fixing "problems in speck" as identified by repology

Most of these are perl packages that need to point to the meta docs site,
and then a fair amount of http addresses that need to be https, and then
the rest are usually documentation sites that no longer exist or were
otherwise changes

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

var/spack/repos/builtin/packages/abinit/package.py

@@ -27,7 +27,7 @@ class Abinit(AutotoolsPackage):
     programs are provided.
     """
 
-    homepage = 'http://www.abinit.org'
+    homepage = 'https://www.abinit.org/'
     url      = 'https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz'
 
     version('9.4.2', sha256='d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc')

var/spack/repos/builtin/packages/ack/package.py

@@ -13,8 +13,8 @@ class Ack(Package):
        source code, ack is written purely in portable Perl 5 and takes
        advantage of the power of Perl's regular expressions."""
 
-    homepage = "http://beyondgrep.com/"
-    url      = "http://beyondgrep.com/ack-2.14-single-file"
+    homepage = "https://beyondgrep.com/"
+    url      = "https://beyondgrep.com/ack-2.14-single-file"
 
     version('2.22', sha256='fd0617585b88517a3d41d3d206c1dc38058c57b90dfd88c278049a41aeb5be38', expand=False)
     version('2.18', sha256='6e41057c8f50f661d800099471f769209480efa53b8a886969d7ec6db60a2208', expand=False)

var/spack/repos/builtin/packages/alglib/package.py

@@ -11,8 +11,8 @@ class Alglib(MakefilePackage):
     """ALGLIB is a cross-platform numerical analysis and data processing
     library."""
 
-    homepage = "http://www.alglib.net"
-    url      = "http://www.alglib.net/translator/re/alglib-3.11.0.cpp.gpl.tgz"
+    homepage = "https://www.alglib.net/"
+    url      = "https://www.alglib.net/translator/re/alglib-3.11.0.cpp.gpl.tgz"
 
     version('3.11.0', sha256='34e391594aac89fb354bdaf58c42849489cd1199197398ba98bb69961f42bdb0')
 

var/spack/repos/builtin/packages/applewmproto/package.py

@@ -13,7 +13,7 @@ class Applewmproto(AutotoolsPackage, XorgPackage):
     to better interact with the Mac OS X Aqua user interface when
     running X11 in a rootless mode."""
 
-    homepage = "http://cgit.freedesktop.org/xorg/proto/applewmproto"
+    homepage = "https://cgit.freedesktop.org/xorg/proto/applewmproto"
     xorg_mirror_path = "proto/applewmproto-1.4.2.tar.gz"
 
     version('1.4.2', sha256='ff8ac07d263a23357af2d6ff0cca3c1d56b043ddf7797a5a92ec624f4704df2e')

var/spack/repos/builtin/packages/asciidoc/package.py

@@ -10,7 +10,7 @@ class Asciidoc(AutotoolsPackage):
     """A presentable text document format for writing articles, UNIX man
     pages and other small to medium sized documents."""
 
-    homepage = "http://asciidoc.org"
+    homepage = "https://asciidoc.org/"
     # Always working URL but strangely with another checksum
     url      = "https://github.com/asciidoc-py/asciidoc-py/archive/8.6.10.tar.gz"
     git      = "https://github.com/asciidoc-py/asciidoc-py.git"

var/spack/repos/builtin/packages/bcache/package.py

@@ -10,7 +10,7 @@ class Bcache(MakefilePackage):
     """Bcache is a patch for the Linux kernel to use SSDs to cache other block
     devices."""
 
-    homepage = "http://bcache.evilpiepirate.org"
+    homepage = "https://bcache.evilpiepirate.org/"
     url      = "https://github.com/g2p/bcache-tools/archive/v1.0.8.tar.gz"
 
     version('1.0.8', sha256='d56923936f37287efc57a46315679102ef2c86cd0be5874590320acd48c1201c')

var/spack/repos/builtin/packages/bib2xhtml/package.py

@@ -6,7 +6,7 @@
 
 class Bib2xhtml(Package):
     """bib2xhtml is a program that converts BibTeX files into HTML."""
-    homepage = "http://www.spinellis.gr/sw/textproc/bib2xhtml/"
+    homepage = "https://www.spinellis.gr/sw/textproc/bib2xhtml/"
     url = 'https://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-79-ge935.tar.gz'
 
     version('3.0-79-ge935', sha256='4a2d2d89dd2f3fed1c735055b806809b5cc1cde32dee1aa5987097ec5bf2181f')

var/spack/repos/builtin/packages/blast-plus/package.py

@@ -20,7 +20,7 @@
 class BlastPlus(AutotoolsPackage):
     """Basic Local Alignment Search Tool."""
 
-    homepage = "http://blast.ncbi.nlm.nih.gov/"
+    homepage = "https://blast.ncbi.nlm.nih.gov/"
     url      = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-src.tar.gz"
 
     maintainers = ['weijianwen']

var/spack/repos/builtin/packages/bohrium/package.py

@@ -15,7 +15,7 @@
 class Bohrium(CMakePackage, CudaPackage):
     """Library for automatic acceleration of array operations"""
 
-    homepage = "http://bh107.org"
+    homepage = "https://github.com/bh107/bohrium"
     url      = "https://github.com/bh107/bohrium/archive/v0.9.0.tar.gz"
     git      = "https://github.com/bh107/bohrium.git"
 

var/spack/repos/builtin/packages/boost/package.py

@@ -18,7 +18,7 @@ class Boost(Package):
        across a broad spectrum of applications. The Boost license
        encourages both commercial and non-commercial use.
     """
-    homepage = "http://www.boost.org"
+    homepage = "https://www.boost.org"
     url      = "http://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.bz2"
     git      = "https://github.com/boostorg/boost.git"
     list_url = "http://sourceforge.net/projects/boost/files/boost/"

var/spack/repos/builtin/packages/byobu/package.py

@@ -10,7 +10,7 @@
 class Byobu(AutotoolsPackage):
     """Byobu: Text-based window manager and terminal multiplexer."""
 
-    homepage = "http://www.byobu.co"
+    homepage = "https://www.byobu.co/"
     url      = "https://launchpad.net/byobu/trunk/5.123/+download/byobu_5.123.orig.tar.gz"
 
     maintainers = ['matthiasdiener']

var/spack/repos/builtin/packages/byte-unixbench/package.py

@@ -9,7 +9,7 @@
 class ByteUnixbench(MakefilePackage):
     """UnixBench is the original BYTE UNIX benchmark suite."""
 
-    homepage = "https://code.google.com/archive/p/byte-unixbench"
+    homepage = "https://github.com/kdlucas/byte-unixbench"
     url      = "https://github.com/kdlucas/byte-unixbench/archive/v5.1.3.tar.gz"
 
     version('5.1.3', sha256='3a6bb00f270a5329682dff20fd2c1ab5332ef046eb54a96a0d7bd371005d31a3')

var/spack/repos/builtin/packages/c-blosc/package.py

@@ -11,7 +11,7 @@
 
 class CBlosc(CMakePackage):
     """Blosc, an extremely fast, multi-threaded, meta-compressor library"""
-    homepage = "http://www.blosc.org"
+    homepage = "https://www.blosc.org"
     url      = "https://github.com/Blosc/c-blosc/archive/v1.11.1.tar.gz"
 
     version('1.21.0', sha256='b0ef4fda82a1d9cbd11e0f4b9685abf14372db51703c595ecd4d76001a8b342d')

var/spack/repos/builtin/packages/c-blosc2/package.py

@@ -10,7 +10,7 @@ class CBlosc2(CMakePackage):
     """Next generation c-blosc with a new API, a new container and
        other bells and whistles"""
 
-    homepage = "http://www.blosc.org"
+    homepage = "https://www.blosc.org/"
     url      = "https://github.com/Blosc/c-blosc2/archive/refs/tags/v2.0.1.tar.gz"
     git      = "https://github.com/Blosc/c-blosc2.git"
 

var/spack/repos/builtin/packages/cfitsio/package.py

@@ -11,8 +11,8 @@ class Cfitsio(AutotoolsPackage):
     data files in FITS (Flexible Image Transport System) data format.
     """
 
-    homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/'
-    url      = 'http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-3.49.tar.gz'
+    homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/'
+    url      = 'https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-3.49.tar.gz'
 
     version('3.49', sha256='5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3')
     version('3.48', sha256='91b48ffef544eb8ea3908543052331072c99bf09ceb139cb3c6977fc3e47aac1')

var/spack/repos/builtin/packages/codec2/package.py

@@ -11,7 +11,7 @@ class Codec2(CMakePackage):
     between 450 and 3200 bit/s. The main application is low bandwidth
     HF/VHF digital radio."""
 
-    homepage = "http://www.rowetel.com/codec2.html"
+    homepage = "https://www.rowetel.com/?page_id=452"
     url      = "https://github.com/drowe67/codec2/archive/v0.9.2.tar.gz"
 
     version('0.9.2', sha256='19181a446f4df3e6d616b50cabdac4485abb9cd3242cf312a0785f892ed4c76c')

var/spack/repos/builtin/packages/dbus/package.py

@@ -16,8 +16,8 @@ class Dbus(Package):
        by any two applications to communicate directly (without going
        through the message bus daemon)."""
 
-    homepage = "http://dbus.freedesktop.org/"
-    url      = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz"
+    homepage = "https://dbus.freedesktop.org/"
+    url      = "https://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz"
 
     version('1.12.8', sha256='e2dc99e7338303393b6663a98320aba6a63421bcdaaf571c8022f815e5896eb3')
     version('1.11.2', sha256='5abc4c57686fa82669ad0039830788f9b03fdc4fff487f0ccf6c9d56ba2645c9')

var/spack/repos/builtin/packages/editline/package.py

@@ -9,7 +9,7 @@
 class Editline(AutotoolsPackage):
     """A readline() replacement for UNIX without termcap (ncurses)"""
 
-    homepage = "http://troglobit.com/editline.html"
+    homepage = "https://troglobit.com/editline.html"
     url      = "https://github.com/troglobit/editline/archive/1.16.0.tar.gz"
 
     version('1.16.0', sha256='33421a1569d025f332a87054bfea28e2c757bdb573f1437bc22c34b798b6383c')

var/spack/repos/builtin/packages/elemental/package.py

@@ -13,7 +13,7 @@ class Elemental(CMakePackage):
     """Elemental: Distributed-memory dense and sparse-direct linear algebra
        and optimization library."""
 
-    homepage = "http://libelemental.org"
+    homepage = "https://libelemental.org"
     url      = "https://github.com/elemental/Elemental/archive/v0.87.7.tar.gz"
     git      = "https://github.com/elemental/Elemental.git"
 

var/spack/repos/builtin/packages/etsf-io/package.py

@@ -15,7 +15,7 @@ class EtsfIo(Package):
     quantum-chemical applications relying upon Density Functional Theory (DFT).
     """
 
-    homepage = "http://www.etsf.eu/resources/software/libraries_and_tools"
+    homepage = "https://github.com/ElectronicStructureLibrary/libetsf_io"
     url = "https://launchpad.net/etsf-io/1.0/1.0.4/+download/etsf_io-1.0.4.tar.gz"
 
     version('1.0.4', sha256='3140c2cde17f578a0e6b63acb27a5f6e9352257a1371a17b9c15c3d0ef078fa4')

var/spack/repos/builtin/packages/exciting/package.py

@@ -15,8 +15,8 @@ class Exciting(MakefilePackage):
     particular focus are excited states within many-body perturbation theory.
     """
 
-    homepage = "http://exciting-code.org/"
-    url      = "http://exciting.wdfiles.com/local--files/nitrogen-14/exciting.nitrogen-14.tar.gz"
+    homepage = "https://exciting-code.org/"
+    url      = "https://exciting.wdfiles.com/local--files/nitrogen-14/exciting.nitrogen-14.tar.gz"
 
     version('14', sha256='a7feaffdc23881d6c0737d2f79f94d9bf073e85ea358a57196d7f7618a0a3eff')
 

var/spack/repos/builtin/packages/exempi/package.py

@@ -14,7 +14,7 @@ class Exempi(AutotoolsPackage):
     a command line tool.
     """
 
-    homepage = "http://libopenraw.freedesktop.org/wiki/Exempi"
+    homepage = "https://libopenraw.freedesktop.org/wiki/Exempi"
     url      = "https://libopenraw.freedesktop.org/download/exempi-2.5.2.tar.bz2"
 
     version('2.5.2', sha256='52f54314aefd45945d47a6ecf4bd21f362e6467fa5d0538b0d45a06bc6eaaed5')

var/spack/repos/builtin/packages/f2c/package.py

@@ -9,8 +9,8 @@
 class F2c(MakefilePackage):
     """F2c converts Fortran 77 source code to C or C++ source files."""
 
-    homepage = "http://www.netlib.org/f2c/"
-    url      = "http://www.netlib.org/f2c/src.tgz"
+    homepage = "https://www.netlib.org/f2c/"
+    url      = "https://www.netlib.org/f2c/src.tgz"
 
     version('master', sha256='d4847456aa91c74e5e61e2097780ca6ac3b20869fae8864bfa8dcc66f6721d35')
 

var/spack/repos/builtin/packages/fastqc/package.py

@@ -9,8 +9,8 @@
 class Fastqc(Package):
     """A quality control tool for high throughput sequence data."""
 
-    homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
-    url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
+    homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+    url = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
 
     version('0.11.9', sha256='15510a176ef798e40325b717cac556509fb218268cfdb9a35ea6776498321369')
     version('0.11.7', sha256='59cf50876bbe5f363442eb989e43ae3eaab8d932c49e8cff2c1a1898dd721112')

var/spack/repos/builtin/packages/faust/package.py

@@ -11,7 +11,7 @@ class Faust(MakefilePackage):
     specifically designed for real-time signal processing and synthesis.
     A distinctive characteristic of Faust is to be fully compiled."""
 
-    homepage = "http://faust.grame.fr/"
+    homepage = "https://faust.grame.fr/"
     url      = "https://github.com/grame-cncm/faust/archive/2.27.2.tar.gz"
 
     version('2.27.2', sha256='3367a868a93b63582bae29ab8783f1df7a10f4084a2bc1d2258ebf3d6a8c31d7')

var/spack/repos/builtin/packages/fenics/package.py

@@ -14,7 +14,7 @@ class Fenics(CMakePackage):
     the code generation interface UFC, the form language UFL and a range of
     additional components."""
 
-    homepage = "http://fenicsproject.org/"
+    homepage = "https://fenicsproject.org/"
     git      = "https://bitbucket.org/fenics-project/dolfin.git"
     url      = "https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-2019.1.0.post0.tar.gz"
 

var/spack/repos/builtin/packages/flann/package.py

@@ -18,7 +18,7 @@ class Flann(CMakePackage):
     C, MATLAB and Python.
     """
 
-    homepage = "http://www.cs.ubc.ca/research/flann/"
+    homepage = "https://github.com/mariusmuja/flann"
     url      = "https://github.com/mariusmuja/flann/archive/1.9.1.tar.gz"
 
     version('1.9.1', sha256='b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3')

var/spack/repos/builtin/packages/fltk/package.py

@@ -18,8 +18,8 @@ class Fltk(Package):
        applications in minutes.
 
     """
-    homepage = 'http://www.fltk.org/'
-    url = 'http://fltk.org/pub/fltk/1.3.3/fltk-1.3.3-source.tar.gz'
+    homepage = 'https://www.fltk.org/'
+    url = 'https://fltk.org/pub/fltk/1.3.3/fltk-1.3.3-source.tar.gz'
 
     version('1.3.3', sha256='f8398d98d7221d40e77bc7b19e761adaf2f1ef8bb0c30eceb7beb4f2273d0d97')
 

var/spack/repos/builtin/packages/fseq/package.py

@@ -9,7 +9,7 @@
 class Fseq(Package):
     """F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags"""
 
-    homepage = "http://fureylab.web.unc.edu/software/fseq/"
+    homepage = "https://fureylab.web.unc.edu/software/fseq/"
     url      = "http://html-large-files-dept-fureylab.cloudapps.unc.edu/fureylabfiles/fseq/fseq_1.84.tgz"
 
     version('1.84', sha256='22d603a51f127cb86cdecde9aeae14d273bb98bcd2b47724763ab3b3241a6e68')

var/spack/repos/builtin/packages/g4abla/package.py

@@ -9,7 +9,7 @@
 
 class G4abla(Package):
     """Geant4 data for nuclear shell effects in INCL/ABLA hadronic mode"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4ABLA.3.0.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4emlow/package.py

@@ -9,7 +9,7 @@
 
 class G4emlow(Package):
     """Geant4 data files for low energy electromagnetic processes."""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4EMLOW.6.50.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4ensdfstate/package.py

@@ -9,7 +9,7 @@
 
 class G4ensdfstate(Package):
     """Geant4 data for nuclides properties"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4ENSDFSTATE.2.1.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4incl/package.py

@@ -10,7 +10,7 @@
 class G4incl(Package):
     """Geant4 data for evaluated particle cross-sections on natural
     composition of elements"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4INCL.1.0.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4ndl/package.py

@@ -9,7 +9,7 @@
 
 class G4ndl(Package):
     """Geant4 Neutron data files with thermal cross sections """
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4NDL.4.5.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4neutronxs/package.py

@@ -10,7 +10,7 @@
 class G4neutronxs(Package):
     """Geant4 data for evaluated neutron cross-sections on natural composition
        of elements"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4NEUTRONXS.1.4.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4particlexs/package.py

@@ -10,7 +10,7 @@
 class G4particlexs(Package):
     """Geant4 data for evaluated particle cross-sections on
     natural composition of elements"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4PARTICLEXS.2.1.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4photonevaporation/package.py

@@ -9,7 +9,7 @@
 
 class G4photonevaporation(Package):
     """Geant4 data for photon evaporation"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4PhotonEvaporation.4.3.2.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4pii/package.py

@@ -9,7 +9,7 @@
 
 class G4pii(Package):
     """Geant4 data for shell ionisation cross-sections"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4PII.1.3.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4radioactivedecay/package.py

@@ -9,7 +9,7 @@
 
 class G4radioactivedecay(Package):
     """Geant4 data files for radio-active decay hadronic processes"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4RadioactiveDecay.5.1.1.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/g4tendl/package.py

@@ -9,7 +9,7 @@
 
 class G4tendl(Package):
     """Geant4 data for incident particles [optional]"""
-    homepage = "http://geant4.web.cern.ch"
+    homepage = "https://geant4.web.cern.ch"
     url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4TENDL.1.3.tar.gz"
 
     tags = ['hep']

var/spack/repos/builtin/packages/gatk/package.py

@@ -12,7 +12,7 @@ class Gatk(Package):
     Variant Discovery in High-Throughput Sequencing Data
     """
 
-    homepage = "https://software.broadinstitute.org/gatk/"
+    homepage = "https://gatk.broadinstitute.org/hc/en-us"
     url = "https://github.com/broadinstitute/gatk/releases/download/4.1.0.0/gatk-4.1.0.0.zip"
     list_url = "https://github.com/broadinstitute/gatk/releases"