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authorzimoun <zimon.toutoune@gmail.com>2022-11-17 03:50:02 +0100
committerRicardo Wurmus <rekado@elephly.net>2022-11-24 12:31:12 +0100
commita62284ad13b139436b2072e53e725e144782d74e (patch)
tree3c9149799b49c1c4b58745a4c46ec73f2305449a /gnu/packages/idutils.scm
parent38fc0acf4d6752a8a3dcdab41eff1b0b5ed5e2d8 (diff)
downloadguix-a62284ad13b139436b2072e53e725e144782d74e.tar.gz
guix-a62284ad13b139436b2072e53e725e144782d74e.zip
gnu: r-adamgui: Update to 1.14.0.
* gnu/packages/bioconductor.scm (r-adamgui): Update to 1.14.0.
Diffstat (limited to 'gnu/packages/idutils.scm')
0 files changed, 0 insertions, 0 deletions
generated by cgit
bstitution)[destination-in-store?] [dump-file/deduplicate*]: New variables. Pass #:dump-file to 'restore-file'. * guix/scripts/substitute.scm (guix-substitute)[deduplicate?]: New variable. Pass #:deduplicate? to 'process-substitution'. * guix/serialization.scm (dump-file): Export and augment 'dump-file'. Ludovic Courtès 2020-12-19daemon: Do not reset timestamps and permissions on substituted items....'guix substitute' now takes care of it via 'restore-file'. * nix/libstore/build.cc (SubstitutionGoal::finished): Remove call to 'canonicalisePathMetaData'. Ludovic Courtès 2020-12-19daemon: Let 'guix substitute' perform hash checks....This way, the hash of the store item can be computed as it is restored, thereby avoiding an additional file tree traversal ('hashPath' call) later on in the daemon. Consequently, it should reduce latency between subsequent substitute downloads. This is a followup to 5ff521452b9ec2aae9ed8e4bb7bdc250a581f203. * guix/scripts/substitute.scm (narinfo-hash-algorithm+value): New procedure. (process-substitution): Wrap INPUT into a hash input port, 'hashed', and read from it. Compare the actual and expected hashes, and print a "hash-mismatch" status line when they differ. When they match, print not just "success" but also the nar hash and size. * nix/libstore/build.cc (class SubstitutionGoal)[expectedHashStr]: Remove. (SubstitutionGoal::finished): Tokenize 'status'. Parse it and handle "success" and "hash-mismatch" accordingly. Call 'hashPath' only when the returned hash is not SHA256. (SubstitutionGoal::handleChildOutput): Remove 'expectedHashStr' handling. * tests/substitute.scm ("substitute, invalid hash"): Rename to... ("substitute, invalid narinfo hash"): ... this. ("substitute, invalid hash"): New test. Ludovic Courtès 2020-12-08daemon: Raise an error if substituter doesn't send the expected hash....It was already impossible in practice for 'expectedHashStr' to be empty if 'status' == "success". * nix/libstore/build.cc (SubstitutionGoal::finished): Throw 'SubstError' when 'expectedHashStr' is empty. Ludovic Courtès 2020-12-08substitute: Cache and reuse connections while substituting....That way, when fetching a series of substitutes from the same server(s), the connection is reused instead of being closed/opened for each substitutes, which saves on network round trips and TLS handshakes. * guix/http-client.scm (http-fetch): Add #:keep-alive? and honor it. * guix/progress.scm (progress-report-port): Add #:close? parameter and honor it. * guix/scripts/substitute.scm (at-most): Return the tail as a second value. (fetch): Add #:port and #:keep-alive? and honor them. (%max-cached-connections): New variable. (open-connection-for-uri/cached, call-with-cached-connection): New procedures. (with-cached-connection): New macro. (process-substitution): Wrap 'fetch' call in 'with-cached-connection'. Pass #:close? to 'progress-report-port'. Ludovic Courtès 2020-12-08daemon: Run 'guix substitute --substitute' as an agent....This avoids spawning one substitute process per substitution. * nix/libstore/build.cc (class Worker)[substituter]: New field. [outPipe, logPipe, pid]: Remove. (class SubstitutionGoal)[expectedHashStr, status, substituter]: New fields. (SubstitutionGoal::timedOut): Adjust to check 'substituter'. (SubstitutionGoal::tryToRun): Remove references to 'outPipe' and 'logPipe'. Run "guix substitute --substitute" as an 'Agent'. Send the request with 'writeLine'. (SubstitutionGoal::finished): Likewise. (SubstitutionGoal::handleChildOutput): Change to fill in 'expectedHashStr' and 'status'. (SubstitutionGoal::handleEOF): Call 'wakeUp' unconditionally. (SubstitutionGoal::~SubstitutionGoal): Adjust to check 'substituter'. * guix/scripts/substitute.scm (process-substitution): Write "success\n" to stdout upon success. (%error-to-file-descriptor-4?): New variable. (guix-substitute): Set 'current-error-port' to file descriptor 4 unless (%error-to-file-descriptor-4?) is false. Remove "--substitute" arguments. Loop reading line from stdin. * tests/substitute.scm <top level>: Call '%error-to-file-descriptor-4?'. (request-substitution): New procedure. ("substitute, no signature") ("substitute, invalid hash") ("substitute, unauthorized key") ("substitute, authorized key") ("substitute, unauthorized narinfo comes first") ("substitute, unsigned narinfo comes first") ("substitute, first narinfo is unsigned and has wrong hash") ("substitute, first narinfo is unsigned and has wrong refs") ("substitute, two invalid narinfos") ("substitute, narinfo with several URLs"): Adjust to new "guix substitute --substitute" calling convention. Ludovic Courtès 2020-12-08daemon: Factorize substituter agent spawning....* nix/libstore/local-store.hh (class LocalStore)[substituter]: New method. [runningSubstituter]: Turn into a shared_ptr. * nix/libstore/local-store.cc (LocalStore::querySubstitutablePaths): Call 'substituter' instead of using inline code. (LocalStore::querySubstitutablePathInfos): Likewise. (LocalStore::substituter): New method. Ludovic Courtès 2020-12-08daemon: Use 'Agent' to spawn 'guix substitute --query'....* nix/libstore/local-store.hh (RunningSubstituter): Remove. (LocalStore)[runningSubstituter]: Change to unique_ptr<Agent>. [setSubstituterEnv, didSetSubstituterEnv]: Remove. [getLineFromSubstituter, getIntLineFromSubstituter]: Take an 'Agent'. * nix/libstore/local-store.cc (LocalStore::~LocalStore): Remove reference to 'runningSubstituter'. (LocalStore::setSubstituterEnv, LocalStore::startSubstituter): Remove. (LocalStore::getLineFromSubstituter): Adjust to 'run' being an 'Agent'. (LocalStore::querySubstitutablePaths): Spawn substituter agent if needed. Adjust to 'Agent' interface. (LocalStore::querySubstitutablePathInfos): Likewise. * nix/libstore/build.cc (SubstitutionGoal::tryToRun): Remove call to 'setSubstituterEnv' and add 'setenv' call for "_NIX_OPTIONS" instead. (SubstitutionGoal::finished): Remove 'readLine' call for 'dummy'. * guix/scripts/substitute.scm (%allow-unauthenticated-substitutes?): Remove second argument to 'make-parameter'. (process-query): Call 'warn-about-missing-authentication' when (%allow-unauthenticated-substitutes?) is #t. (guix-substitute): Wrap body in 'parameterize'. Set 'guix-warning-port' too. No longer exit when 'substitute-urls' returns the empty list. No longer print newline initially. * tests/substitute.scm (test-quit): Parameterize 'current-error-port' to account for the port changes in 'guix-substitute'. Ludovic Courtès 2020-12-08daemon: 'Agent' constructor takes a list of environment variables....* nix/libutil/util.hh (struct Agent)[Agent]: Add 'env' parameter. * nix/libutil/util.cc (Agent::Agent): Honor it. Ludovic Courtès 2020-12-01daemon: Remove unneeded forward declaration....This is a followup to ee9dff34f9317509cb2b833d07a0d5e01a36a4ae. * nix/libstore/build.cc: Remove 'struct Agent' forward declaration. Ludovic Courtès 2020-11-29daemon: Remove pre-Guix hack....* nix/libstore/build.cc (DerivationGoal::startBuilder): Remove "NIX_OUTPUT_CHECKED" hack. Ludovic Courtès 2020-11-29Use substitute servers on the local network....* guix/scripts/discover.scm: New file. * Makefile.am (MODULES): Add it. * nix/nix-daemon/guix-daemon.cc (options): Add "discover" option, (parse-opt): parse it, (main): start "guix discover" process when the option is set. * guix/scripts/substitute.scm (%local-substitute-urls): New variable, (substitute-urls): add it. * gnu/services/base.scm (<guix-configuration>): Add "discover?" field, (guix-shepherd-service): honor it. * doc/guix.texi (Invoking guix-daemon): Document "discover" option, (Base Services): ditto. Mathieu Othacehe 2020-10-27maint: Add 'etc/gnu-store.mount.in' to the distribution....Reported by Vagrant Cascadian. * nix/local.mk (EXTRA_DIST): Add 'etc/gnu-store.mount.in'. Ludovic Courtès 2020-10-09nix: Honor '--rounds' when also using '--check'....Fixes <https://issues.guix.gnu.org/40144>. Until now, the '--rounds' option, when also using '--check', was ignored. This change makes it possible to use both, so that an item that has already been built once can be rebuilt as many times as desired. * nix/libstore/build.cc: Remove the conditionals causing the daemon to complete a build task early when 'buildMode' is equal to 'nix::bmCheck'. Reported-by: Brice Waegeneire <brice@waegenei.re> Maxim Cournoyer 2020-10-01daemon: Try to execute derivation builders only for matching OS kernels....Fixes <https://bugs.gnu.org/43668>. Previously, guix-daemon would try to run GNU/Hurd executables on GNU/Linux. execve(2) would succeed, but the executable would immediately crash. This change prevents it from attempting to execute "i586-gnu" code on "*-linux", while preserving the binfmt_misc-friendly behavior implemented in commit 7bf2a70a4ffd976d50638d3b9f2ec409763157df. * nix/libstore/build.cc (sameOperatingSystemKernel): New function. (DerivationGoal::runChild): Call 'execve' only when 'sameOperatingSystemKernel' returns true. Ludovic Courtès 2020-09-17guix-install.sh: Support OpenRC....* etc/guix-install.sh (chk_init_sys): Detect OpenRC. (sys_enable_guix_daemon): Install & enable the Guix daemon on such systems. * etc/openrc/guix-daemon.in: New file. * nix/local.mk: Add a rule for it. (openrcservicedir, nodist_openrcservice_DATA): New variables. (CLEANFILES, EXTRA_DIST): Add them. * .gitignore: Ignore etc/openrc/guix-daemon. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr> Morgan Smith 2020-09-14daemon: Spawn 'guix authenticate' once for all....Previously, we'd spawn 'guix authenticate' once for each item that has to be signed (when exporting) or authenticated (when importing). Now, we spawn it once for all and then follow a request/reply protocol. This reduces the wall-clock time of: guix archive --export -r $(guix build coreutils -d) from 30s to 2s. * guix/scripts/authenticate.scm (sign-with-key): Return the signature instead of displaying it. Raise a &formatted-message instead of calling 'leave'. (validate-signature): Likewise. (read-command): New procedure. (define-enumerate-type, reply-code): New macros. (guix-authenticate)[send-reply]: New procedure. Change to read commands from current-input-port. * nix/libstore/local-store.cc (runAuthenticationProgram): Remove. (authenticationAgent, readInteger, readAuthenticateReply): New functions. (signHash, verifySignature): Rewrite in terms of the agent. * tests/store.scm ("import not signed"): Remove 'pk' call. ("import signed by unauthorized key"): Check the error message of C. * tests/guix-authenticate.sh: Rewrite using the new protocol. fixlet Ludovic Courtès 2020-09-14daemon: Move 'Agent' to libutil....* nix/libstore/build.cc (DerivationGoal::tryBuildHook): Add "offload" to 'args' and pass settings.guixProgram as the first argument to Agent::Agent. (pathNullDevice, commonChildInit, Agent, Agent::Agent) (Agent::~Agent): Move to... * nix/libutil/util.cc: ... here. * nix/libutil/util.hh (struct Agent, commonChildInit): New declarations. Ludovic Courtès 2020-09-14daemon: Isolate signing and signature verification functions....* nix/libstore/local-store.cc (signHash, verifySignature): New functions. (LocalStore::exportPath): Use 'signHash' instead of inline code. (LocalStore::importPath): Use 'verifySignature' instead of inline code. Ludovic Courtès 2020-09-14daemon: Generalize 'HookInstance' to 'Agent'....* nix/libstore/build.cc (HookInstance): Rename to... (Agent): ... this. Rename 'toHook' and 'fromHook' similarly and update users. Change constructor to require a command and an argument list. (DerivationGoal::tryBuildHook): Pass arguments to the 'Agent' constructor. Ludovic Courtès 2020-09-11daemon: Simplify interface with 'guix authenticate'....There's no reason at this point to mimic the calling convention of the 'openssl' command. * nix/libstore/local-store.cc (LocalStore::exportPath): Add only "sign" and HASH to ARGS. Remove 'tmpDir' and 'hashFile'. (LocalStore::importPath): Add only "verify" and SIGNATURE to * guix/scripts/authenticate.scm (guix-authenticate): Adjust accordingly; remove the OpenSSL-style clauses. (read-hash-data): Remove. (sign-with-key): Replace 'port' with 'sha256' and adjust accordingly. (validate-signature): Export SIGNATURE to be a canonical sexp. * tests/guix-authenticate.sh: Adjust tests accordingly. Ludovic Courtès 2020-06-27daemon: Recognize SHA3 and BLAKE2s....* nix/libutil/hash.hh (HashType): Add htSHA3_256, htSHA3_512, and htBLAKE2s_256. * nix/libutil/hash.cc (parseHashType, printHashType): Recognize them. * tests/store.scm ("add-to-store"): Test these algorithms. Ludovic Courtès 2020-06-27daemon: Remove OpenSSL hash compatibility wrappers....* nix/libutil/hash.cc (struct Ctx): Copy from gcrypt-hash.hh. (start, update, finish): Use gcrypt functions directly instead of OpenSSL-like wrappers. * nix/libutil/gcrypt-hash.cc, nix/libutil/gcrypt-hash.hh, nix/libutil/md5.h, nix/libutil/sha1.h, nix/libutil/sha256.h, nix/libutil/sha512.h: Remove. * nix/local.mk (libutil_a_SOURCES, libutil_headers): Adjust accordingly. Ludovic Courtès 2020-06-27daemon: Map directly to gcrypt hash functions....* nix/libutil/hash.hh (HashType): Map directly to GCRY_MD_ values. (md5HashSize, sha1HashSize, sha256HashSize, sha512HashSize): Remove. * nix/libutil/hash.cc (Hash::Hash): Use 'gcry_md_get_algo_dlen'. Ludovic Courtès 2020-06-25daemon: Correctly handle EMLINK corner case when deduplicating....Suggested by Caleb Ristvedt <caleb.ristvedt@cune.org>. * nix/libstore/optimise-store.cc (LocalStore::optimisePath_): Save errno from 'rename' before calling 'unlink'. Ludovic Courtès 2020-06-24nix: Tweak .gitignore files....Remove .gitignore entries where they match source files that are tracked in Git. This is relevant to me at least, as some code searching tools use .gitignore files and will ignore matched files. Christopher Baines 2020-06-06daemon: Handle EXDEV when moving to trash directory....Fixes <https://bugs.gnu.org/41607>. Reported by Stephen Scheck <singularsyntax@gmail.com>. * nix/libstore/gc.cc (LocalStore::deletePathRecursive): When we try to move a dead directory into the trashDir using rename(2) but it returns an EXDEV error, just delete the directory instead. This can happen in a Docker container when the directory is not on the "top layer". Chris Marusich 2020-05-23build: Add a comment above the sysvinit section....* nix/local.mk (sysvinitservicedir): Add a comment. Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr> Vincent Legoll 2020-05-17etc: Install mount unit only if it exists....This follows up on 1a1faa78b0498fbb71f1533beb4b65817c1d3f2a, and avoids the (non-fatal) error seen in <https://issues.guix.gnu.org/41356>. /gnu/store will remain writable on new foreign distribution installations until the next release. * etc/guix-install.sh (sys_enable_guix_daemon): Check for ‘gnu-store.mount’ presence before trying to cp it. Update forgotten copyright header. Tobias Geerinckx-Rice 2020-05-16etc: Add a systemd unit to bind-mount @storedir@ read-only....* etc/gnu-store.mount.in: New file. * nix/local.mk (nodist_systemdservice_DATA): Add it. (etc/%.mount): New rule for it. * etc/guix-install.sh (sys_enable_guix_daemon): Install it. * doc/guix.texi (Binary Installation): Document it. * .gitignore: Ignore changes to it. Tobias Geerinckx-Rice 2020-03-26daemon: Avoid kill -1 bug on the Hurd....This allows for native builds on the Hurd, doing sudo ./pre-inst-env guix-daemon --disable-chroot --build-users-group=guixbuild & ./pre-inst-env guix build hello * nix/libutil/util.cc (killUser)[__GNU__]: Avoid kill -1 bug; kill only current process and ignore SIGKILL status in parent. Co-authored-by: Jan Nieuwenhuizen <janneke@gnu.org> Manolis Ragkousis 2020-03-26daemon: Do not use clone on the Hurd....Checking for CLONE_NEWNS is only needed for using tha Linux specific clone(2), otherwise we can use fork(2). Using clone on the Hurd needs some work, only support LINUX for now. See https://lists.gnu.org/archive/html/guix-devel/2020-03/msg00190.html * nix/libstore/build.cc (CHROOT_ENABLED): Break into CHROOT_ENABLED and CLONE_ENABLED. (DerivationGoal::startBuilder): Replace CHROOT_ENABLED with __linux__. (DerivationGoal::runChild): Only define pivot_root() if SYS_pivot_root is defined. Co-authored-by: Jan Nieuwenhuizen <janneke@gnu.org> Manolis Ragkousis 2020-03-11Add system start-up files for guix-daemon....* etc/init.d/guix-daemon.in: New file. * nix/local.mk (etc/init.d/guix-daemon): New rule. (nodist_sysvinitservice_DATA): Add etc/init.d/guix-daemon.in . (CLEANFILES): Add etc/init.d/guix-daemon . * .gitignore: Add etc/init.d/guix-daemon . Danny Milosavljevic 2020-02-26daemon: Drop 'AT_STATX_DONT_SYNC' flag upon EINVAL....Fixes <https://bugs.gnu.org/39727>. Reported by Paul Garlick <pgarlick@tourbillion-technology.com>. * nix/libstore/gc.cc (LocalStore::removeUnusedLinks) [HAVE_STATX]: Add 'statx_flags' static variables. Clear 'AT_STATX_DONT_SYNC' flag from 'statx_flags' when 'statx' returns EINVAL. Ludovic Courtès 2020-01-12daemon: Fix the displayed GC estimated progress....* nix/libstore/gc.cc (LocalStore::deletePathRecursive): Fix computation of 'fraction'. Take 'bytesInvalidated' into account. Ludovic Courtès 2020-01-12daemon: Account for deleted store files when deduplication is on....Previously, a store item that is a regular file would not be accounted for in the 'bytesFreed' value computed by 'deletePath' because its 'st_nlink' count would always be >= 2. This commit fixes that. * nix/libutil/util.hh (deletePath): Add optional 'linkThreshold' argument. * nix/libutil/util.cc (_deletePath): Add 'linkThreshold' argument and honor it. Pass it down in recursive call. (deletePath): Add 'linkThreshold' and honor it. * nix/libstore/gc.cc (LocalStore::deleteGarbage): Pass 'linkThreshold' argument to 'deletePath', with a value of 2 when PATH is a store item and deduplication is on. Ludovic Courtès 2019-11-29daemon: 'pathExists' uses 'statx' when available....* nix/libutil/util.cc (pathExists) [HAVE_STATX]: New code. Ludovic Courtès 2019-11-27daemon: 'deletePath' uses 'statx' when available....* nix/libutil/util.cc (_deletePath) [HAVE_STATX]: Use 'statx'. Ludovic Courtès 2019-11-27daemon: GC remove-unused-links phase uses 'statx' when available....* config-daemon.ac: Check for 'statx'. * nix/libstore/gc.cc (LocalStore::removeUnusedLinks) [HAVE_STATX]: Use 'statx' instead of 'lstat'. Ludovic Courtès 2019-11-26daemon: boost::format: Fix typo "referred"....* nix/boost/format/exceptions.hpp (too_few_args): Fix typo. (too_many_args): Fix typo. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Vagrant Cascadian 2019-11-26guix build, daemon: Rename "--no-build-hook" to "--no-offload"....This is a followup to bc69ea2d605810cc32e13ed03d5848b8dc358b61. * guix/scripts/build.scm (show-build-options-help): Rename "--no-build-hook" to "--no-offload". (%standard-build-options): Likewise, and warn when "--no-build-hook" is passed. * nix/nix-daemon/guix-daemon.cc (options): Add "--no-offload" and mark "--no-build-hook" as hidden. * guix/scripts/offload.scm: Adjust comment. * doc/guix.texi (Invoking guix-daemon, Common Build Options): Replace "--no-build-hook" with "--no-offload". * etc/completion/fish/guix.fish, etc/completion/zsh/_guix: Adjust accordingly. Ludovic Courtès 2019-11-22daemon: GC displays how much it has collected....* nix/libstore/gc.cc (LocalStore::deletePathRecursive): Display the percentage reached relative to 'maxFreed', or the total amount of data deleted when 'maxFreed' is ULLONG_MAX. Ludovic Courtès