From e8b75faf7c75041003aac10c212412653725475f Mon Sep 17 00:00:00 2001 From: Travers Date: Sat, 28 Sep 2024 13:29:59 -0700 Subject: [PATCH] update qsbase URL --- ChangeLog | 52 +++++++++---------- R/zz_help_files.R | 2 +- README.md | 2 +- .../correctness_testing_extended.R | 22 ++++---- src/BLOSC/shuffle_routines.h | 2 +- src/extra_functions.h | 2 +- src/qs_common.h | 2 +- src/qs_deserialization.h | 2 +- src/qs_deserialization_stream.h | 2 +- src/qs_deserialize_common.h | 2 +- src/qs_functions.cpp | 2 +- src/qs_mt_deserialization.h | 2 +- src/qs_mt_serialization.h | 2 +- src/qs_serialization.h | 2 +- src/qs_serialization_stream.h | 2 +- tests/correctness_testing.R | 2 +- vignettes/vignette.rmd | 2 +- 17 files changed, 52 insertions(+), 52 deletions(-) diff --git a/ChangeLog b/ChangeLog index 4e70326..9125596 100644 --- a/ChangeLog +++ b/ChangeLog @@ -6,11 +6,11 @@ Version 0.27.1 (2024-06-04) * Add function `set_trust_promises` to allow for serialization and deserialization of PROMSXP Version 0.26.3 (2024-05-15) - * When serializing, eval promises immediately (https://github.com/traversc/qs/issues/94) - * Return NULL and issue a warning when unserializing a PROMSXP (see https://github.com/traversc/qs/issues/93) + * When serializing, eval promises immediately (https://github.com/qsbase/qs/issues/94) + * Return NULL and issue a warning when unserializing a PROMSXP (see https://github.com/qsbase/qs/issues/93) Version 0.26.2 (2024-03-18) - * Change check for requiring `-latomic` flag to use `AC_COMPILE_IFELSE` (https://github.com/traversc/qs/issues/88, https://github.com/traversc/qs/issues/91, https://github.com/traversc/qs/issues/76) + * Change check for requiring `-latomic` flag to use `AC_COMPILE_IFELSE` (https://github.com/qsbase/qs/issues/88, https://github.com/qsbase/qs/issues/91, https://github.com/qsbase/qs/issues/76) Version 0.26.1 (2024-03-07) * Add ALTREP serialization @@ -21,12 +21,12 @@ Version 0.25.7 (2023-12-05) Version 0.25.6 (2023-11-27) * Fix tests to account for ALTREP serialization - * Add filenames to error messages (https://github.com/traversc/qs/issues/75) - * Fix unit tests for big endian system (https://github.com/traversc/qs/issues/77) - * Check for GCC and add `-latomic` flag which is sometimes required (https://github.com/traversc/qs/issues/76) + * Add filenames to error messages (https://github.com/qsbase/qs/issues/75) + * Fix unit tests for big endian system (https://github.com/qsbase/qs/issues/77) + * Check for GCC and add `-latomic` flag which is sometimes required (https://github.com/qsbase/qs/issues/76) Version 0.25.5 (2023-2-20) - * Add function `qread_url`, a helper function that reads `qs` objects from the internet (https://github.com/traversc/qs/issues/49) + * Add function `qread_url`, a helper function that reads `qs` objects from the internet (https://github.com/qsbase/qs/issues/49) * Add `qattributes` function for extracting attributes of a saved object Version 0.25.4 (2022-8-9) @@ -50,7 +50,7 @@ Version 0.25.1 (2021-7-20) * Remove `R_restoreHashCount` function, as it is not part of the new R API Version 0.24.4 (2021-3-13) - * Throw a proper error message for DBFS issues (https://github.com/traversc/qs/issues/51) + * Throw a proper error message for DBFS issues (https://github.com/qsbase/qs/issues/51) Version 0.24.3 (2021-3-8) * Add github actions to test compilation on different R versions @@ -58,39 +58,39 @@ Version 0.24.3 (2021-3-8) Version 0.24.1 (2021-3-5) * Add additional error checks on failure to read or write data * Update xxhash version to 0.8.0 - * Reduce R version requirement from R 3.5.0 to R 3.0.2 (https://github.com/traversc/qs/pull/36) + * Reduce R version requirement from R 3.5.0 to R 3.0.2 (https://github.com/qsbase/qs/pull/36) Version 0.23.6 (2020-2-7) - * Add BNDCELLS (aka immediate bindings) support added in R 4.0 (https://github.com/traversc/qs/issues/50) + * Add BNDCELLS (aka immediate bindings) support added in R 4.0 (https://github.com/qsbase/qs/issues/50) Version 0.23.5 (2020-12-9) - * Correct issue in `qsavem` function (https://github.com/traversc/qs/issues/46) + * Correct issue in `qsavem` function (https://github.com/qsbase/qs/issues/46) Version 0.23.4 (2020-10-8) - * Correct documentation of `qreadm` and `qsavem` functions (https://github.com/traversc/qs/issues/44) + * Correct documentation of `qreadm` and `qsavem` functions (https://github.com/qsbase/qs/issues/44) Version 0.23.3 (2020-9-24) - * Fix to https://github.com/traversc/qs/issues/43 + * Fix to https://github.com/qsbase/qs/issues/43 Version 0.23.1 (2020-7-14) - * Fix to `qsavem` / `qload` functions (https://github.com/traversc/qs/issues/39) + * Fix to `qsavem` / `qload` functions (https://github.com/qsbase/qs/issues/39) * Update xxhash bundled library to v0.7.4 Version 0.22.1 (2020-5-31) - * Added `qsavem` and `qload`/`qreadm` functions for saving and reading multiple objects at once. Thanks to Bryce Chamberlain (https://github.com/traversc/qs/pull/36) + * Added `qsavem` and `qload`/`qreadm` functions for saving and reading multiple objects at once. Thanks to Bryce Chamberlain (https://github.com/qsbase/qs/pull/36) * `qs` now depends on R 3.5 and later. For earlier versions of R, use `remotes::install_github("traversc/qs@legacy")` * Improved alt-rep string functionality using the stringfish package (https://cran.r-project.org/package=stringfish) Version 0.21.2 (2020-3-8) * Added implementations of base 85 and base 91 ASCII encoding. See `?base91_encoding` and `?base85_encoding` - * Fixed a typo in the benchmarking code (https://github.com/traversc/qs/issues/32) and updated the readme benchmark to the latest version - * Added a more descriptive error when trying to read a non-existent file (https://github.com/traversc/qs/pull/34) + * Fixed a typo in the benchmarking code (https://github.com/qsbase/qs/issues/32) and updated the readme benchmark to the latest version + * Added a more descriptive error when trying to read a non-existent file (https://github.com/qsbase/qs/pull/34) * Compile LZ4 library in C++ instead of C to avoid U.B. issue (https://github.com/lz4/lz4/issues/847) Version 0.21.1 (2020-2-6) - * Fix for active bindings in R6/environments (https://github.com/traversc/qs/issues/29) - * Correct several documentation errors (https://github.com/traversc/qs/issues/28) - * Fix for incorrect serialization of "names" attribute in S4 Raster class (https://github.com/traversc/qs/issues/27) + * Fix for active bindings in R6/environments (https://github.com/qsbase/qs/issues/29) + * Correct several documentation errors (https://github.com/qsbase/qs/issues/28) + * Fix for incorrect serialization of "names" attribute in S4 Raster class (https://github.com/qsbase/qs/issues/27) Version 0.20.2 (2019-12-1) * Fix to minor bug involving serialization of locked environments @@ -102,7 +102,7 @@ Version 0.20.1 (2019-12-1) * S4SXP (non-simple S4 objects with slots) are efficiently serialized, instead of previously relying on R serialization Version 0.19.1 (2019-9-2) - * Exposed C++ API for use in other Rcpp packages and Rcpp scripts (https://github.com/traversc/qs/issues/18) + * Exposed C++ API for use in other Rcpp packages and Rcpp scripts (https://github.com/qsbase/qs/issues/18) Version 0.18.4 (2019-8-22) * Fixed an rchk issue with a missing `PROTECT` call during serialization @@ -110,7 +110,7 @@ Version 0.18.4 (2019-8-22) Version 0.18.3 (2019-8-20) * `qsave` now returns invisibly the number of bytes written to file - * Fixed an issue with deserialization of large S4 objects (https://github.com/traversc/qs/issues/14) + * Fixed an issue with deserialization of large S4 objects (https://github.com/qsbase/qs/issues/14) * Additional serialization and deserialization functions for advanced usage: * `qserialize` and `qdeserialize` reads and writes objects in memory to raw vectors * `qsave_fd` and `qread_fd` reads and write objects to file descriptors @@ -118,7 +118,7 @@ Version 0.18.3 (2019-8-20) * `qread_ptr` reads objects from a void pointer Version 0.18.2 (2019-7-19) - * Changed license to GPL-3 (https://github.com/traversc/qs/issues/13) + * Changed license to GPL-3 (https://github.com/qsbase/qs/issues/13) Version 0.18.1 (2019-7-14) * Revised header format in order to include more information -- files created by 0.18.1 cannot by read by earlier versions @@ -147,7 +147,7 @@ Version 0.16.3 (2019-6-21) * The goal is R should not crash even if a file is corrupted Version 0.16.2 (2019-6-15) - * Added `Set_elt` method for alt-rep string class (https://github.com/traversc/qs/issues/9) + * Added `Set_elt` method for alt-rep string class (https://github.com/qsbase/qs/issues/9) * Code cleanup: * Additional error checking during compression and de-compression * Use of RAII for protection stack handling @@ -158,7 +158,7 @@ Version 0.16.1 (2019-5-15) * Support for zstd streaming interface. As opposed to block compression routines, streaming compression offers better compression ratio but is not as fast * Re-factor configure script to not be so messy - * Changed file suffixes in examples from "q" to "qs" (https://github.com/traversc/qs/issues/5) + * Changed file suffixes in examples from "q" to "qs" (https://github.com/qsbase/qs/issues/5) * (Not included) brotli compression library was evaluated, but did not offer better performance compared to zstd on average * Updated zstd to version 1.4.0 (from 1.3.8) and lz4 to 1.9.1 (from 1.8.2) * Updated benchmarks to include zstd streaming interface and newer versions of zstd and lz4 @@ -170,7 +170,7 @@ Version 0.15.1 (2019-04-07) * Added support for lz4HC (high compression lz4 variant, but slower compression) * Additional error check handling to verify file integrity; see `qinspect` function * Additional documentation and examples - * Normalize file paths before attempting to write or read (https://github.com/traversc/qs/issues/4) + * Normalize file paths before attempting to write or read (https://github.com/qsbase/qs/issues/4) * Added star name database from the International Astronomical Union; see `?starnames` Version 0.14.1 (2019-03-03) diff --git a/R/zz_help_files.R b/R/zz_help_files.R index 800bbad..5a34386 100644 --- a/R/zz_help_files.R +++ b/R/zz_help_files.R @@ -15,7 +15,7 @@ # along with this program. If not, see . # # You can contact the author at: -# https://github.com/traversc/qs +# https://github.com/qsbase/qs # Since roxygen2 doesn't parse the `@usage` block, it doesn't know what the usage is, and hence it doesn't find any parameters to inherit, so we can't rely on diff --git a/README.md b/README.md index d8150bf..6e1c31f 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ Using qs ================ -[![R-CMD-check](https://github.com/traversc/qs/workflows/R-CMD-check/badge.svg)](https://github.com/traversc/qs/actions) +[![R-CMD-check](https://github.com/qsbase/qs/workflows/R-CMD-check/badge.svg)](https://github.com/qsbase/qs/actions) [![CRAN-Status-Badge](https://www.r-pkg.org/badges/version/qs)](https://cran.r-project.org/package=qs) [![CRAN-Downloads-Badge](https://cranlogs.r-pkg.org/badges/qs)](https://cran.r-project.org/package=qs) [![CRAN-Downloads-Total-Badge](https://cranlogs.r-pkg.org/badges/grand-total/qs)](https://cran.r-project.org/package=qs) diff --git a/inst/extra_tests/correctness_testing_extended.R b/inst/extra_tests/correctness_testing_extended.R index fb0a984..6fdaafd 100644 --- a/inst/extra_tests/correctness_testing_extended.R +++ b/inst/extra_tests/correctness_testing_extended.R @@ -124,7 +124,7 @@ for(i in 1:10) { rm(g1, g2, gb1, gb2) gc() -print("github.com/traversc/qs/issues/9") +print("github.com/qsbase/qs/issues/9") x <- data.table(x = 1:26, y = letters) qsave_rand(x, file=myfile) xu <- qread(myfile, use_alt_rep = T) @@ -133,7 +133,7 @@ stopifnot(identical(c("a", "y"), colnames(xu))) data.table::setnames(xu, 2, "b") stopifnot(identical(c("a", "b"), colnames(xu))) -print("github.com/traversc/qs/issues/23") +print("github.com/qsbase/qs/issues/23") for(i in 1:10) { z <- data.table(x=nanotime(runif(1e6)*1e18)) qsave_rand(z, file=myfile) @@ -146,9 +146,9 @@ gc() # large S4 objects -# https://github.com/traversc/qs/issues/14 +# https://github.com/qsbase/qs/issues/14 # Data is private, so not uploaded online -print("github.com/traversc/qs/issues/14 (this takes a long time)") +print("github.com/qsbase/qs/issues/14 (this takes a long time)") if (Sys.info()[['sysname']] != "Windows") { system("cat /mnt/n/R_stuff/qs_extended_tests/issue_14_data.rds > /dev/null") r <- mcreadRDS("/mnt/n/R_stuff/qs_extended_tests/issue_14_data.rds") @@ -172,9 +172,9 @@ gc() # gc() # Efficient serialization of ggplot objects -# https://github.com/traversc/qs/issues/21 +# https://github.com/qsbase/qs/issues/21 # Data is private, so not uploaded online -print("github.com/traversc/qs/issues/21") +print("github.com/qsbase/qs/issues/21") print("testing issue 21 no longer works because of deprecated plot object") # print("reading in initial data") # if (Sys.info()[['sysname']] != "Windows") { @@ -204,7 +204,7 @@ print("testing issue 21 no longer works because of deprecated plot object") # gc() # } -print("https://github.com/traversc/qs/issues/6") +print("https://github.com/qsbase/qs/issues/6") RiskModel <- R6Class( classname = "RiskModel", public = list( @@ -237,7 +237,7 @@ for(i in 1:5) { gc() } -print("https://github.com/traversc/qs/issues/27") +print("https://github.com/qsbase/qs/issues/27") nx <- ny <- 2 N <- nx * ny template <- raster(nrows = ny, ncols = nx, xmn = -nx / 2, xmx = nx / 2, @@ -249,14 +249,14 @@ qsave(DEM, file = myfile) DEM2 <- qread(myfile) all.equal(DEM@legend@names, DEM2@legend@names) -print("https://github.com/traversc/qs/issues/29") +print("https://github.com/qsbase/qs/issues/29") XClass <- R6Class( "XClass", active = list(r=function() runif(1)) ) x <- XClass$new() qsave(x, file=myfile) x2 <- qread(myfile) stopifnot(is.numeric(x2$r)) -print("https://github.com/traversc/qs/issues/43") +print("https://github.com/qsbase/qs/issues/43") for(i in 1:200) { a <- paste0(rep(".", i), collapse = "") x <- list(a = a, # a= '....................................................................', @@ -274,7 +274,7 @@ f2 <- compiler::cmpfun(function(x) { x <- x + 1.0; environment() }) # .Internal(inspect(f3(TRUE))) # this doesn't work? -print("https://github.com/traversc/qs/issues/50") +print("https://github.com/qsbase/qs/issues/50") for(i in 1:200) { x2 <- qs::qdeserialize(qs::qserialize(f1(1L))) stopifnot(identical(x2$x, 2L)) diff --git a/src/BLOSC/shuffle_routines.h b/src/BLOSC/shuffle_routines.h index 4b6c140..ad24db2 100644 --- a/src/BLOSC/shuffle_routines.h +++ b/src/BLOSC/shuffle_routines.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ /* The following shuffle routines were adapted from the Blosc meta-compression library diff --git a/src/extra_functions.h b/src/extra_functions.h index 2f76823..f63bbd1 100644 --- a/src/extra_functions.h +++ b/src/extra_functions.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ // These are extra functions that are not directly related to qs serialization diff --git a/src/qs_common.h b/src/qs_common.h index b0a7f15..ed96e41 100644 --- a/src/qs_common.h +++ b/src/qs_common.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: -https://github.com/traversc/qs +https://github.com/qsbase/qs */ #ifndef QS_COMMON_H diff --git a/src/qs_deserialization.h b/src/qs_deserialization.h index 971878a..31147ec 100644 --- a/src/qs_deserialization.h +++ b/src/qs_deserialization.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ #include "qs_common.h" diff --git a/src/qs_deserialization_stream.h b/src/qs_deserialization_stream.h index 18430b7..28a5b6f 100644 --- a/src/qs_deserialization_stream.h +++ b/src/qs_deserialization_stream.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ #include "qs_common.h" diff --git a/src/qs_deserialize_common.h b/src/qs_deserialize_common.h index b642065..f50f47d 100644 --- a/src/qs_deserialize_common.h +++ b/src/qs_deserialize_common.h @@ -647,7 +647,7 @@ SEXP processBlock(T * const sobj) { // SET_OBJECT(obj, 1); // this flag seems kind of pointless } if( !trust_promises_global && (TYPEOF(obj) == PROMSXP)) { - Rcpp::warning("PROMSXP detected, replacing with NULL (see https://github.com/traversc/qs/issues/93)"); + Rcpp::warning("PROMSXP detected, replacing with NULL (see https://github.com/qsbase/qs/issues/93)"); return R_NilValue; } else { return obj; diff --git a/src/qs_functions.cpp b/src/qs_functions.cpp index 9be29cd..43b0357 100644 --- a/src/qs_functions.cpp +++ b/src/qs_functions.cpp @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ #include "qs_common.h" diff --git a/src/qs_mt_deserialization.h b/src/qs_mt_deserialization.h index 89750cf..c9054dd 100644 --- a/src/qs_mt_deserialization.h +++ b/src/qs_mt_deserialization.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ #include "qs_common.h" diff --git a/src/qs_mt_serialization.h b/src/qs_mt_serialization.h index ec72370..3de1116 100644 --- a/src/qs_mt_serialization.h +++ b/src/qs_mt_serialization.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ #include "qs_common.h" diff --git a/src/qs_serialization.h b/src/qs_serialization.h index 8dd5775..4d12e4a 100644 --- a/src/qs_serialization.h +++ b/src/qs_serialization.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ #include "qs_common.h" diff --git a/src/qs_serialization_stream.h b/src/qs_serialization_stream.h index 309649c..326e63a 100644 --- a/src/qs_serialization_stream.h +++ b/src/qs_serialization_stream.h @@ -15,7 +15,7 @@ along with this program. If not, see . You can contact the author at: - https://github.com/traversc/qs + https://github.com/qsbase/qs */ #include "qs_common.h" diff --git a/tests/correctness_testing.R b/tests/correctness_testing.R index a8a2c40..e8ce6c3 100644 --- a/tests/correctness_testing.R +++ b/tests/correctness_testing.R @@ -536,7 +536,7 @@ for (q in 1:reps) { # some one off tests # test 1: alt rep implementation -# https://github.com/traversc/qs/issues/9 +# https://github.com/qsbase/qs/issues/9 # stringfish character vectors -- require R > 3.5.0 if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) { diff --git a/vignettes/vignette.rmd b/vignettes/vignette.rmd index 9e58a0e..8013574 100644 --- a/vignettes/vignette.rmd +++ b/vignettes/vignette.rmd @@ -16,7 +16,7 @@ IS_GITHUB <- Sys.getenv("IS_GITHUB") != "" ```{r results='asis', echo=FALSE, eval=IS_GITHUB} cat(' -[![R-CMD-check](https://github.com/traversc/qs/workflows/R-CMD-check/badge.svg)](https://github.com/traversc/qs/actions) +[![R-CMD-check](https://github.com/qsbase/qs/workflows/R-CMD-check/badge.svg)](https://github.com/qsbase/qs/actions) [![CRAN-Status-Badge](https://www.r-pkg.org/badges/version/qs)](https://cran.r-project.org/package=qs) [![CRAN-Downloads-Badge](https://cranlogs.r-pkg.org/badges/qs)](https://cran.r-project.org/package=qs) [![CRAN-Downloads-Total-Badge](https://cranlogs.r-pkg.org/badges/grand-total/qs)](https://cran.r-project.org/package=qs)