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MarcusKlikMarcusKlik
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Merge branch 'hotfix'
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‎.Rbuildignore‎

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@@ -18,3 +18,4 @@ LZ4/LICENSE$
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^_pkgdown\.yml$
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^CRAN-RELEASE$
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^revdep$
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^\.github$

‎.github/.gitignore‎

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*.html

‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [develop, release, hotfix, master]
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pull_request:
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branches: [develop, release, hotfix, master]
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name: R-CMD-check
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-pandoc@v1
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- uses: r-lib/actions/setup-r@v1
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v1
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with:
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extra-packages: rcmdcheck
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- uses: r-lib/actions/check-r-package@v1
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- name: Show testthat output
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if: always()
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run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@main
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with:
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name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check

‎DESCRIPTION‎

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@@ -5,21 +5,20 @@ Description: Multithreaded serialization of compressed data frames using the
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'fst' format. The 'fst' format allows for random access of stored data and
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compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD
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compression library is owned by Facebook Inc.
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Version: 0.9.4
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Date: 2020-08-26
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Version: 0.9.6
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Date: 2022-02-01
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Authors@R: c(
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person("Mark", "Klik", email = "[email protected]", role = c("aut", "cre", "cph")),
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person("Yann", "Collet", role = c("ctb", "cph"),
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comment = "Yann Collet is author of the bundled LZ4 and ZSTD code and copyright holder of LZ4"),
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person("Facebook, Inc.", role = "cph", comment = "Bundled ZSTD code"))
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LazyData: true
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Depends:
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R (>= 3.0.0)
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Imports:
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Rcpp
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LinkingTo: Rcpp
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SystemRequirements: little-endian platform
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RoxygenNote: 7.1.1
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RoxygenNote: 7.1.2
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Suggests:
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testthat,
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bit64,

‎NEWS.md‎

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# fst 0.9.6
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Version 0.9.6 is a minor update to 'hotfix' an issue with the use of `sample.int()`. All calls to `sample.int()` now
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explicitly reference a length one size object.
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# fst 0.9.4
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Version 0.9.4 is a minor update to 'hotfix' an issue with suggested packages as reported by CRAN.

‎README.Rmd‎

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<img src="fst.png" align="right" height="196" width="196" />
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[![Linux/OSX Build Status](https://travis-ci.org/fstpackage/fst.svg?branch=develop)](https://travis-ci.org/fstpackage/fst)
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[![Windows Build status](https://ci.appveyor.com/api/projects/status/6g6kp8onpb26jhnm/branch/develop?svg=true)](https://ci.appveyor.com/project/fstpackage/fst/branch/develop)
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[![Build Status](https://github.com/fstpackage/fst/actions/workflows/R-CMD-check.yaml/badge.svg?branch=develop)](https://github.com/fstpackage/fst/actions/workflows/R-CMD-check.yaml)
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[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
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[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/fst)](https://cran.r-project.org/package=fst)
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[![codecov](https://codecov.io/gh/fstpackage/fst/branch/develop/graph/badge.svg)](https://codecov.io/gh/fstpackage/fst)

‎README.md‎

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<img src="fst.png" align="right" height="196" width="196" />
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[![Linux/OSX Build
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Status](https://travis-ci.org/fstpackage/fst.svg?branch=develop)](https://travis-ci.org/fstpackage/fst)
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[![Windows Build
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status](https://ci.appveyor.com/api/projects/status/6g6kp8onpb26jhnm/branch/develop?svg=true)](https://ci.appveyor.com/project/fstpackage/fst/branch/develop)
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[![Build
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Status](https://github.com/fstpackage/fst/actions/workflows/R-CMD-check.yaml/badge.svg?branch=develop)](https://github.com/fstpackage/fst/actions/workflows/R-CMD-check.yaml)
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[![License: AGPL
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v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
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[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/fst)](https://cran.r-project.org/package=fst)
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[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/fst)](https://cran.r-project.org/package=fst)
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[![codecov](https://codecov.io/gh/fstpackage/fst/branch/develop/graph/badge.svg)](https://codecov.io/gh/fstpackage/fst)
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[![downloads](http://cranlogs.r-pkg.org/badges/fst)](http://cran.rstudio.com/web/packages/fst/index.html)
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[![total\_downloads](https://cranlogs.r-pkg.org/badges/grand-total/fst)](http://cran.rstudio.com/web/packages/fst/index.html)
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[![total_downloads](https://cranlogs.r-pkg.org/badges/grand-total/fst)](http://cran.rstudio.com/web/packages/fst/index.html)
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## Overview
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The figure below compares the read and write performance of the *fst*
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package to various alternatives.
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| Method | Format | Time (ms) | Size (MB) | Speed (MB/s) | N |
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| :------------- | :------ | :-------- | :-------- | :----------- | :------ |
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| readRDS | bin | 1577 | 1000 | 633 | 112 |
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| saveRDS | bin | 2042 | 1000 | 489 | 112 |
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| fread | csv | 2925 | 1038 | 410 | 232 |
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| fwrite | csv | 2790 | 1038 | 358 | 241 |
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| read\_feather | bin | 3950 | 813 | 253 | 112 |
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| write\_feather | bin | 1820 | 813 | 549 | 112 |
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| **read\_fst** | **bin** | **457** | **303** | **2184** | **282** |
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| **write\_fst** | **bin** | **314** | **303** | **3180** | **291** |
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| Method | Format | Time (ms) | Size (MB) | Speed (MB/s) | N |
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|:--------------|:--------|:----------|:----------|:-------------|:--------|
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| readRDS | bin | 1577 | 1000 | 633 | 112 |
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| saveRDS | bin | 2042 | 1000 | 489 | 112 |
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| fread | csv | 2925 | 1038 | 410 | 232 |
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| fwrite | csv | 2790 | 1038 | 358 | 241 |
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| read_feather | bin | 3950 | 813 | 253 | 112 |
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| write_feather | bin | 1820 | 813 | 549 | 112 |
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| **read_fst** | **bin** | **457** | **303** | **2184** | **282** |
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| **write_fst** | **bin** | **314** | **303** | **3180** | **291** |
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These benchmarks were performed on a laptop (i7 4710HQ @2.5 GHz) with a
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reasonably fast SSD (M.2 Samsung SM951) using the dataset defined below.
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## Basic usage
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Using *fst* is simple. Data can be stored and retrieved using methods
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*write\_fst* and *read\_fst*:
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*write_fst* and *read_fst*:
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``` r
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# Generate some random data frame with 10 million rows and various column types
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This reads rows 2000 to 5000 from columns *Logical* and *Factor* without
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actually touching any other data in the stored file. That means that a
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subset can be read from file **without reading the complete file
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first**. This is different from, say, *readRDS* or *read\_feather* where
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first**. This is different from, say, *readRDS* or *read_feather* where
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you have to read the complete file or column before you can make a
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subset.
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‎cran-checklist.md‎

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- Travis Linux and OSX
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- AppVeyor (Windows Server)
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- latest R dev version on Windows
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* Build packages with dependencies on fst
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* Test packages with dependencies on fst using revdepcheck::revdep_check()
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* Merge develop branch into release branch
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* Bump version to even value in DESCRIPTION and check package startup message
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* Update README.Rmd and verify generated README.md on Github (release)

‎cran-comments.md‎

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## Resubmission
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This resubmission of fst (v0.9.4) addresses the submission comments of Dr. Uwe Ligges on the package title and URL.
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## Submission
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This submission of fst (v0.9.4) addresses Prof. Brian Ripley's request to fix problems shown in updated CRAN checks. Packages that are in Suggests are now used conditionally in the package code and tests.
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This submission of fst (v0.9.6) addresses package build errors caused by the incorrect use of the size argument in
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sample.int() as reported by Prof Ripley.
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## Test environments
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* OSX on travis-ci (version 10.13.6)
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* Ubuntu 16.04.6 LTS on travis-ci
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* macOS 11.6.2 20G314 using R 4.1.2 on github build infrastructure
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* Ubuntu 20.04.3 LTS using R version 4.0.5 on github build infrastructure
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* Ubuntu 20.04.3 LTS using R 4.1.2 on github build infrastructure
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* Ubuntu 20.04.3 LTS using R dev (2022-01-30 r81596) on github build infrastructure
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* Microsoft Windows Server 2019 10.0.17763 Datacenter using R 4.1.2 on github build infrastructure
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* Ubuntu 18.04 locally using clang-10.0
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* Docker with the rocker/r-devel-ubsan-clang instrumented image
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* Local Ubuntu with instrumented image using clang-10
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* Windows 10 local R 3.6.4
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* Windows 10 local R-dev 4.0.2
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* Windows 10 local R 3.6.3
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* Singularity-container package for running rchk on Ubuntu 18.04
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* Valgrind on Ubuntu 18.04
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* Rhub (all available systems)
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There are no errors or warnings.
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## Downstream dependencies
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I have run R CMD check on downstream dependencies and found no issues. The notes on the grattan and tidyfst packages are unrelated to fst.
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-- CHECKED 15 packages --
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disk.frame 0.3.7
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drake 7.12.4
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epwshiftr 0.1.1
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expss 0.10.6
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grattan 1.9.0.0 -> 1 note unrelated to fst
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hdd 0.1.0
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heims 0.4.0
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lazyarray 1.1.0
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prt 0.1.0
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qtl2fst 0.22-7
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raveio 0.0.3
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readabs 0.4.3
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rio 0.5.16
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tidyfst 0.9.8 -> 1 note unrelated to fst
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tidyft 0.4.5 -> 1 note unrelated to fst
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## revdepcheck results
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We checked 29 reverse dependencies (26 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
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* We saw 0 new problems
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* We failed to check 0 packages

‎src/RcppExports.cpp‎

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using namespace Rcpp;
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#ifdef RCPP_USE_GLOBAL_ROSTREAM
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Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
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Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
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#endif
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// fstlib_version
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int fstlib_version();
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RcppExport SEXP _fst_fstlib_version() {

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