From 8463df97c6f26ec4d22cd5828bb0574fd5e450d2 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Mon, 4 Oct 2021 02:51:45 +0200
Subject: IMPORTANT: Updates to almost all software
This commit primarily affects the configuration step of Maneage'd projects,
and in particular, updated versions of the many of the software (see
P.S.). So it shouldn't affect your high-level analysis other than the
version bumps of the software you use (and the software's possibly
improve/changed behavior).
The following software (and thus their dependencies) couldn't be updated as
described below:
- Cryptography: isn't building because it depends on a new
setuptools-rust package that has problems
(https://savannah.nongnu.org/bugs/index.php?61731), so it has been
commented in 'versions.conf'.
- SecretStorage: because it depends on Cryptography.
- Keyring: because it depends on SecretStorage.
- Astroquery: because it depends on Keyring.
This is a "squashed" commit after rebasing a development branch of 60
commits corresponding to a roughly two-month time interval. The following
people contributed to this branch.
- Boudewijn Roukema added all the R software infrastructure and the R
packages, as well as greatly helping in fixing many bugs during the
update.
- Raul Infante-Sainz helped in testing and debugging the build.
- Pedram Ashofteh Ardakani found and fixed a bug.
- Zahra Sharbaf helped in testing and found several bugs.
Below a description of the most noteworthy points is given.
- Software tarballs: all updated software now have a unified format
tarball (ustar; if not possible, pax) and unified compression (Lzip) in
Maneage's software repository in Zenodo
(https://doi.org/10.5281/zenodo.3883409). For more on this See
https://savannah.nongnu.org/task/?15699 . This won't affect any extra
software you would like to add; you can use any format recognized by
GNU Tar, and all common compression algorithms. This new requirement is
only for software that get merged to the core Maneage branch.
- Metastore (and thus libbsd and libmd) moved to highlevel: Metastore
(and the packages it depends on) is a high-level product that is only
relevant during the project development (like Emacs!): when the user
wants the file meta data (like dates) to be unchanged after checking
out branches. So it should be considered a high-level software, not
basic. Metastore also usually causes many more headaches and error
messages, so personally, I have stopped using it! Instead I simply
merge my branches in a separate clone, then pull the merge commit: in
this way, the files of my project aren't re-written during the checkout
phase and therefore their dates are untouched (which can conflict with
Make's dates on configuration files).
- The un-official cloned version of Flex (2.6.4-91 until this commit) was
causing problems in the building of Netpbm, so with this commit, it has
been moved back to version 2.6.4.
- Netpbm's official page had version 10.73.38 as the latest stable
tarball that was just released in late 2021. But I couldn't find our
previously-used version 10.86.99 anywhere (to see when it was released
and why we used it! Its at last more than one year old!). So the
official stable version is being used now.
- Improved instructions in 'README.md' for building software environment
in a Docker container (while having project source and output data
products on the local system; including the usage of the host's
'/dev/shm' to speed up temporary operations).
- Until now, the convention in Maneage was to put eight SPACE characters
before the comment lines within recipes. This was done because by
default GNU Emacs (also many other editors) show a TAB as eight
characters. However, in other text editors, online browsers, or even
the Git diff, a TAB can correspond to a different number of
characters. In such cases, the Maneage recipes wouldn't look too
interesting (the comments and the recipe commands would show a
different indentation!).
With this commit, all the comment lines in the Makefiles within the
core Maneage branch have a hash ('#') as their first character and a
TAB as the second. This allows the comment lines in recipes to have the
same indentation as code; making the code much more easier to read in a
general scenario including a 'git diff' (editor agnostic!).
P.S. List of updated software with their old and new versions
- Software with no version update are not mentioned.
- The old version of newly added software are shown with '--'.
Name (Basic) Old version New version
------------ ----------- -----------
Bzip2 1.0.6 1.0.8
CURL 7.71.1 7.79.1
Dash 0.5.10.2 0.5.11.5
File 5.39 5.41
Flock 0.2.3 0.4.0
GNU Bash 5.0.18 5.1.8
GNU Binutils 2.35 2.37
GNU Coreutils 8.32 9.0
GNU GCC 10.2.0 11.2.0
GNU M4 1.4.18 1.4.19
GNU Readline 8.0 8.1.1
GNU Tar 1.32 1.34
GNU Texinfo 6.7 6.8
GNU diffutils 3.7 3.8
GNU findutils 4.7.0 4.8.0
GNU gmp 6.2.0 6.2.1
GNU grep 3.4 3.7
GNU gzip 1.10 1.11
GNU libunistring 0.9.10 1.0
GNU mpc 1.1.0 1.2.1
GNU mpfr 4.0.2 4.1.0
GNU nano 5.2 6.0
GNU ncurses 6.2 6.3
GNU wget 1.20.3 1.21.2
Git 2.28.0 2.34.0
Less 563 590
Libxml2 2.9.9 2.9.12
Lzip 1.22-rc2 1.22
OpenSLL 1.1.1a 3.0.0
Patchelf 0.10 0.13
Perl 5.32.0 5.34.0
Podlators -- 4.14
Name (Highlevel) Old version New version
---------------- ----------- -----------
Apachelog4cxx 0.10.0-603 0.12.1
Astrometry.net 0.80 0.85
Boost 1.73.0 1.77.0
CFITSIO 3.48 4.0.0
Cmake 3.18.1 3.21.4
Eigen 3.3.7 3.4.0
Expat 2.2.9 2.4.1
FFTW 3.3.8 3.3.10
Flex 2.6.4-91 2.6.4
Fontconfig 2.13.1 2.13.94
Freetype 2.10.2 2.11.0
GNU Astronomy Utilities 0.12 0.16.1-e0f1
GNU Autoconf 2.69.200-babc 2.71
GNU Automake 1.16.2 1.16.5
GNU Bison 3.7 3.8.2
GNU Emacs 27.1 27.2
GNU GDB 9.2 11.1
GNU GSL 2.6 2.7
GNU Help2man 1.47.11 1.48.5
Ghostscript 9.52 9.55.0
ICU -- 70.1
ImageMagick 7.0.8-67 7.1.0-13
Libbsd 0.10.0 0.11.3
Libffi 3.2.1 3.4.2
Libgit2 1.0.1 1.3.0
Libidn 1.36 1.38
Libjpeg 9b 9d
Libmd -- 1.0.4
Libtiff 4.0.10 4.3.0
Libx11 1.6.9 1.7.2
Libxt 1.2.0 1.2.1
Netpbm 10.86.99 10.73.38
OpenBLAS 0.3.10 0.3.18
OpenMPI 4.0.4 4.1.1
Pixman 0.38.0 0.40.0
Python 3.8.5 3.10.0
R 4.0.2 4.1.2
SWIG 3.0.12 4.0.2
Util-linux 2.35 2.37.2
Util-macros 1.19.2 1.19.3
Valgrind 3.15.0 3.18.1
WCSLIB 7.3 7.7
Xcb-proto 1.14 1.14.1
Xorgproto 2020.1 2021.5
Name (Python) Old version New version
------------- ----------- -----------
Astropy 4.0 5.0
Beautifulsoup4 4.7.1 4.10.0
Beniget -- 0.4.1
Cffi 1.12.2 1.15.0
Cryptography 2.6.1 36.0.1
Cycler 0.10.0 0.11.0+}
Cython 0.29.21 0.29.24
Esutil 0.6.4 0.6.9
Extension-helpers -- 0.1
Galsim 2.2.1 2.3.3
Gast -- 0.5.3
Jinja2 -- 3.0.3
MPI4py 3.0.3 3.1.3
Markupsafe -- 2.0.1
Numpy 1.19.1 1.21.3
Packaging -- 21.3
Pillow -- 8.4.0
Ply -- 3.11
Pyerfa -- 2.0.0.1
Pyparsing 2.3.1 3.0.4
Pythran -- 0.11.0
Scipy 1.5.2 1.7.3
Setuptools 41.6.0 58.3.0
Six 1.12.0 1.16.0
Uncertainties 3.1.2 3.1.6
Wheel -- 0.37.0
Name (R) Old version New version
-------- ----------- -----------
Cli -- 2.5.0
Colorspace -- 2.0-1
Cowplot -- 1.1.1
Crayon -- 1.4.1
Digest -- 0.6.27
Ellipsis -- 0.3.2
Fansi -- 0.5.0
Farver -- 2.1.0
Ggplot2 -- 3.3.4
Glue -- 1.4.2
GridExtra -- 2.3
Gtable -- 0.3.0
Isoband -- 0.2.4
Labeling -- 0.4.2
Lifecycle -- 1.0.0
Magrittr -- 2.0.1
MASS -- 7.3-54
Mgcv -- 1.8-36
Munsell -- 0.5.0
Pillar -- 1.6.1
R-Pkgconfig -- 2.0.3
R6 -- 2.5.0
RColorBrewer -- 1.1-2
Rlang -- 0.4.11
Scales -- 1.1.1
Tibble -- 3.1.2
Utf8 -- 1.2.1
Vctrs -- 0.3.8
ViridisLite -- 0.4.0
Withr -- 2.4.2
---
reproduce/software/patches/README.md | 6 ++++
.../patches/valgrind-3.15.0-mpi-fix1.patch | 37 ----------------------
.../patches/valgrind-3.15.0-mpi-fix2.patch | 23 --------------
3 files changed, 6 insertions(+), 60 deletions(-)
create mode 100644 reproduce/software/patches/README.md
delete mode 100644 reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
delete mode 100644 reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
(limited to 'reproduce/software/patches')
diff --git a/reproduce/software/patches/README.md b/reproduce/software/patches/README.md
new file mode 100644
index 0000000..804d7ec
--- /dev/null
+++ b/reproduce/software/patches/README.md
@@ -0,0 +1,6 @@
+Patches to apply to software source
+===================================
+
+This directory is for keeping patches that may be necessary for some
+versions of some software. So it may be empty in some instances (when no
+software in that commit needs a patch).
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
deleted file mode 100644
index 94dcab5..0000000
--- a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
+++ /dev/null
@@ -1,37 +0,0 @@
----
- mpi/libmpiwrap.c | 12 +++++++++++-
- 1 file changed, 11 insertions(+), 1 deletion(-)
- Patch by Samuel Thibault:
- https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=10
- and hacked further by Boud Roukema 2020-05-10.
---- a/mpi/libmpiwrap.c
-+++ b/mpi/libmpiwrap.c
-@@ -278,8 +278,12 @@ static void showTy ( FILE* f, MPI_Dataty
- else if (ty == MPI_LONG_INT) fprintf(f,"LONG_INT");
- else if (ty == MPI_SHORT_INT) fprintf(f,"SHORT_INT");
- else if (ty == MPI_2INT) fprintf(f,"2INT");
-+# if defined(MPI_UB_ENABLED_IN_MPI1)
- else if (ty == MPI_UB) fprintf(f,"UB");
-+# endif
-+# if defined(MPI_LB_ENABLED_IN_MPI1)
- else if (ty == MPI_LB) fprintf(f,"LB");
-+# endif
- # if defined(MPI_WCHAR)
- else if (ty == MPI_WCHAR) fprintf(f,"WCHAR");
- # endif
-@@ -733,8 +737,14 @@ void walk_type ( void(*f)(void*,long), c
- f(base + offsetof(Ty,loc), sizeof(int));
- return;
- }
-- if (ty == MPI_LB || ty == MPI_UB)
-+#if defined(MPI_LB_ENABLED_IN_MPI1)
-+ if (ty == MPI_LB)
-+ return; /* have zero size, so nothing needs to be done */
-+#endif
-+#if defined(MPI_UB_ENABLED_IN_MPI1)
-+ if (ty == MPI_UB)
- return; /* have zero size, so nothing needs to be done */
-+#endif
- goto unhandled;
- /*NOTREACHED*/
- }
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
deleted file mode 100644
index 12b50a2..0000000
--- a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Index: valgrind-3.15.0/mpi/Makefile.am
-===================================================================
- Patch by Samuel Thibault:
- https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=22
---- valgrind-3.15.0.orig/mpi/Makefile.am
-+++ valgrind-3.15.0/mpi/Makefile.am
-@@ -42,14 +42,14 @@ libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@
- libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
- libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CFLAGS = \
- $(CFLAGS_MPI) $(MPI_FLAG_M3264_PRI) -Wno-deprecated-declarations
--libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDFLAGS = $(LDFLAGS_MPI)
-+libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDADD = $(LDFLAGS_MPI)
- endif
- if BUILD_MPIWRAP_SEC
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_SOURCES = libmpiwrap.c
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CFLAGS = \
- $(CFLAGS_MPI) $(MPI_FLAG_M3264_SEC) -Wno-deprecated-declarations
--libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDFLAGS = $(LDFLAGS_MPI)
-+libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDADD = $(LDFLAGS_MPI)
- endif
-
- #----------------------------------------------------------------------------
--
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