 @@ set -e
-# Input arguments.
-bdir=$1
-ddir=$2
-downloader="$3"
-user_backup_urls="$4"
+# Input arguments (the 'IFS's are to allow space in the name).
+IFS='"' bdir="$1"
+IFS='"' ddir="$2"
+IFS='"' downloader="$3"
+IFS='"' user_backup_urls="$4"
# Basic directories/files
-topdir=$(pwd)
-sdir=$bdir/software
-tardir=$sdir/tarballs
-instdir=$sdir/installed
-tmpblddir=$sdir/build-tmp
+topdir="$(pwd)"
+sdir="$bdir"/software
+tardir="$sdir"/tarballs
+instdir="$sdir"/installed
+tmpblddir="$sdir"/build-tmp
confdir=reproduce/software/config
-ibidir=$instdir/version-info/proglib
+ibidir="$instdir"/version-info/proglib
downloadwrapper=reproduce/analysis/bash/download-multi-try
# Derived directories
-bindir=$instdir/bin
-urlfile=$confdir/urls.conf
-versionsfile=$confdir/versions.conf
-checksumsfile=$confdir/checksums.conf
-backupfile=$confdir/servers-backup.conf
+bindir="$instdir"/bin
+urlfile="$confdir"/urls.conf
+versionsfile="$confdir"/versions.conf
+checksumsfile="$confdir"/checksums.conf
+backupfile="$confdir"/servers-backup.conf
@@ -87,21 +87,21 @@ done
# Download the necessary tarball.
download_tarball() {
# Basic definitions
- maneagetar=$tardir/$tarball
+ maneagetar="$tardir"/"$tarball"
# See if the tarball already exists in Maneage.
if [ -f "$maneagetar" ]; then
just_a_place_holder=1
else
- ucname=$tardir/$tarball.unchecked
+ ucname="$tardir"/"$tarball.unchecked"
# If the URL is empty, use the top backup server
if [ x$w = x ]; then
bservers="$backupservers"
- tarballurl=$topbackupserver/$tarball
+ tarballurl="$topbackupserver"/"$tarball"
else
bservers="$backupservers_all"
- tarballurl=$url/$tarball
+ tarballurl="$url"/"$tarball"
fi
# See if it is in the input-software directory, if so, make a link, if
@@ -111,19 +111,19 @@ download_tarball() {
# link and link to an actual file.
if [ -f "$ddir/$tarball" ]; then
if type realpath > /dev/null 2> /dev/null; then
- ln -sf "$(realpath $ddir/$tarball)" "$ucname"
+ ln -sf "$(realpath "$ddir/$tarball")" "$ucname"
else
- cp $ddir/$tarball $ucname
+ cp "$ddir/$tarball" "$ucname"
fi
else
- $downloadwrapper "$downloader" nolock $tarballurl $ucname \
+ $downloadwrapper "$downloader" nolock $tarballurl "$ucname" \
"$bservers"
fi
# Make sure this is the correct tarball.
if type sha512sum > /dev/null 2> /dev/null; then
checksum=$(sha512sum "$ucname" | awk '{print $1}')
- expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' $checksumsfile)
+ expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' "$checksumsfile")
if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar"
else
echo "ERROR: Non-matching checksum: $tarball"
@@ -137,9 +137,9 @@ download_tarball() {
# If the tarball is newer than the (possibly existing) program (the version
# has changed), then delete the program.
- if [ -f $ibidir/$progname ]; then
- if [ $maneagetar -nt $ibidir/$progname ]; then
- rm $ibidir/$progname
+ if [ -f "$ibidir/$progname" ]; then
+ if [ "$maneagetar" -nt "$ibidir/$progname" ]; then
+ rm "$ibidir/$progname"
fi
fi
}
@@ -151,39 +151,39 @@ download_tarball() {
# Build the program from the tarball. This function takes one argument
# which is the configure-time options.
build_program() {
- if ! [ -f $ibidir/$progname ]; then
+ if ! [ -f "$ibidir/$progname" ]; then
# Options
configoptions=$1
# Go into the temporary building directory.
- cd $tmpblddir
+ cd "$tmpblddir"
unpackdir="$progname"-"$version"
# Some implementations of 'tar' don't recognize Lzip, so we need to
# manually call Lzip first, then call tar afterwards.
- csuffix=$(echo $tarball | sed -e's/\./ /g' | awk '{print $NF}')
- rm -rf $unpackdir
+ csuffix=$(echo "$tarball" | sed -e's/\./ /g' | awk '{print $NF}')
+ rm -rf "$unpackdir"
if [ x$csuffix = xlz ]; then
intarrm=1
- intar=$(echo $tarball | sed -e's/.lz//')
- lzip -c -d $tardir/$tarball > $intar
+ intar=$(echo "$tarball" | sed -e's/.lz//')
+ lzip -c -d "$tardir/$tarball" > $intar
else
intarrm=0
- intar=$tardir/$tarball
+ intar="$tardir"/"$tarball"
fi
# Unpack the tarball and go into it.
- tar xf $intar
- if [ x$intarrm = x1 ]; then rm $intar; fi
- cd $unpackdir
+ tar xf "$intar"
+ if [ x$intarrm = x1 ]; then rm "$intar"; fi
+ cd "$unpackdir"
# build the project, either with Make and either without it.
if [ x$progname = xlzip ]; then
- ./configure --build --check --installdir=$instdir/bin $configoptions
+ ./configure --build --check --installdir="$instdir/bin" $configoptions
else
# All others accept the configure script.
- ./configure --prefix=$instdir $configoptions
+ ./configure --prefix="$instdir" $configoptions
# To build GNU Make, we don't want to assume the existance of a
# Make program, so we use its 'build.sh' script and its own built
@@ -198,9 +198,9 @@ build_program() {
fi
# Clean up the source directory
- cd $topdir
- rm -rf $tmpblddir/$unpackdir
- echo "$progname_tex $version" > $ibidir/$progname
+ cd "$topdir"
+ rm -rf "$tmpblddir/$unpackdir"
+ echo "$progname_tex $version" > "$ibidir/$progname"
fi
}
@@ -219,7 +219,7 @@ build_program() {
progname="lzip"
progname_tex="Lzip"
url=$(awk '/^'$progname'-url/{print $3}' $urlfile)
-version=$(awk '/^'$progname'-version/{print $3}' $versionsfile)
+version=$(awk '/^'$progname'-version/{print $3}' "$versionsfile")
tarball=$progname-$version.tar
download_tarball
build_program