From 7d01ee66d46c30152f1a8c855c20042e376d207c Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Wed, 18 Jul 2018 14:11:16 -0400 Subject: gnu: Add avogadro. * gnu/packages/chemistry.scm (avogadro): New variable. * gnu/packages/patches/avogadro-boost148.patch, gnu/packages/patches/avogadro-eigen3-update.patch, gnu/packages/patches/avogadro-python-eigen-lib.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. --- gnu/local.mk | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 60db25a60c..b1bd1c089c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -584,6 +584,9 @@ dist_patch_DATA = \ %D%/packages/patches/audacity-build-with-system-portaudio.patch \ %D%/packages/patches/automake-skip-amhello-tests.patch \ %D%/packages/patches/avahi-localstatedir.patch \ + %D%/packages/patches/avogadro-boost148.patch \ + %D%/packages/patches/avogadro-eigen3-update.patch \ + %D%/packages/patches/avogadro-python-eigen-lib.patch \ %D%/packages/patches/avidemux-install-to-lib.patch \ %D%/packages/patches/awesome-reproducible-png.patch \ %D%/packages/patches/azr3.patch \ -- cgit v1.2.3 From 6635a3cc7f92a0c2b389761ecc599f5922186cf9 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 27 Aug 2018 15:12:04 -0400 Subject: gnu: python-pygit2: Update to 0.26.4. * gnu/packages/python.scm (python-pygit2, python2-pygit2): Update to 0.26.4. [source]: Remove 'python-pygit2-disable-network-tests.patch'. * gnu/packages/patches/python-pygit2-disable-network-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../python-pygit2-disable-network-tests.patch | 43 ---------------------- gnu/packages/python.scm | 6 +-- 3 files changed, 2 insertions(+), 48 deletions(-) delete mode 100644 gnu/packages/patches/python-pygit2-disable-network-tests.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index b1bd1c089c..d0e84c5972 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1087,7 +1087,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-mox3-python3.6-compat.patch \ %D%/packages/patches/python-paste-remove-website-test.patch \ %D%/packages/patches/python-paste-remove-timing-test.patch \ - %D%/packages/patches/python-pygit2-disable-network-tests.patch \ %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch \ %D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \ %D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch \ diff --git a/gnu/packages/patches/python-pygit2-disable-network-tests.patch b/gnu/packages/patches/python-pygit2-disable-network-tests.patch deleted file mode 100644 index 5578e4c375..0000000000 --- a/gnu/packages/patches/python-pygit2-disable-network-tests.patch +++ /dev/null @@ -1,43 +0,0 @@ -Disable tests trying to look up remote servers. - -diff --git a/test/test_credentials.py b/test/test_credentials.py ---- a/test/test_credentials.py -+++ b/test/test_credentials.py -@@ -68,6 +68,7 @@ class CredentialCreateTest(utils.NoRepoTestCase): - self.assertEqual((username, None, None, None), cred.credential_tuple) - - -+@unittest.skipIf(True, "network tests are not supported in Guix") - class CredentialCallback(utils.RepoTestCase): - def test_callback(self): - class MyCallbacks(pygit2.RemoteCallbacks): -@@ -92,6 +93,7 @@ class CredentialCallback(utils.RepoTestCase): - remote = self.repo.create_remote("github", url) - self.assertRaises(TypeError, lambda: remote.fetch(callbacks=MyCallbacks())) - -+@unittest.skipIf(True, "network tests are not supported in Guix") - class CallableCredentialTest(utils.RepoTestCase): - - def test_user_pass(self): -diff --git a/test/test_repository.py b/test/test_repository.py ---- a/test/test_repository.py -+++ b/test/test_repository.py -@@ -573,6 +573,7 @@ class CloneRepositoryTest(utils.NoRepoTestCase): - self.assertTrue('refs/remotes/custom_remote/master' in repo.listall_references()) - self.assertIsNotNone(repo.remotes["custom_remote"]) - -+ @unittest.skipIf(True, "network tests are not supported in Guix") - def test_clone_with_credentials(self): - repo = clone_repository( - "https://bitbucket.org/libgit2/testgitrepository.git", -diff --git a/test/test_submodule.py b/test/test_submodule.py ---- a/test/test_submodule.py -+++ b/test/test_submodule.py -@@ -42,6 +42,7 @@ SUBM_PATH = 'submodule' - SUBM_URL = 'https://github.com/libgit2/pygit2' - SUBM_HEAD_SHA = '819cbff552e46ac4b8d10925cc422a30aa04e78e' - -+@unittest.skipIf(True, "network tests are not supported in Guix") - class SubmoduleTest(utils.SubmoduleRepoTestCase): - - def test_lookup_submodule(self): diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3c46102da1..6ab6763a96 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3265,16 +3265,14 @@ association studies (GWAS) on extremely large data sets.") (define-public python-pygit2 (package (name "python-pygit2") - (version "0.26.0") + (version "0.26.4") (source (origin (method url-fetch) (uri (pypi-uri "pygit2" version)) (sha256 (base32 - "1cbc488ra3kg7r3qky17ms0szi3cda2d96qfkv1l9djsy9hnvw57")) - (patches - (search-patches "python-pygit2-disable-network-tests.patch")))) + "145k3fsd21274swia7mcc7n3kzlbd47xmg55mxsjdb5d9b7fr858")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six) -- cgit v1.2.3 From 526ce419303ac511be8d51b41471022bed472e6b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 28 Aug 2018 00:18:34 +0200 Subject: gnu: GRUB: Check for errors from efibootmgr. * gnu/packages/patches/grub-check-error-efibootmgr.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/bootloaders.scm (grub)[source](patches): New field. --- gnu/local.mk | 1 + gnu/packages/bootloaders.scm | 3 +- .../patches/grub-check-error-efibootmgr.patch | 176 +++++++++++++++++++++ 3 files changed, 179 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/grub-check-error-efibootmgr.patch (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index d0e84c5972..a2e538570b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -769,6 +769,7 @@ dist_patch_DATA = \ %D%/packages/patches/grep-timing-sensitive-test.patch \ %D%/packages/patches/groff-source-date-epoch.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ + %D%/packages/patches/grub-check-error-efibootmgr.patch \ %D%/packages/patches/gsl-test-i686.patch \ %D%/packages/patches/gspell-dash-test.patch \ %D%/packages/patches/guile-1.8-cpp-4.5.patch \ diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 727789a96e..e9abf399ab 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -85,7 +85,8 @@ (uri (string-append "mirror://gnu/grub/grub-" version ".tar.xz")) (sha256 (base32 - "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1")))) + "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1")) + (patches (search-patches "grub-check-error-efibootmgr.patch")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/patches/grub-check-error-efibootmgr.patch b/gnu/packages/patches/grub-check-error-efibootmgr.patch new file mode 100644 index 0000000000..b2fd160c9a --- /dev/null +++ b/gnu/packages/patches/grub-check-error-efibootmgr.patch @@ -0,0 +1,176 @@ +Without this patch, GRUB may proceed to wipe all firmware boot entries +and report a successful installation, even if efibootmgr hit an error. + +Origin URL: +https://git.sv.gnu.org/cgit/grub.git/commit/?id=6400613ad0b463abc93362086a491cd2a5e99b0d + +From 6400613ad0b463abc93362086a491cd2a5e99b0d Mon Sep 17 00:00:00 2001 +From: Steve McIntyre +Date: Wed, 31 Jan 2018 21:49:36 +0000 +Subject: Make grub-install check for errors from efibootmgr + +Code is currently ignoring errors from efibootmgr, giving users +clearly bogus output like: + + Setting up grub-efi-amd64 (2.02~beta3-4) ... + Installing for x86_64-efi platform. + Could not delete variable: No space left on device + Could not prepare Boot variable: No space left on device + Installation finished. No error reported. + +and then potentially unbootable systems. If efibootmgr fails, grub-install +should know that and report it! + +We've been using similar patch in Debian now for some time, with no ill effects. + +diff --git a/grub-core/osdep/unix/platform.c b/grub-core/osdep/unix/platform.c +index a3fcfca..ca448bc 100644 +--- a/grub-core/osdep/unix/platform.c ++++ b/grub-core/osdep/unix/platform.c +@@ -78,19 +78,20 @@ get_ofpathname (const char *dev) + dev); + } + +-static void ++static int + grub_install_remove_efi_entries_by_distributor (const char *efi_distributor) + { + int fd; + pid_t pid = grub_util_exec_pipe ((const char * []){ "efibootmgr", NULL }, &fd); + char *line = NULL; + size_t len = 0; ++ int rc; + + if (!pid) + { + grub_util_warn (_("Unable to open stream from %s: %s"), + "efibootmgr", strerror (errno)); +- return; ++ return errno; + } + + FILE *fp = fdopen (fd, "r"); +@@ -98,7 +99,7 @@ grub_install_remove_efi_entries_by_distributor (const char *efi_distributor) + { + grub_util_warn (_("Unable to open stream from %s: %s"), + "efibootmgr", strerror (errno)); +- return; ++ return errno; + } + + line = xmalloc (80); +@@ -119,23 +120,25 @@ grub_install_remove_efi_entries_by_distributor (const char *efi_distributor) + bootnum = line + sizeof ("Boot") - 1; + bootnum[4] = '\0'; + if (!verbosity) +- grub_util_exec ((const char * []){ "efibootmgr", "-q", ++ rc = grub_util_exec ((const char * []){ "efibootmgr", "-q", + "-b", bootnum, "-B", NULL }); + else +- grub_util_exec ((const char * []){ "efibootmgr", ++ rc = grub_util_exec ((const char * []){ "efibootmgr", + "-b", bootnum, "-B", NULL }); + } + + free (line); ++ return rc; + } + +-void ++int + grub_install_register_efi (grub_device_t efidir_grub_dev, + const char *efifile_path, + const char *efi_distributor) + { + const char * efidir_disk; + int efidir_part; ++ int ret; + efidir_disk = grub_util_biosdisk_get_osdev (efidir_grub_dev->disk); + efidir_part = efidir_grub_dev->disk->partition ? efidir_grub_dev->disk->partition->number + 1 : 1; + +@@ -151,23 +154,26 @@ grub_install_register_efi (grub_device_t efidir_grub_dev, + grub_util_exec ((const char * []){ "modprobe", "-q", "efivars", NULL }); + #endif + /* Delete old entries from the same distributor. */ +- grub_install_remove_efi_entries_by_distributor (efi_distributor); ++ ret = grub_install_remove_efi_entries_by_distributor (efi_distributor); ++ if (ret) ++ return ret; + + char *efidir_part_str = xasprintf ("%d", efidir_part); + + if (!verbosity) +- grub_util_exec ((const char * []){ "efibootmgr", "-q", ++ ret = grub_util_exec ((const char * []){ "efibootmgr", "-q", + "-c", "-d", efidir_disk, + "-p", efidir_part_str, "-w", + "-L", efi_distributor, "-l", + efifile_path, NULL }); + else +- grub_util_exec ((const char * []){ "efibootmgr", ++ ret = grub_util_exec ((const char * []){ "efibootmgr", + "-c", "-d", efidir_disk, + "-p", efidir_part_str, "-w", + "-L", efi_distributor, "-l", + efifile_path, NULL }); + free (efidir_part_str); ++ return ret; + } + + void +diff --git a/include/grub/util/install.h b/include/grub/util/install.h +index 5910b0c..0dba8b6 100644 +--- a/include/grub/util/install.h ++++ b/include/grub/util/install.h +@@ -210,7 +210,7 @@ grub_install_create_envblk_file (const char *name); + const char * + grub_install_get_default_x86_platform (void); + +-void ++int + grub_install_register_efi (grub_device_t efidir_grub_dev, + const char *efifile_path, + const char *efi_distributor); +diff --git a/util/grub-install.c b/util/grub-install.c +index 5e4cdfd..690f180 100644 +--- a/util/grub-install.c ++++ b/util/grub-install.c +@@ -1848,9 +1848,13 @@ main (int argc, char *argv[]) + if (!removable && update_nvram) + { + /* Try to make this image bootable using the EFI Boot Manager, if available. */ +- grub_install_register_efi (efidir_grub_dev, +- "\\System\\Library\\CoreServices", +- efi_distributor); ++ int ret; ++ ret = grub_install_register_efi (efidir_grub_dev, ++ "\\System\\Library\\CoreServices", ++ efi_distributor); ++ if (ret) ++ grub_util_error (_("efibootmgr failed to register the boot entry: %s"), ++ strerror (ret)); + } + + grub_device_close (ins_dev); +@@ -1871,6 +1875,7 @@ main (int argc, char *argv[]) + { + char * efifile_path; + char * part; ++ int ret; + + /* Try to make this image bootable using the EFI Boot Manager, if available. */ + if (!efi_distributor || efi_distributor[0] == '\0') +@@ -1887,8 +1892,11 @@ main (int argc, char *argv[]) + efidir_grub_dev->disk->name, + (part ? ",": ""), (part ? : "")); + grub_free (part); +- grub_install_register_efi (efidir_grub_dev, +- efifile_path, efi_distributor); ++ ret = grub_install_register_efi (efidir_grub_dev, ++ efifile_path, efi_distributor); ++ if (ret) ++ grub_util_error (_("efibootmgr failed to register the boot entry: %s"), ++ strerror (ret)); + } + break; + -- cgit v1.2.3