Merge branch 'hotfix'

Author: MarcusKlik

.Rbuildignore

@@ -14,6 +14,7 @@ LZ4/LICENSE$
 \.png$
 \.yml$
 ^dataset\.fst$
-^res - readme\.fst$
+^res_readme\.fst$
 ^_pkgdown\.yml$
 ^CRAN-RELEASE$
+^revdep$

.travis.yml

@@ -1,12 +1,12 @@
-language: R
+language: r
 cache: packages
-sudo: false
 warnings_are_errors: true
 
 r:
   - oldrel
   - release
   - devel
+
 os:
   - linux
   - osx
@@ -15,12 +15,11 @@ matrix:
   exclude:
   - r: devel
     os: osx
+  - r: oldrel
+    os: osx
 
-before_install:
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install llvm &&
-    export PATH="/usr/local/opt/llvm/bin:$PATH" &&
-    export LDFLAGS="-L/usr/local/opt/llvm/lib" &&
-    export CPPFLAGS="-I/usr/local/opt/llvm/include"; fi
+brew_packages:
+  - llvm
 
 r_packages:
   - covr

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: fst
 Type: Package
-Title: Lightning Fast Serialization of Data Frames for R
+Title: Lightning Fast Serialization of Data Frames
 Description: Multithreaded serialization of compressed data frames using the
     'fst' format. The 'fst' format allows for random access of stored data and
     compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD
     compression library is owned by Facebook Inc.
-Version: 0.9.2
-Date: 2020-03-31
+Version: 0.9.4
+Date: 2020-08-26
 Authors@R: c(
     person("Mark", "Klik", email = "[email protected]", role = c("aut", "cre", "cph")),
     person("Yann", "Collet", role = c("ctb", "cph"),
@@ -19,7 +19,7 @@ Imports:
     Rcpp
 LinkingTo: Rcpp
 SystemRequirements: little-endian platform
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Suggests:
     testthat,
     bit64,
@@ -32,5 +32,5 @@ Encoding: UTF-8
 Copyright: This package includes sources from the LZ4 library written
     by Yann Collet, sources of the ZSTD library owned by Facebook, Inc.
     and sources of the fstlib library owned by Mark Klik
-URL: https://fstpackage.github.io
+URL: http://www.fstpackage.org
 BugReports: https://github.com/fstpackage/fst/issues

NEWS.md

@@ -1,9 +1,16 @@
 
+# fst 0.9.4
+
+Version 0.9.4 is a minor update to 'hotfix' an issue with suggested packages as reported by CRAN.
+
+## Bugs solved
+
+* Packages `nanotime`, `bit64` and `lintr` are now used conditionally as is required for packages suggested in DESCRIPTION, see 'Writing R Extensions' 1.1.3.1 (thanks @CRAN for reporting)
+
+
 # fst 0.9.2
 
-Version 0.9.2 of the `fst` package brings support for zero-row table serialization and compression for long vectors. In
-addition, `fst` was prepared for the change in the default settings for the stringsAsFactors argument (data.frame) in
-R 4.0.0.
+Version 0.9.2 of the `fst` package brings support for zero-row table serialization and compression for long vectors. In addition, `fst` was prepared for the change in the default settings for the stringsAsFactors argument (data.frame) in R 4.0.0.
 
 ## Library updates
 

R/RcppExports.R

@@ -21,12 +21,12 @@ fsthasher <- function(rawVec, seed, blockHash) {
     .Call(`_fst_fsthasher`, rawVec, seed, blockHash)
 }
 
-fstcomp <- function(rawVec, compressor, compression, hash, r_container) {
-    .Call(`_fst_fstcomp`, rawVec, compressor, compression, hash, r_container)
+fstcomp <- function(rawVec, compressor, compression, hash) {
+    .Call(`_fst_fstcomp`, rawVec, compressor, compression, hash)
 }
 
-fstdecomp <- function(rawVec, r_container) {
-    .Call(`_fst_fstdecomp`, rawVec, r_container)
+fstdecomp <- function(rawVec) {
+    .Call(`_fst_fstdecomp`, rawVec)
 }
 
 getnrofthreads <- function() {

R/compress.R

@@ -44,8 +44,7 @@ compress_fst <- function(x, compressor = "ZSTD", compression = 0, hash = FALSE)
     stop("Parameter x is not set to a raw vector.")
   }
 
-  container <- as.list(1)
-  compressed_vec <- fstcomp(x, compressor, as.integer(compression), hash, container)
+  compressed_vec <- fstcomp(x, compressor, as.integer(compression), hash)
 
   if (inherits(compressed_vec, "fst_error")) {
     stop(compressed_vec)
@@ -67,8 +66,7 @@ decompress_fst <- function(x) {
     stop("Parameter x should be a raw vector with compressed data.")
   }
 
-  container <- as.list(1)
-  decompressed_vec <- fstdecomp(x, container)
+  decompressed_vec <- fstdecomp(x)
 
   if (inherits(decompressed_vec, "fst_error")) {
     stop(decompressed_vec)

README.Rmd

@@ -36,7 +36,7 @@ require(data.table)
 require(fst)
 require(knitr)
 
-speed_results <- read_fst("res - readme.fst", as.data.table = TRUE)
+speed_results <- read_fst("res_readme.fst", as.data.table = TRUE)
 
 speeds <- speed_results[NrOfRows == 5e7, list(
   `Time (ms)` = as.integer(median(Time)),

cran-checklist.md

@@ -15,20 +15,20 @@
 * Update README.Rmd and verify generated README.md on Github (release)
 * Update cran_comments.md
 * Build docs folder using pkgdown::build_site()
-* Update NEWS.md and make sure to remove '(in development)' in the version title
-  and update the version number
+* Update NEWS.md and make sure to remove '(in development)' in the version title and update version number
 * Credit all GitHub contributions in NEWS.md
 * Submit to CRAN
 
 # After releasing to CRAN
 
 * Update NEWS.md with the release date
+* Build docs folder using pkgdown::build_site(). Check that the package date is correct.
 * Merge branch release into master
 * Tag the release on Github
-* Commit the fstpackage.github.io repository with the latest docs
-* Merge branch master into release
+* Commit latest docs to the fstpackage.github.io and fstpackage.github.io/fst repository
 * Go to the repository release page and create a new release with tag version vx.y.z.
   Copy and paste the contents of the relevant NEWS.md section into the release notes.
+* Merge branch master into release
 * Add '(in development)' to version title in NEWS.md and update to odd version number
 * Check package startup message
 * Merge release branch into develop

cran-comments.md

@@ -1,29 +1,23 @@
 
-## Resubmission 2
+## Resubmission
 
-Resubmission 1 failed on clang-10 ubsan warnings ("adding offset to a null pointer"). These warnings have been fixed locally and checked on a local instrumented build using clang-10 on Ubuntu 18.04.4 (thanks Prof Hornik and Prof Ripley for the pointers).
-
-## Resubmission 1
-
-The pre-checks for my original submission failed on a specific warning in the included ZSTD compressor component (from Facebook). To remedy this, I've adapted the C++ macro responsible for the warning and all corresponding calls. This could be safely done as the macro is only activated in a specially prepared DEBUG build and therefore it is not used bycalls from the fst package. I have raised an issue with the ZSTD team addressing this problem (see https://github.com/facebook/zstd/issues/2035).
+This resubmission of fst (v0.9.4) addresses the submission comments of Dr. Uwe Ligges on the package title and URL.
 
 ## Submission
 
-This submission of fst (v0.9.2) addresses Dr. Kurt Hornik's request to fix problems shown for the r-devel checks. These issues are related to the new stringsAsFactors = FALSE default, which is planned for R 4.0.0.
+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.
 
 ## Test environments 
 
 * OSX on travis-ci (version 10.13.6)
-* Ubuntu Ubuntu 16.04.6 LTS on travis-ci
-* Ubuntu 19.10 locally
-* Ubuntu 19.10 locally using clang-6.0
+* Ubuntu 16.04.6 LTS on travis-ci
+* Ubuntu 18.04 locally using clang-10.0
 * Docker with the rocker/r-devel-ubsan-clang instrumented image
-* Local Ubuntu with instrumenten image using clang-10
+* Local Ubuntu with instrumented image using clang-10
 * Windows 10 local R 3.6.4
-* Windows 10 local R-dev 4.0.0 pre-release (r77640)
-* Windows Server 2012 R2 x64 (build 9600) on AppVeyor (R 3.6.3)
-* Singularity-container package for running rchk on Ubuntu 18.10
-* Valgrind on Ubuntu 19.10.
+* Windows 10 local R-dev 4.0.2
+* Singularity-container package for running rchk on Ubuntu 18.04
+* Valgrind on Ubuntu 18.04
 * Rhub (all available systems)
 
 ## R CMD check results
@@ -34,14 +28,20 @@ There are no errors or warnings.
 
 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.
 
--- CHECKED 9 packages --
-
-disk.frame 0.3.4
-drake 7.11.0
-expss 0.10.1
-grattan 1.8.0.0 ->  1 note unrelated to fst
-hdd 0.1.0
-heims 0.4.0
-readabs 0.4.3
-rio 0.5.16
-tidyfst 0.7.7 ->  1 note unrelated to fst
+-- CHECKED 15 packages --
+
+disk.frame  0.3.7
+drake       7.12.4
+epwshiftr   0.1.1
+expss       0.10.6
+grattan     1.9.0.0 ->  1 note unrelated to fst
+hdd         0.1.0
+heims       0.4.0
+lazyarray   1.1.0
+prt         0.1.0
+qtl2fst     0.22-7
+raveio      0.0.3
+readabs     0.4.3
+rio         0.5.16
+tidyfst     0.9.8 ->  1 note unrelated to fst
+tidyft      0.4.5 ->  1 note unrelated to fst