summaryrefslogtreecommitdiff
AgeCommit message (Collapse)AuthorFilesLines
2021-09-18(math/R-mnormt) Updated from 1.5.6 to 2.0.2mef2-9/+9
2020-06-24: 2.0.1 R version requirement is reduced from 4.0.0 to 2.2.0 2020-06-24: 2.0.1 fixed a bug which effectively prevented using dmtruncnorm and dmtrunct with an argument 'x' of vector type; various improvements in the documentation of recintab and mom2cum. 2020-06-02: 2.0.0 support for the truncated versions of the multivariate normal and the t distributions is introduced; for the truncated normal distribution, functions recintab and mom2cum allow computation of corresponding moments and cumulants; the latter function can also be used for obtaining the cumulants of other distributions of which the moments are known. 2020-04-29: 1.5-7 improved R coding of sadmvn and sadmvt, with increased use of biv.nt.prob; fixed a bug of pmnorm affecting a peculiar input set; a new function is introduced: sample_Mardia_measures.
2021-09-18Added math/R-tmvnsim version 1.0.2mef2-2/+4
2021-09-18(math/R-tmvnsim) import R-tmvnsim-1.0.2mef3-0/+29
Importance sampling from the truncated multivariate normal using the GHK (Geweke-Hajivassiliou-Keane) simulator. Unlike Gibbs sampling which can get stuck in one truncation sub-region depending on initial values, this package allows truncation based on disjoint regions that are created by truncation of absolute values. The GHK algorithm uses simple Cholesky transformation followed by recursive simulation of univariate truncated normals hence there are also no convergence issues. Importance sample is returned along with sampling weights, based on which, one can calculate integrals over truncated regions for multivariate normals.
2021-09-18doc: Updated math/R-lmm to 1.3mef2-3/+3
2021-09-18(math/R-lmm) Updated 1.2 to 1.3mef2-8/+7
Version 1.3 2020-07-05 Apply 'gfortran -c -fc-prototypes-external lmm.f' to extract C prototype
2021-09-18biology/biolibc: Update to 0.2.0.11bacon4-10/+10
Regenerate man pages with improved auto-c2man Improved formatting and added missing return value sections
2021-09-18doc: Updated devel/libxtend to 0.1.3.5bacon1-1/+2
2021-09-18devel/libxtend: Update to 0.1.3.5bacon4-11/+11
dsv_read_field*(): Treat multiple space characters as one delimiter Regenerate man pages with improved auto-c2man Improved formatting and added missing return value sections
2021-09-17Updated net/dnsmasq, textproc/py-phonenumbersadam1-1/+3
2021-09-17py-phonenumbers: updated to 8.12.31adam3-11/+8
What's new in 8.12.24 Merge to upstream commit e9d8d84f531b; relevant code changes: Updated As-You-Type-Formatter to exclude patterns where some digits would be dropped in the output. This also fixes the bug where an extra country code is added in some cases to the user's output. b/183053929
2021-09-17dnsmasq: updated to 2.86adam2-7/+7
version 2.86 Handle DHCPREBIND requests in the DHCPv6 server code. Thanks to Aichun Li for spotting this omission, and the initial patch. Fix bug which caused dnsmasq to lose track of processes forked to handle TCP DNS connections under heavy load. The code checked that at least one free process table slot was available before listening on TCP sockets, but didn't take into account that more than one TCP connection could arrive, so that check was not sufficient to ensure that there would be slots for all new processes. It compounded this error by silently failing to store the process when it did run out of slots. Even when this bug is triggered, all the right things happen, and answers are still returned. Only under very exceptional circumstances, does the bug manifest itself: see https://lists.thekelleys.org.uk/pipermail/dnsmasq-discuss/2021q2/014976.html Thanks to Tijs Van Buggenhout for finding the conditions under which the bug manifests itself, and then working out exactly what was going on. Major rewrite of the DNS server and domain handling code. This should be largely transparent, but it drastically improves performance and reduces memory foot-print when configuring large numbers domains of the form local=/adserver.com/ or local=/adserver.com/# Lookup times now grow as log-to-base-2 of the number of domains, rather than greater than linearly, as before. The change makes multiple addresses associated with a domain work address=/example.com/1.2.3.4 address=/example.com/5.6.7.8 It also handles multiple upstream servers for a domain better; using the same try/retry algorithms as non domain-specific servers. This also applies to DNSSEC-generated queries. Finally, some of the oldest and gnarliest code in dnsmasq has had a significant clean-up. It's far from perfect, but it _is_ better. Revise resource handling for number of concurrent DNS queries. This used to have a global limit, but that has a problem when using different servers for different upstream domains. Queries which are routed by domain to an upstream server which is not responding will build up and trigger the limit, which breaks DNS service for all other domains which could be handled by other servers. The change is to make the limit per server-group, where a server group is the set of servers configured for a particular domain. In the common case, where only default servers are declared, there is no effective change. Improve efficiency of DNSSEC. The sharing point for DNSSEC RR data used to be when it entered the cache, having been validated. After that queries requiring the KEY or DS records would share the cached values. There is a common case in dual-stack hosts that queries for A and AAAA records for the same domain are made simultaneously. If required keys were not in the cache, this would result in two requests being sent upstream for the same key data (and all the subsequent chain-of-trust queries.) Now we combine these requests and elide the duplicates, resulting in fewer queries upstream and better performance. To keep a better handle on what's going on, the "extra" logging mode has been modified to associate queries and answers for DNSSEC queries in the same way as ordinary queries. The requesting address and port have been removed from DNSSEC logging lines, since this is no longer strictly defined. Connection track mark based DNS query filtering. Thanks to Etan Kissling for implementing this It extends query filtering support beyond what is currently possible with the `--ipset` configuration option, by adding support for: 1) Specifying allowlists on a per-client basis, based on their associated Linux connection track mark. 2) Dynamic configuration of allowlists via Ubus. 3) Reporting when a DNS query resolves or is rejected via Ubus. 4) DNS name patterns containing wildcards. Disallowed queries are not forwarded; they are rejected with a REFUSED error code. Allow smaller than 64 prefix lengths in synth-domain, with caveats. --synth-domain=1234:4567::/56,example.com is now valid. Make domains generated by --synth-domain appear in replies when in authoritative mode. Ensure CAP_NET_ADMIN capability is available when conntrack is configured. Thanks to Yick Xie for spotting the lack of this. When --dhcp-hostsfile --dhcp-optsfile and --addn-hosts are given a directory as argument, define the order in which files within that directory are read (alphabetical order of filename). Thanks to Ed Wildgoose for the initial patch and motivation for this.
2021-09-17doc: Updated sysutils/macchina to 1.1.6pin1-1/+2
2021-09-17sysutils/macchina: update to 1.1.6pin3-201/+103
v1.1.6 -Update libmacchina dependency to v2.1.4, finally fixing the brightness readout. v1.1.5 -Update to latest libmacchina, libc, serde_json and dirs versions -Import libmacchina's backlight method (#102) -netbsd/terminal: Traverse /proc to which terminal the user is operating in, ignoring the shell. -netbsd/resolution: Remove this method for the time being On my previous commit I wrote the following, "As of version 1.0.0 macchina uses google-speech to support text-to-speech. I've disabled this feature, please let me know if you think this should be on." This was a mistake from my side, the feature was available but, disabled by default in versions 1.0.0 to 1.1.5. The relevant code is only compiled into the binary if, and only if, the feature is enabled at compile time. This feature and the code have been removed on version 1.1.6
2021-09-17Updated lang/nodejs12, lang/nodejsadam1-1/+3
2021-09-17nodejs: updated to 14.17.6adam3-10/+11
Version 14.17.6 'Fermium' (LTS) This is a security release. Notable Changes These are vulnerabilities in the node-tar, arborist, and npm cli modules which are related to the initial reports and subsequent remediation of node-tar vulnerabilities CVE-2021-32803 and CVE-2021-32804. Subsequent internal security review of node-tar and additional external bounty reports have resulted in another 5 CVE being remediated in core npm CLI dependencies including node-tar, and npm arborist. Version 14.17.5 'Fermium' (LTS) This is a security release. Notable Changes CVE-2021-3672/CVE-2021-22931: Improper handling of untypical characters in domain names (High) Node.js was vulnerable to Remote Code Execution, XSS, application crashes due to missing input validation of hostnames returned by Domain Name Servers in the Node.js DNS library which can lead to the output of wrong hostnames (leading to Domain Hijacking) and injection vulnerabilities in applications using the library. You can read more about it at https://nvd.nist.gov/vuln/detail/CVE-2021-22931. CVE-2021-22930: Use after free on close http2 on stream canceling (High) Node.js was vulnerable to a use after free attack where an attacker might be able to exploit memory corruption to change process behavior. This release includes a follow-up fix for CVE-2021-22930 as the issue was not completely resolved by the previous fix. You can read more about it at https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2021-22930. CVE-2021-22939: Incomplete validation of rejectUnauthorized parameter (Low) If the Node.js HTTPS API was used incorrectly and "undefined" was in passed for the "rejectUnauthorized" parameter, no error was returned and connections to servers with an expired certificate would have been accepted. You can read more about it at https://nvd.nist.gov/vuln/detail/CVE-2021-22939.
2021-09-17nodejs12: updated to 12.22.6adam3-27/+9
Version 12.22.6 'Erbium' (LTS) This is a security release. Notable Changes These are vulnerabilities in the node-tar, arborist, and npm cli modules which are related to the initial reports and subsequent remediation of node-tar vulnerabilities CVE-2021-32803 and CVE-2021-32804. Subsequent internal security review of node-tar and additional external bounty reports have resulted in another 5 CVE being remediated in core npm CLI dependencies including node-tar, and npm arborist. Version 12.22.5 'Erbium' (LTS) This is a security release. Notable Changes CVE-2021-3672/CVE-2021-22931: Improper handling of untypical characters in domain names (High) Node.js was vulnerable to Remote Code Execution, XSS, application crashes due to missing input validation of hostnames returned by Domain Name Servers in the Node.js DNS library which can lead to the output of wrong hostnames (leading to Domain Hijacking) and injection vulnerabilities in applications using the library. You can read more about it at https://nvd.nist.gov/vuln/detail/CVE-2021-22931. CVE-2021-22930: Use after free on close http2 on stream canceling (High) Node.js was vulnerable to a use after free attack where an attacker might be able to exploit memory corruption to change process behavior. This release includes a follow-up fix for CVE-2021-22930 as the issue was not completely resolved by the previous fix. You can read more about it at https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2021-22930. CVE-2021-22939: Incomplete validation of rejectUnauthorized parameter (Low) If the Node.js HTTPS API was used incorrectly and "undefined" was in passed for the "rejectUnauthorized" parameter, no error was returned and connections to servers with an expired certificate would have been accepted. You can read more about it at https://nvd.nist.gov/vuln/detail/CVE-2021-22939. Version 12.22.4 'Erbium' (LTS) This is a security release. Notable Changes CVE-2021-22930: Use after free on close http2 on stream canceling (High) Node.js is vulnerable to a use after free attack where an attacker might be able to exploit the memory corruption, to change process behavior. You can read more about it in https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2021-22930
2021-09-17doc: Updated www/webkit-gtk to 2.32.4leot1-1/+2
2021-09-17webkit-gtk: Update to 2.32.4leot3-10/+10
Changes: 2.32.4 ------ - Do not append .asc extension to downloaded text/plain files. - Fix several crashes and rendering issues.
2021-09-17Updated graphics/gd, www/py-flask-restfuladam1-1/+3
2021-09-17py-flask-restful: updated to 0.3.9adam2-7/+7
Version 0.3.9 Compatibility with Flask 2.0
2021-09-17gd: updated to 2.3.3adam3-10/+8
2.3.3: The LibGD team is proud to announce the 2.3.3 release of libgd. This release brings a few fixes as well as improved compilations and builds on all platforms. On Windows, vcpkg to install libGd dependencies is now well supported. Fixed * update cmake to generate config.h in the build dir * gdPutBuf return value check * HEIF builds fail with latest distros * segfault in heif tests due to missing label.heic * Test failure avif/compare_avif_to_png with libavif-0.8.2 * imagecopyresampled() produce artifacts on transparent PNG * Fixes to build v2.3.0 on Windows with MinGW-w64 * optimize option in gif animation causes segfault * _gdContributionsCalc() always uses DEFAULT_BOX_RADIUS * gdImageRotateInterpolated() converts the source image to truecolor * CMake and Makefiles build broken on Windows * gdImageScaleTwoPass() looses top row and left column
2021-09-17Revbump all Go packages after go117 updatebsiegert99-185/+198
2021-09-17doc: Updated lang/go117 to 1.17.1bsiegert1-1/+2
2021-09-17go117: update to 1.17.1 (security).bsiegert3-8/+13
go1.17.1 (released 2021-09-09) includes a security fix to the archive/zip package, as well as bug fixes to the compiler, linker, the go command, and to the crypto/rand, embed, go/types, html/template, and net/http packages.
2021-09-17doc: Updated lang/go116 to 1.16.8bsiegert1-1/+2
2021-09-17Update go116 to 1.16.8 (security).bsiegert2-7/+7
go1.16.8 (released 2021-09-09) includes a security fix to the archive/zip package, as well as bug fixes to the archive/zip, go/internal/gccgoimporter, html/template, net/http, and runtime/pprof packages.
2021-09-17Updated net/qbittorrent, www/apache24adam2-3/+4
2021-09-17qbittorrent: updated to 4.3.8adam2-7/+7
v4.3.8 - BUGFIX: Delay processing of watched folders - BUGFIX: Use the same icon for selecting folders/files (Chocobo1) - BUGFIX: Use default upper limits for ddns entries (Chocobo1) - WEBUI: Expose SSRF mitigation - WEBUI: Update webui libraries (Chocobo1) - WEBUI: Group trackers by hostname - WEBUI: Improve "last activity" calculation in WebAPI - WINDOWS: NSIS: Add Polish translation
2021-09-17apache24: updated to 2.4.49adam2-7/+7
Changes with Apache 2.4.49 *) SECURITY: CVE-2021-40438 (cve.mitre.org) mod_proxy: Server Side Request Forgery (SSRF) vulnerabilty [Yann Ylavic] *) SECURITY: CVE-2021-39275 (cve.mitre.org) core: ap_escape_quotes buffer overflow *) SECURITY: CVE-2021-36160 (cve.mitre.org) mod_proxy_uwsgi: Out of bound read vulnerability [Yann Ylavic] *) SECURITY: CVE-2021-34798 (cve.mitre.org) core: null pointer dereference on malformed request *) SECURITY: CVE-2021-33193 (cve.mitre.org) mod_http2: Request splitting vulnerability with mod_proxy [Stefan Eissing] *) core/mod_proxy/mod_ssl: Adding `outgoing` flag to conn_rec, indicating a connection is initiated by the server to somewhere, in contrast to incoming connections from clients. Adding 'ap_ssl_bind_outgoing()` function that marks a connection as outgoing and is used by mod_proxy instead of the previous optional function `ssl_engine_set`. This enables other SSL module to secure proxy connections. The optional functions `ssl_engine_set`, `ssl_engine_disable` and `ssl_proxy_enable` are now provided by the core to have backward compatibility with non-httpd modules that might use them. mod_ssl itself no longer registers these functions, but keeps them in its header for backward compatibility. The core provided optional function wrap any registered function like it was done for `ssl_is_ssl`. [Stefan Eissing] *) mod_ssl: Support logging private key material for use with wireshark via log file given by SSLKEYLOGFILE environment variable. Requires OpenSSL 1.1.1. PR 63391. [Joe Orton] *) mod_proxy: Do not canonicalize the proxied URL when both "nocanon" and "ProxyPassInterpolateEnv On" are configured. PR 65549. [Joel Self <joelself gmail.com>] *) mpm_event: Fix children processes possibly not stopped on graceful restart. PR 63169. [Joel Self <joelself gmail.com>] *) mod_proxy: Fix a potential infinite loop when tunneling Upgrade(d) protocols from mod_proxy_http, and a timeout triggering falsely when using mod_proxy_wstunnel, mod_proxy_connect or mod_proxy_http with upgrade= setting. PRs 65521 and 65519. [Yann Ylavic] *) mod_unique_id: Reduce the time window where duplicates may be generated PR 65159 [Christophe Jaillet] *) mpm_prefork: Block signals for child_init hooks to prevent potential threads created from there to catch MPM's signals. [Ruediger Pluem, Yann Ylavic] *) Revert "mod_unique_id: Fix potential duplicated ID generation under heavy load. PR 65159" added in 2.4.47. This causes issue on Windows. [Christophe Jaillet] *) mod_proxy_uwsgi: Fix PATH_INFO setting for generic worker. [Yann Ylavic] *) mod_md: Certificate/keys pairs are verified as matching before a renewal is accepted as successful or a staged renewal is replacing the existing certificates. This avoid potential mess ups in the md store file system to render the active certificates non-working. [@mkauf] *) mod_proxy: Faster unix socket path parsing in the "proxy:" URL. [Yann Ylavic] *) mod_ssl: tighten the handling of ALPN for outgoing (proxy) connections. If ALPN protocols are provided and sent to the remote server, the received protocol selected is inspected and checked for a match. Without match, the peer handshake fails. An exception is the proposal of "http/1.1" where it is accepted if the remote server did not answer ALPN with a selected protocol. This accomodates for hosts that do not observe/support ALPN and speak http/1.x be default. *) mod_proxy: Fix possible reuse/merging of Proxy(Pass)Match worker instances with others when their URLs contain a '$' substitution. PR 65419 + 65429. [Yann Ylavic] *) mod_dav: Add method_precondition hook. WebDAV extensions define conditions that must exist before a WebDAV method can be executed. This hook allows a WebDAV extension to verify these preconditions. [Graham Leggett] *) Add hooks deliver_report and gather_reports to mod_dav.h. Allows other modules apart from versioning implementations to handle the REPORT method. [Graham Leggett] *) Add dav_get_provider(), dav_open_lockdb(), dav_close_lockdb() and dav_get_resource() to mod_dav.h. [Graham Leggett] *) core: fix ap_escape_quotes substitution logic. [Eric Covener] *) Easy patches: synch 2.4.x and trunk - mod_auth_basic: Use ap_cstr_casecmp instead of strcasecmp. - mod_ldap: log and abort locking errors. - mod_ldap: style fix for r1831165 - mod_ldap: build break fix for r1831165 - mod_deflate: Avoid hard-coded "%ld" format strings in mod_deflate's logging statements - mod_deflate: Use apr_uint64_t instead of uint64_t (follow up to r1849590) - mod_forensic: Follow up to r1856490: missing one mod_log_forensic test_char_table case. - mod_rewrite: Save a few cycles. - mod_request: Fix a comment (missing '_' in 'keep_body') and some style issues - core: remove extra whitespace in HTTP_NOT_IMPLEMENTED [Christophe Jaillet] *) core/mpm: add hook 'child_stopping` that gets called when the MPM is stopping a child process. The additional `graceful` parameter allows registered hooks to free resources early during a graceful shutdown. [Yann Ylavic, Stefan Eissing] *) mod_proxy: Fix icomplete initialization of BalancerMember(s) from the balancer-manager, which can lead to a crash. [Yann Ylavic] *) mpm_event: Fix graceful stop/restart of children processes if connections are in lingering close for too long. [Yann Ylavic] *) mod_md: fixed a potential null pointer dereference if ACME/OCSP server returned 2xx responses without content type. Reported by chuangwen. [chuangwen, Stefan Eissing] *) mod_md: - Domain names in `<MDomain ...>` can now appear in quoted form. - Fixed a failure in ACME challenge selection that aborted further searches when the tls-alpn-01 method did not seem to be suitable. - Changed the tls-alpn-01 setup to only become unsuitable when none of the dns names showed support for a configured 'Protocols ... acme-tls/1'. This allows use of tls-alpn-01 for dns names that are not mapped to a VirtualHost. [Stefan Eissing] *) Add CPING to health check logic. [Jean-Frederic Clere] *) core: Split ap_create_request() from ap_read_request(). [Graham Leggett] *) core, h2: common ap_parse_request_line() and ap_check_request_header() code. [Yann Ylavic] *) core: Add StrictHostCheck to allow unconfigured hostnames to be rejected. [Eric Covener] *) htcacheclean: Improve help messages. [Christophe Jaillet]
2021-09-17qvwm: add missing libraries for the SunOS linkernia1-1/+3
2021-09-17luakit: add missing libraries on SunOSnia1-1/+3
2021-09-17rxvt-unicode: needs libXt for Intrinsic.hnia1-1/+2
2021-09-17doc: Added sysutils/syslog-ng-snmp version 3.34.1wiz1-1/+2
2021-09-17sysutils/Makefile: + syslog-ng-snmpwiz1-1/+2
2021-09-17sysutils/syslog-ng-snmp: import syslog-ng-snmp-3.34.1wiz3-0/+22
Based on files provided by Chavdar Ivanov. Syslog-ng tries to fill the gaps original syslogd's were lacking: * powerful configurability * filtering based on message content * message integrity, message encryption * portability * better network forwarding This package contains the snmp module.
2021-09-17syslog-ng: do not override COMMENT (for modules)wiz2-4/+6
Disable SNMP by default. Add comments for upcoming package.
2021-09-17pax11publish.1 is only installed if we build with x11.schmonz1-2/+2
2021-09-17Fix macOS build. NFCI elsewhere.schmonz7-100/+171
2021-09-17ardour: Point at LOCAL_PORTS since someone uploaded a non-matchingnia1-2/+2
distfile over mine.
2021-09-17Fix build for non-amd64 NetBSD architectures (already reported upstream)martin2-1/+22
2021-09-17gpac: Fix building on notdarwin.nia10-26/+204
2021-09-16doc: Updated math/R-lme4 to 1.1.27.1mef2-3/+3
2021-09-16(math/R-lme4) Updated 1.1.21 to 1.1.27.1mef2-8/+18
HANGES IN VERSION 1.1-27.1: USER-VISIBLE CHANGES: * 'influence.merMod' allows user-specified starting parameters * cleaned up performance vignette BUG FIXES: * 'cooks.distance' now works with objects computed by 'influence' method * 'influence.merMod' now works with 'glmer' models using 'nAGQ=0' * 'predict' (with new data) and 'simulate' methods now work for models with >100 levels in a random effect grouping variable (GH #631) CHANGES IN VERSION 1.1-27 (2021-05-15): USER-VISIBLE CHANGES: * improvements from Lionel Henry (via https://github.com/lme4/lme4/pull/587) to fix corner cases in data checking; also resolves GH #601 (allFit scoping) * 'getME(., "lower")' now has names (request of GH #609) * improved detection of 'NaN' in internal calculations (typically due to underflow/overflow or out-of-bounds linear predictors from non-constraining link functions such as identity-link Gamma models) * 'influence.merMod' allows parallel computation * the 'statmod' package is no longer required unless attempting to simulate results from a model with an inverse Gaussian response BUG FIXES: * long formulas work better in 'anova' headings (GH #611) CHANGES IN VERSION 1.1-26 (2020-11-30): BUG FIXES: * 'predict', 'model.frame(.,fixed.only=TRUE)' work with variable names containing spaces (GH #605) * 'simulate' works when original response variable was logical * 'densityplot' handles partly broken profiles more robustly NEW FEATURES: * 'thpr' method for 'densityplot()' (for plotting profiles scaled as densities) gets new arguments CHANGES IN VERSION 1.1-25 (2020-10-23): * Set more tests to run only if environment variable 'LME4_TEST_LEVEL'>1 CHANGES IN VERSION 1.1-24 (never on CRAN): USER-VISIBLE CHANGES: * 'anova()' now returns a p-value of 'NA' if the df difference between two models is 0 (implying they are equivalent models) (GH#583, @MetaEntropy) * speedup in 'coef()' for large models, by skipping conditional variance calculation (Alexander Bauer) * 'simulate.formula' machinery has changed slightly, for compatibility with the 'ergm' package (Pavel Krivitsky) * informational messages about (non-)convergence improved (GH #599) * improved error messages for 0 non-NA cases in data (GH #533) NEW FEATURES: * 'getME(.,"devfun")' now works for 'glmer' objects. Additionally, 'profile'/'confint' for GLMMs no longer depend on objects in the fitting environment remaining unchanged (GH #589). This change also affects likelihood profiling machinery; results of 'glmer' profiling/CIs may not match results from previous versions exactly. BUG FIXES: * improved handling/documentation of 'glmer.nb' controls (GH #556) * 'predict' works better for 'gamm4' objects (GH #575) * resolved some long-standing UBSAN issues (GH #561) CHANGES IN VERSION 1.1-23 (2020-03-06): This is primarily for CRAN compliance (previous submission was retracted to allow time for downstream package adjustments). * Some PROTECT/UNPROTECT fixes CHANGES IN VERSION 1.1-22 (never on CRAN): USER-VISIBLE CHANGES: * prediction now works better for factors with many levels (GH#467, solution by @sihoward) * minor changes to argument order in '[g]lmerControl'; default tolerance for convergence checks increased from 0.001 to 0.002 for 'glmerControl' (now consistent with 'lmerControl') * 'lmer(*, family="<fam>")' is no longer valid; it had been deprecated since 2013-06. * 'lmer()', 'glmer()', and 'nlmer()' no longer have a formal '...' argument. This defunctifies the use of a 'sparseX = .' argument and will reveal some user errors, where extraneous arguments were previously disregarded. * In 'isSingular(x, tol)', the default tolerance ('tol') has been increased from '1e-5' to '1e-4', the default of 'check.conv.singular' in 'g?lmerControl()'. * for clarity and consistency with base R methods, some column names of 'anova()' output are changed: "Df" becomes "npar", "Chi Df" becomes "Df" (GH #528) * 'simulate()' now works with inverse-Gaussian models (GH #284 revisited, @nahorp/Florian Hartig) * single-model mode of 'anova()' now warns about unused arguments in ... (e.g. 'type="III"') * default tolerances for 'nloptwrap'/BOBYQA optimizer tightened ('xtol_abs' and 'ftol_abs' were 1e-6, now 1e-8). (To revert to former tolerances, use 'control=lmerControl(optimizer="nloptwrap", optCtrl=list(xtol_abs=1e-6, ftol_abs=1e-6))'.) BUG FIXES: * improved checking for missing data (@lionel-) * internal 'checkZrank()' should be able to deal with ('Matrix' package) 'rankMatrix()' returning 'NA'. * 'allFit(fm)' now works for a model that had an explicit 'control = lmerControl(..)' call. * internal 'getStart()' now works when model's 'start' was specified as a list, and when called from 'drop1()' on a submodel, fixing GH #521. * internal function 'mkdevfun' now works even if there is an extraneous 'getCall' function defined in the global environment (GH #535) * 'allFit()' works even if a variable with symbol 'i' is used somewhere in the original model call (GH #538, reported by Don Cohen); generally more robust * 'glmer.nb' works even if an alternative version of 'negative.binomial' (other than the one from 'MASS') is loaded in the workspace (e.g. by the 'GLMMadaptive' package) (GH#516) * 'level' argument is now honoured by 'confint(..., type="boot", level=...)' (GH #543)
2021-09-16doc: Updated math/R-intervals to 0.15.2mef2-3/+3
2021-09-16(math/R-intervals) Updated 0.15.1 to 0.15.2, NEWS not updatedmef2-9/+8
2021-09-16doc: Updated math/R-gtools to 3.9.2mef2-3/+3
2021-09-16(math/R-gtools) Updated 3.8.1 to 3.9.2mef2-9/+12
gtools 3.9.2 - 2021-06-03 ------------------------- Bug fixes: - Fix missing man page and export for `combinations` and `permutations`. Behind the scenes: - Fixed more spelling/typographical errors, mostly in `NEWS.md`. - Speed up `checkRversion` by removing checks for versions 2.x and 3.x. gtools 3.9.1 - 2021-06-01 ------------------------- Bug fixes: - Use valid HTTP request for example in `setTCPNoDelay` to prevent errors when running tests. Behind the scenes: - Fixed numerous spelling/typographical errors. - Update obsolete http URLs to https gtools 3.9.0 - 2021-05-31 ------------------------- New functions: - New `script_file` and `script_path` functions to obtain the directory or full path to the currently executing script. - New 'stat_mode` function to calculate the statistical mode (most frequently occurring value). - New `capwords` function to apply title capitalization rules to a character vector. - Move `baseOf` from `gplots` as requested by Steffen Möller. #2 New parameters: - Add `scientific` parameter to `mixedsort` and `mixedorder` to control whether numbers in scientific notation are recognized. Resolved #7. - Enhance `invalid` to detect `try-error` objects. #6 Bug fixes: - Add support for R version 4 to `checkRVersion`. Resolved #5. - Correct bug in `lastAdd` by explicitly checking for a `.Last` of mode function. Behind the scenes: - Modernize package code by using `roxygen2` for documentation and managing the NAMESPACE. - Modernize C function registration. - Replace http URLs with `https` and resolve broken links. - Add github actions to automated testing - Use pkgdown to generate HTML documentation. - Use `styler` package to standardize R code formatting. gtools 3.8.2 - 2020-03-23 ------------------------- Minor changes to support R 4.0
2021-09-16doc: Updated math/R-gstat to 2.0.7mef2-3/+3
2021-09-16(math/R-gstat) Updated 2.0.2 to 2.0.7mef2-10/+18
# version 2.0-7 * return `NA` as estimate when prediction/simulation fails; #80 # version 2.0-6 * fixes `object 'ret' not found` bug introduced by #63; #65 #66 #70 # version 2.0-5 * use multiple cores in `variogramST`, using pkg future; #63 by @sigmafelix * fix bug with conditional simulation using `stars` target grid and nsim=1, #58 # version 2.0-4 * fix CRAN warning issue # version 2.0-3 * fix bug in support for `sf` objects; #46 * fix `krigeTg` for the case when data or newdata are of class `sf` or `sfc`; #51
2021-09-16doc: Updated math/R-geoR to 1.8.1mef2-3/+3