Last updated on 2025-12-28 11:49:39 CET.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| glow | 2 | 11 | ||
| qs | 6 | 1 | 5 | 1 |
| qs2 | 8 | 5 | ||
| seqtrie | 3 | 10 | ||
| stringfish | 8 | 5 |
Current CRAN status: NOTE: 2, OK: 11
Version: 0.13.0
Check: installed package size
Result: NOTE
installed size is 11.5Mb
sub-directories of 1Mb or more:
doc 1.3Mb
libs 9.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: ERROR: 6, WARN: 1, NOTE: 5, OK: 1
Version: 0.27.3
Check: compiled code
Result: WARN
File ‘qs/libs/qs.so’:
Found non-API calls to R: ‘ATTRIB’, ‘CLOENV’, ‘ENCLOS’, ‘FRAME’,
‘HASHTAB’, ‘IS_S4_OBJECT’, ‘LEVELS’, ‘OBJECT’, ‘PRENV’,
‘Rf_allocSExp’, ‘SETLEVELS’, ‘SET_ATTRIB’, ‘SET_CLOENV’,
‘SET_ENCLOS’, ‘SET_FRAME’, ‘SET_HASHTAB’, ‘SET_OBJECT’,
‘SET_PRENV’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’
These entry points may be removed soon:
‘SET_FRAME’, ‘SET_HASHTAB’, ‘SET_ENCLOS’, ‘SET_S4_OBJECT’, ‘FRAME’, ‘HASHTAB’, ‘IS_S4_OBJECT’, ‘CLOENV’, ‘ENCLOS’, ‘OBJECT’, ‘SET_CLOENV’, ‘LEVELS’, ‘SETLEVELS’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.27.3
Check: tests
Result: ERROR
Running ‘correctness_testing.R’ [178s/189s]
Running ‘qattributes_testing.R’ [39s/47s]
Running ‘qsavemload_testing.R’ [2s/2s]
Running the tests in ‘tests/qattributes_testing.R’ failed.
Complete output:
> total_time <- Sys.time()
>
> suppressMessages(library(Rcpp))
> suppressMessages(library(dplyr))
> suppressMessages(library(data.table))
> suppressMessages(library(qs))
> suppressMessages(library(stringfish))
> options(warn = 1)
>
> do_gc <- function() {
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ gc(full = TRUE)
+ } else {
+ gc()
+ }
+ }
>
> # because sourceCpp uses setwd, we need absolute path to R_TESTS when run within R CMD check
> R_TESTS <- Sys.getenv("R_TESTS") # startup.Rs
> if (nzchar(R_TESTS)) {
+ R_TESTS_absolute <- normalizePath(R_TESTS)
+ Sys.setenv(R_TESTS = R_TESTS_absolute)
+ }
> sourceCpp(code="#include <Rcpp.h>
+ using namespace Rcpp;
+ // [[Rcpp::plugins(cpp11)]]
+ // [[Rcpp::export(rng=false)]]
+ CharacterVector splitstr(std::string x, std::vector<double> cuts){
+ CharacterVector ret(cuts.size() - 1);
+ for(uint64_t i=1; i<cuts.size(); i++) {
+ ret[i-1] = x.substr(std::round(cuts[i-1])-1, std::round(cuts[i])-std::round(cuts[i-1]));
+ }
+ return ret;
+ }
+ // [[Rcpp::export(rng=false)]]
+ int setlev(SEXP x, int i) {
+ return SETLEVELS(x,i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ void setobj(SEXP x, int i) {
+ return SET_OBJECT(x, i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ List generateList(std::vector<int> list_elements){
+ auto randchar = []() -> char
+ {
+ const char charset[] =
+ \"0123456789\"
+ \"ABCDEFGHIJKLMNOPQRSTUVWXYZ\"
+ \"abcdefghijklmnopqrstuvwxyz\";
+ const size_t max_index = (sizeof(charset) - 1);
+ return charset[ rand() % max_index ];
+ };
+ List ret(list_elements.size());
+ std::string str(10,0);
+ for(size_t i=0; i<list_elements.size(); i++) {
+ switch(list_elements[i]) {
+ case 1:
+ ret[i] = R_NilValue;
+ break;
+ case 2:
+ std::generate_n( str.begin(), 10, randchar );
+ ret[i] = str;
+ break;
+ case 3:
+ ret[i] = rand();
+ break;
+ case 4:
+ ret[i] = static_cast<double>(rand());
+ break;
+ }
+ }
+ return ret;
+ }")
> if (nzchar(R_TESTS)) Sys.setenv(R_TESTS = R_TESTS)
>
> args <- commandArgs(T)
> if (nzchar(R_TESTS) || ((length(args) > 0) && args[1] == "check")) { # do fewer tests within R CMD check so it completes within a reasonable amount of time
+ reps <- 2
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6)
+ test_points_slow <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16) # for Character Vector, stringfish and list
+ max_size <- 1e6
+ } else {
+ reps <- 3
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6, 1e7)
+ test_points_slow <- test_points
+ max_size <- 1e7
+ }
> myfile <- tempfile()
>
> obj_size <- 0
> get_obj_size <- function() {
+ get("obj_size", envir = globalenv())
+ }
> set_obj_size <- function(x) {
+ assign("obj_size", get_obj_size() + as.numeric(object.size(x)), envir = globalenv())
+ return(get_obj_size());
+ }
> random_object_generator <- function(N, with_envs = FALSE) { # additional input: global obj_size, max_size
+ if (sample(3, 1) == 1) {
+ ret <- as.list(1:N)
+ } else if (sample(2, 1) == 1) {
+ ret <- as.pairlist(1:N)
+ } else {
+ ret <- as.pairlist(1:N)
+ setlev(ret, sample(2L^12L, 1L) - 1L)
+ setobj(ret, 1L)
+ }
+
+ for (i in 1:N) {
+ if (get_obj_size() > get("max_size", envir = globalenv())) break;
+ otype <- sample(12, size = 1)
+ z <- NULL
+ is_attribute <- ifelse(i == 1, F, sample(c(F, T), size = 1))
+ if (otype == 1) {z <- rnorm(1e4); set_obj_size(z);}
+ else if (otype == 2) { z <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (otype == 3) { z <- sample(c(T, F, NA), size = 1e4, replace = T); set_obj_size(z); }
+ else if (otype == 4) { z <- (sample(256, size = 1e4, replace = T) - 1) %>% as.raw; set_obj_size(z); }
+ else if (otype == 5) { z <- replicate(sample(1e4, size = 1), {rep(letters, length.out = sample(10, size = 1)) %>% paste(collapse = "")}); set_obj_size(z); }
+ else if (otype == 6) { z <- rep(letters, length.out = sample(1e4, size = 1)) %>% paste(collapse = ""); set_obj_size(z); }
+ else if (otype == 7) { z <- as.formula("y ~ a + b + c : d", env = globalenv()); attr(z, "blah") <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (with_envs && otype %in% c(8, 9)) { z <- function(x) {x + runif(1)} }
+ # else if(with_envs && otype %in% c(10,11)) { z <- new.env(); z$x <- random_object_generator(N, with_envs); makeActiveBinding("y", function() runif(1), z) }
+ else { z <- random_object_generator(N, with_envs) }
+ if (is_attribute) {
+ attr(ret[[i - 1]], runif(1) %>% as.character()) <- z
+ } else {
+ ret[[i]] <- z
+ }
+ }
+ return(ret)
+ }
>
> rand_strings <- function(n) {
+ s <- sample(0:100, size = n, replace = T)
+ x <- lapply(unique(s), function(si) {
+ stringfish::random_strings(sum(s == si), si, vector_mode = "normal")
+ }) %>% unlist %>% sample
+ x[sample(n, size = n/10)] <- NA
+ return(x)
+ }
>
> nested_tibble <- function() {
+ sub_tibble <- function(nr = 600, nc = 4) {
+ z <- lapply(1:nc, function(i) rand_strings(nr)) %>%
+ setNames(make.unique(paste0(sample(letters, nc), rand_strings(nc)))) %>%
+ bind_cols %>%
+ as_tibble
+ }
+ tibble(
+ col1 = rand_strings(100),
+ col2 = rand_strings(100),
+ col3 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col4 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col5 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4))
+ ) %>% setNames(make.unique(paste0(sample(letters, 5), rand_strings(5))))
+ }
>
> printCarriage <- function(x) {
+ cat(x, "\r")
+ }
>
> attributes_serialize_identical <- function(attributes, full_object) {
+ identical(serialize(attributes(full_object), NULL), serialize(attributes, NULL))
+ }
>
> attributes_identical <- function(attributes, full_object) {
+ identical(attributes, attributes(full_object))
+ }
>
> ################################################################################################
>
> qsave_rand <- function(x, file) {
+ alg <- sample(c("lz4", "zstd", "lz4hc", "zstd_stream", "uncompressed"), 1)
+ # alg <- "zstd_stream"
+ nt <- sample(5,1)
+ sc <- sample(0:15,1)
+ cl <- sample(10,1)
+ ch <- sample(c(T,F),1)
+ qsave(x, file = file, preset = "custom", algorithm = alg,
+ compress_level = cl, shuffle_control = sc, nthreads = nt, check_hash = ch)
+ }
>
> qattributes_rand <- function(file) {
+ # ar <- sample(c(T,F),1)
+ # don't use altrep to avoid serialization differences
+ # attributes_serialize_identical won't pass with ALTREP
+ ar <- FALSE
+ nt <- sample(5,1)
+ qattributes(file, use_alt_rep = ar, nthreads = nt, strict = T)
+ }
>
> ################################################################################################
>
> for (q in 1:reps) {
+ cat("Rep", q, "of", reps, "\n")
+ # String correctness
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rep(letters, length.out = tp) %>% paste(collapse = "")
+ x1 <- c(NA, "", x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("strings: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Character vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ # qs_use_alt_rep(F)
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Character Vectors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # stringfish character vectors -- require R > 3.5.0
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ x1 <- stringfish::convert_to_sf(x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Stringfish: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+ }
+
+ # Integers
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- sample(1:tp, replace = T)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Integers: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Doubles
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rnorm(tp)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Numeric: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Logical
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+
+ x1 <- sample(c(T, F, NA), replace = T, size = tp)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Logical: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ # List
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- generateList(sample(1:4, replace = T, size = tp))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("List: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.frame(str = x1,num = runif(1:1000), stringsAsFactors = F)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Data.frame test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.table(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_serialize_identical(z, x1))
+ }
+ cat("Data.table test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- tibble(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Tibble test")
+ cat("\n")
+
+ # Encoding test
+ if (Sys.info()[['sysname']] != "Windows") {
+ for (i in 1:3) {
+ x1 <- "己所不欲，勿施于人" # utf 8
+ x2 <- x1
+ Encoding(x2) <- "latin1"
+ x3 <- x1
+ Encoding(x3) <- "bytes"
+ x4 <- rep(x1, x2, length.out = 1e4) %>% paste(collapse = ";")
+ x1 <- c(x1, x2, x3, x4)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage("Encoding test")
+ } else {
+ printCarriage("(Encoding test not run on windows)")
+ }
+ cat("\n")
+
+ # complex vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ re <- rnorm(tp)
+ im <- runif(tp)
+ x1 <- complex(real = re, imaginary = im)
+ x1 <- c(NA_complex_, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Complex: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # factors
+ for (tp in test_points) {
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- factor(rep(letters, length.out = tp), levels = sample(letters), ordered = TRUE)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Factors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Random objects
+ time <- vector("numeric", length = 8)
+ for (i in 1:8) {
+ # qs_use_alt_rep(sample(c(T, F), size = 1))
+ obj_size <- 0
+ x1 <- random_object_generator(12)
+ printCarriage(sprintf("Random objects: %s bytes", object.size(x1) %>% as.numeric))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Random objects: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # nested attributes
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- as.list(1:26)
+ attr(x1[[26]], letters[26]) <- rnorm(100)
+ for (i in 25:1) {
+ attr(x1[[i]], letters[i]) <- x1[[i + 1]]
+ }
+ time[i] <- Sys.time()
+ for(j in 1:length(x1)) {
+ qsave_rand(x1[[j]], file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1[[j]]))
+ }
+ }
+ printCarriage(sprintf("Nested attributes: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # alt-rep -- should serialize the unpacked object
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- 1:max_size
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Alt rep integer: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+
+ # Environment test
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- new.env()
+ x1[["a"]] <- 1:max_size
+ x1[["b"]] <- runif(max_size)
+ x1[["c"]] <- stringfish::random_strings(1e4, vector_mode = "normal")
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z[["a"]], x1[["a"]]))
+ stopifnot(attributes_identical(z[["b"]], x1[["b"]]))
+ stopifnot(attributes_identical(z[["c"]], x1[["c"]]))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("Environment test: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- nested_tibble()
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z, x1))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("nested tibble test: %s s", signif(mean(time), 4)))
+ cat("\n")
+ }
Rep 1 of 2
strings: 0, 0.05082 s
strings: 1, 0.04919 s
strings: 2, 0.008973 s
strings: 4, 0.005316 s
strings: 8, 0.003118 s
strings: 31, 0.009231 s
strings: 33, 0.002765 s
strings: 32, 0.006517 s
strings: 255, 0.007391 s
strings: 257, 0.01696 s
strings: 256, 0.000517 s
strings: 65535, 0.01118 s
strings: 65537, 0.01243 s
strings: 65536, 0.004347 s
strings: 1e+06, 0.01022 s
Character Vectors: 0, 0.004165 s
Character Vectors: 1, 0.003115 s
Character Vectors: 2, 0.002115 s
Character Vectors: 4, 0.001147 s
Character Vectors: 8, 0.001371 s
Character Vectors: 31, 0.001967 s
Character Vectors: 33, 0.001322 s
Character Vectors: 32, 0.005508 s
Character Vectors: 255, 0.004501 s
Character Vectors: 257, 0.001548 s
Character Vectors: 256, 0.002847 s
Character Vectors: 65535, 0.004328 s
Character Vectors: 65537, 0.009387 s
Character Vectors: 65536, 0.003019 s
Stringfish: 0, 0.005564 s
Stringfish: 1, 0.001372 s
Stringfish: 2, 0.00573 s
Stringfish: 4, 0.004982 s
Stringfish: 8, 0.002257 s
Stringfish: 31, 0.0015 s
Stringfish: 33, 0.002526 s
Stringfish: 32, 0.002396 s
Stringfish: 255, 0.004095 s
Stringfish: 257, 0.004547 s
Stringfish: 256, 0.001465 s
Stringfish: 65535, 0.00436 s
Stringfish: 65537, 0.002645 s
Stringfish: 65536, 0.007699 s
Integers: 0, 0.002357 s
Integers: 1, 0.005929 s
Integers: 2, 0.001978 s
Integers: 4, 0.004432 s
Integers: 8, 0.006345 s
Integers: 31, 0.005554 s
Integers: 33, 0.003979 s
Integers: 32, 0.006441 s
Integers: 255, 0.0256 s
Integers: 257, 0.01089 s
Integers: 256, 0.006044 s
Integers: 65535, 0.01006 s
Integers: 65537, 0.004668 s
Integers: 65536, 0.003862 s
Integers: 1e+06, 0.02997 s
Numeric: 0, 0.005556 s
Numeric: 1, 0.01232 s
Numeric: 2, 0.002847 s
Numeric: 4, 0.008062 s
Numeric: 8, 0.008895 s
Numeric: 31, 0.005278 s
Numeric: 33, 0.006554 s
Numeric: 32, 0.005155 s
Numeric: 255, 0.006816 s
Numeric: 257, 0.006588 s
Numeric: 256, 0.01038 s
Numeric: 65535, 0.01922 s
Numeric: 65537, 0.01018 s
Numeric: 65536, 0.003398 s
Numeric: 1e+06, 0.3119 s
Logical: 0, 0.006727 s
Logical: 1, 0.005169 s
Logical: 2, 0.00521 s
Logical: 4, 0.004765 s
Logical: 8, 0.003067 s
Logical: 31, 0.001708 s
Logical: 33, 0.02264 s
Logical: 32, 0.006852 s
Logical: 255, 0.004009 s
Logical: 257, 0.002161 s
Logical: 256, 0.00761 s
Logical: 65535, 0.005156 s
Logical: 65537, 0.00699 s
Logical: 65536, 0.009592 s
Logical: 1e+06, 0.0419 s
List: 0, 0.001232 s
List: 1, 0.01558 s
List: 2, 0.007583 s
List: 4, 0.0004638 s
List: 8, 0.006926 s
List: 31, 0.001081 s
List: 33, 0.002559 s
List: 32, 0.004397 s
List: 255, 0.02702 s
List: 257, 0.003988 s
List: 256, 0.008714 s
List: 65535, 0.02735 s
List: 65537, 0.032 s
List: 65536, 0.02981 s
Data.frame test
Error: attributes_serialize_identical(z, x1) is not TRUE
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.27.3
Check: tests
Result: ERROR
Running ‘correctness_testing.R’ [156s/161s]
Running ‘qattributes_testing.R’ [34s/38s]
Running ‘qsavemload_testing.R’ [1s/2s]
Running the tests in ‘tests/qattributes_testing.R’ failed.
Complete output:
> total_time <- Sys.time()
>
> suppressMessages(library(Rcpp))
> suppressMessages(library(dplyr))
> suppressMessages(library(data.table))
> suppressMessages(library(qs))
> suppressMessages(library(stringfish))
> options(warn = 1)
>
> do_gc <- function() {
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ gc(full = TRUE)
+ } else {
+ gc()
+ }
+ }
>
> # because sourceCpp uses setwd, we need absolute path to R_TESTS when run within R CMD check
> R_TESTS <- Sys.getenv("R_TESTS") # startup.Rs
> if (nzchar(R_TESTS)) {
+ R_TESTS_absolute <- normalizePath(R_TESTS)
+ Sys.setenv(R_TESTS = R_TESTS_absolute)
+ }
> sourceCpp(code="#include <Rcpp.h>
+ using namespace Rcpp;
+ // [[Rcpp::plugins(cpp11)]]
+ // [[Rcpp::export(rng=false)]]
+ CharacterVector splitstr(std::string x, std::vector<double> cuts){
+ CharacterVector ret(cuts.size() - 1);
+ for(uint64_t i=1; i<cuts.size(); i++) {
+ ret[i-1] = x.substr(std::round(cuts[i-1])-1, std::round(cuts[i])-std::round(cuts[i-1]));
+ }
+ return ret;
+ }
+ // [[Rcpp::export(rng=false)]]
+ int setlev(SEXP x, int i) {
+ return SETLEVELS(x,i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ void setobj(SEXP x, int i) {
+ return SET_OBJECT(x, i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ List generateList(std::vector<int> list_elements){
+ auto randchar = []() -> char
+ {
+ const char charset[] =
+ \"0123456789\"
+ \"ABCDEFGHIJKLMNOPQRSTUVWXYZ\"
+ \"abcdefghijklmnopqrstuvwxyz\";
+ const size_t max_index = (sizeof(charset) - 1);
+ return charset[ rand() % max_index ];
+ };
+ List ret(list_elements.size());
+ std::string str(10,0);
+ for(size_t i=0; i<list_elements.size(); i++) {
+ switch(list_elements[i]) {
+ case 1:
+ ret[i] = R_NilValue;
+ break;
+ case 2:
+ std::generate_n( str.begin(), 10, randchar );
+ ret[i] = str;
+ break;
+ case 3:
+ ret[i] = rand();
+ break;
+ case 4:
+ ret[i] = static_cast<double>(rand());
+ break;
+ }
+ }
+ return ret;
+ }")
> if (nzchar(R_TESTS)) Sys.setenv(R_TESTS = R_TESTS)
>
> args <- commandArgs(T)
> if (nzchar(R_TESTS) || ((length(args) > 0) && args[1] == "check")) { # do fewer tests within R CMD check so it completes within a reasonable amount of time
+ reps <- 2
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6)
+ test_points_slow <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16) # for Character Vector, stringfish and list
+ max_size <- 1e6
+ } else {
+ reps <- 3
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6, 1e7)
+ test_points_slow <- test_points
+ max_size <- 1e7
+ }
> myfile <- tempfile()
>
> obj_size <- 0
> get_obj_size <- function() {
+ get("obj_size", envir = globalenv())
+ }
> set_obj_size <- function(x) {
+ assign("obj_size", get_obj_size() + as.numeric(object.size(x)), envir = globalenv())
+ return(get_obj_size());
+ }
> random_object_generator <- function(N, with_envs = FALSE) { # additional input: global obj_size, max_size
+ if (sample(3, 1) == 1) {
+ ret <- as.list(1:N)
+ } else if (sample(2, 1) == 1) {
+ ret <- as.pairlist(1:N)
+ } else {
+ ret <- as.pairlist(1:N)
+ setlev(ret, sample(2L^12L, 1L) - 1L)
+ setobj(ret, 1L)
+ }
+
+ for (i in 1:N) {
+ if (get_obj_size() > get("max_size", envir = globalenv())) break;
+ otype <- sample(12, size = 1)
+ z <- NULL
+ is_attribute <- ifelse(i == 1, F, sample(c(F, T), size = 1))
+ if (otype == 1) {z <- rnorm(1e4); set_obj_size(z);}
+ else if (otype == 2) { z <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (otype == 3) { z <- sample(c(T, F, NA), size = 1e4, replace = T); set_obj_size(z); }
+ else if (otype == 4) { z <- (sample(256, size = 1e4, replace = T) - 1) %>% as.raw; set_obj_size(z); }
+ else if (otype == 5) { z <- replicate(sample(1e4, size = 1), {rep(letters, length.out = sample(10, size = 1)) %>% paste(collapse = "")}); set_obj_size(z); }
+ else if (otype == 6) { z <- rep(letters, length.out = sample(1e4, size = 1)) %>% paste(collapse = ""); set_obj_size(z); }
+ else if (otype == 7) { z <- as.formula("y ~ a + b + c : d", env = globalenv()); attr(z, "blah") <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (with_envs && otype %in% c(8, 9)) { z <- function(x) {x + runif(1)} }
+ # else if(with_envs && otype %in% c(10,11)) { z <- new.env(); z$x <- random_object_generator(N, with_envs); makeActiveBinding("y", function() runif(1), z) }
+ else { z <- random_object_generator(N, with_envs) }
+ if (is_attribute) {
+ attr(ret[[i - 1]], runif(1) %>% as.character()) <- z
+ } else {
+ ret[[i]] <- z
+ }
+ }
+ return(ret)
+ }
>
> rand_strings <- function(n) {
+ s <- sample(0:100, size = n, replace = T)
+ x <- lapply(unique(s), function(si) {
+ stringfish::random_strings(sum(s == si), si, vector_mode = "normal")
+ }) %>% unlist %>% sample
+ x[sample(n, size = n/10)] <- NA
+ return(x)
+ }
>
> nested_tibble <- function() {
+ sub_tibble <- function(nr = 600, nc = 4) {
+ z <- lapply(1:nc, function(i) rand_strings(nr)) %>%
+ setNames(make.unique(paste0(sample(letters, nc), rand_strings(nc)))) %>%
+ bind_cols %>%
+ as_tibble
+ }
+ tibble(
+ col1 = rand_strings(100),
+ col2 = rand_strings(100),
+ col3 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col4 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col5 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4))
+ ) %>% setNames(make.unique(paste0(sample(letters, 5), rand_strings(5))))
+ }
>
> printCarriage <- function(x) {
+ cat(x, "\r")
+ }
>
> attributes_serialize_identical <- function(attributes, full_object) {
+ identical(serialize(attributes(full_object), NULL), serialize(attributes, NULL))
+ }
>
> attributes_identical <- function(attributes, full_object) {
+ identical(attributes, attributes(full_object))
+ }
>
> ################################################################################################
>
> qsave_rand <- function(x, file) {
+ alg <- sample(c("lz4", "zstd", "lz4hc", "zstd_stream", "uncompressed"), 1)
+ # alg <- "zstd_stream"
+ nt <- sample(5,1)
+ sc <- sample(0:15,1)
+ cl <- sample(10,1)
+ ch <- sample(c(T,F),1)
+ qsave(x, file = file, preset = "custom", algorithm = alg,
+ compress_level = cl, shuffle_control = sc, nthreads = nt, check_hash = ch)
+ }
>
> qattributes_rand <- function(file) {
+ # ar <- sample(c(T,F),1)
+ # don't use altrep to avoid serialization differences
+ # attributes_serialize_identical won't pass with ALTREP
+ ar <- FALSE
+ nt <- sample(5,1)
+ qattributes(file, use_alt_rep = ar, nthreads = nt, strict = T)
+ }
>
> ################################################################################################
>
> for (q in 1:reps) {
+ cat("Rep", q, "of", reps, "\n")
+ # String correctness
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rep(letters, length.out = tp) %>% paste(collapse = "")
+ x1 <- c(NA, "", x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("strings: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Character vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ # qs_use_alt_rep(F)
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Character Vectors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # stringfish character vectors -- require R > 3.5.0
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ x1 <- stringfish::convert_to_sf(x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Stringfish: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+ }
+
+ # Integers
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- sample(1:tp, replace = T)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Integers: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Doubles
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rnorm(tp)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Numeric: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Logical
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+
+ x1 <- sample(c(T, F, NA), replace = T, size = tp)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Logical: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ # List
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- generateList(sample(1:4, replace = T, size = tp))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("List: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.frame(str = x1,num = runif(1:1000), stringsAsFactors = F)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Data.frame test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.table(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_serialize_identical(z, x1))
+ }
+ cat("Data.table test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- tibble(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Tibble test")
+ cat("\n")
+
+ # Encoding test
+ if (Sys.info()[['sysname']] != "Windows") {
+ for (i in 1:3) {
+ x1 <- "己所不欲，勿施于人" # utf 8
+ x2 <- x1
+ Encoding(x2) <- "latin1"
+ x3 <- x1
+ Encoding(x3) <- "bytes"
+ x4 <- rep(x1, x2, length.out = 1e4) %>% paste(collapse = ";")
+ x1 <- c(x1, x2, x3, x4)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage("Encoding test")
+ } else {
+ printCarriage("(Encoding test not run on windows)")
+ }
+ cat("\n")
+
+ # complex vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ re <- rnorm(tp)
+ im <- runif(tp)
+ x1 <- complex(real = re, imaginary = im)
+ x1 <- c(NA_complex_, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Complex: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # factors
+ for (tp in test_points) {
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- factor(rep(letters, length.out = tp), levels = sample(letters), ordered = TRUE)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Factors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Random objects
+ time <- vector("numeric", length = 8)
+ for (i in 1:8) {
+ # qs_use_alt_rep(sample(c(T, F), size = 1))
+ obj_size <- 0
+ x1 <- random_object_generator(12)
+ printCarriage(sprintf("Random objects: %s bytes", object.size(x1) %>% as.numeric))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Random objects: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # nested attributes
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- as.list(1:26)
+ attr(x1[[26]], letters[26]) <- rnorm(100)
+ for (i in 25:1) {
+ attr(x1[[i]], letters[i]) <- x1[[i + 1]]
+ }
+ time[i] <- Sys.time()
+ for(j in 1:length(x1)) {
+ qsave_rand(x1[[j]], file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1[[j]]))
+ }
+ }
+ printCarriage(sprintf("Nested attributes: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # alt-rep -- should serialize the unpacked object
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- 1:max_size
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Alt rep integer: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+
+ # Environment test
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- new.env()
+ x1[["a"]] <- 1:max_size
+ x1[["b"]] <- runif(max_size)
+ x1[["c"]] <- stringfish::random_strings(1e4, vector_mode = "normal")
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z[["a"]], x1[["a"]]))
+ stopifnot(attributes_identical(z[["b"]], x1[["b"]]))
+ stopifnot(attributes_identical(z[["c"]], x1[["c"]]))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("Environment test: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- nested_tibble()
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z, x1))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("nested tibble test: %s s", signif(mean(time), 4)))
+ cat("\n")
+ }
Rep 1 of 2
strings: 0, 0.01085 s
strings: 1, 0.006962 s
strings: 2, 0.002808 s
strings: 4, 0.002623 s
strings: 8, 0.001477 s
strings: 31, 0.001711 s
strings: 33, 0.006057 s
strings: 32, 0.006155 s
strings: 255, 0.003673 s
strings: 257, 0.00862 s
strings: 256, 0.008873 s
strings: 65535, 0.004765 s
strings: 65537, 0.006333 s
strings: 65536, 0.007996 s
strings: 1e+06, 0.004169 s
Character Vectors: 0, 0.004814 s
Character Vectors: 1, 0.0002366 s
Character Vectors: 2, 0.003968 s
Character Vectors: 4, 0.0003866 s
Character Vectors: 8, 0.001806 s
Character Vectors: 31, 0.002256 s
Character Vectors: 33, 9.012e-05 s
Character Vectors: 32, 0.00252 s
Character Vectors: 255, 0.003198 s
Character Vectors: 257, 0.001387 s
Character Vectors: 256, 0.00246 s
Character Vectors: 65535, 0.003739 s
Character Vectors: 65537, 0.004092 s
Character Vectors: 65536, 0.003651 s
Stringfish: 0, 0.0001485 s
Stringfish: 1, 0.0022 s
Stringfish: 2, 0.000121 s
Stringfish: 4, 0.001541 s
Stringfish: 8, 0.001065 s
Stringfish: 31, 0.002141 s
Stringfish: 33, 0.0005921 s
Stringfish: 32, 0.00125 s
Stringfish: 255, 0.001854 s
Stringfish: 257, 0.004307 s
Stringfish: 256, 8.79e-05 s
Stringfish: 65535, 0.002119 s
Stringfish: 65537, 0.001854 s
Stringfish: 65536, 0.003106 s
Integers: 0, 0.006641 s
Integers: 1, 0.008951 s
Integers: 2, 0.00269 s
Integers: 4, 0.005495 s
Integers: 8, 0.0005256 s
Integers: 31, 0.003309 s
Integers: 33, 0.003532 s
Integers: 32, 0.002321 s
Integers: 255, 0.001837 s
Integers: 257, 0.003143 s
Integers: 256, 0.004272 s
Integers: 65535, 0.003764 s
Integers: 65537, 0.006934 s
Integers: 65536, 0.01165 s
Integers: 1e+06, 0.01543 s
Numeric: 0, 0.002245 s
Numeric: 1, 0.002659 s
Numeric: 2, 0.004527 s
Numeric: 4, 0.0006354 s
Numeric: 8, 0.003986 s
Numeric: 31, 0.001292 s
Numeric: 33, 0.0007136 s
Numeric: 32, 0.007763 s
Numeric: 255, 0.008098 s
Numeric: 257, 0.003168 s
Numeric: 256, 0.01041 s
Numeric: 65535, 0.003644 s
Numeric: 65537, 0.005891 s
Numeric: 65536, 0.01924 s
Numeric: 1e+06, 0.1566 s
Logical: 0, 0.005451 s
Logical: 1, 0.006072 s
Logical: 2, 0.002644 s
Logical: 4, 0.002863 s
Logical: 8, 0.002292 s
Logical: 31, 0.003339 s
Logical: 33, 0.003329 s
Logical: 32, 0.007279 s
Logical: 255, 0.003617 s
Logical: 257, 0.003521 s
Logical: 256, 0.005711 s
Logical: 65535, 0.0006626 s
Logical: 65537, 0.002672 s
Logical: 65536, 0.005417 s
Logical: 1e+06, 0.03373 s
List: 0, 0.007847 s
List: 1, 0.006476 s
List: 2, 0.004522 s
List: 4, 0.00282 s
List: 8, 0.002148 s
List: 31, 0.0009642 s
List: 33, 0.005905 s
List: 32, 0.002962 s
List: 255, 0.0004397 s
List: 257, 0.01159 s
List: 256, 0.01384 s
List: 65535, 0.02417 s
List: 65537, 0.02377 s
List: 65536, 0.02196 s
Data.frame test
Error: attributes_serialize_identical(z, x1) is not TRUE
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.27.3
Check: tests
Result: ERROR
Running ‘correctness_testing.R’ [265s/354s]
Running ‘qattributes_testing.R’ [57s/73s]
Running ‘qsavemload_testing.R’
Running the tests in ‘tests/qattributes_testing.R’ failed.
Complete output:
> total_time <- Sys.time()
>
> suppressMessages(library(Rcpp))
> suppressMessages(library(dplyr))
> suppressMessages(library(data.table))
> suppressMessages(library(qs))
> suppressMessages(library(stringfish))
> options(warn = 1)
>
> do_gc <- function() {
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ gc(full = TRUE)
+ } else {
+ gc()
+ }
+ }
>
> # because sourceCpp uses setwd, we need absolute path to R_TESTS when run within R CMD check
> R_TESTS <- Sys.getenv("R_TESTS") # startup.Rs
> if (nzchar(R_TESTS)) {
+ R_TESTS_absolute <- normalizePath(R_TESTS)
+ Sys.setenv(R_TESTS = R_TESTS_absolute)
+ }
> sourceCpp(code="#include <Rcpp.h>
+ using namespace Rcpp;
+ // [[Rcpp::plugins(cpp11)]]
+ // [[Rcpp::export(rng=false)]]
+ CharacterVector splitstr(std::string x, std::vector<double> cuts){
+ CharacterVector ret(cuts.size() - 1);
+ for(uint64_t i=1; i<cuts.size(); i++) {
+ ret[i-1] = x.substr(std::round(cuts[i-1])-1, std::round(cuts[i])-std::round(cuts[i-1]));
+ }
+ return ret;
+ }
+ // [[Rcpp::export(rng=false)]]
+ int setlev(SEXP x, int i) {
+ return SETLEVELS(x,i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ void setobj(SEXP x, int i) {
+ return SET_OBJECT(x, i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ List generateList(std::vector<int> list_elements){
+ auto randchar = []() -> char
+ {
+ const char charset[] =
+ \"0123456789\"
+ \"ABCDEFGHIJKLMNOPQRSTUVWXYZ\"
+ \"abcdefghijklmnopqrstuvwxyz\";
+ const size_t max_index = (sizeof(charset) - 1);
+ return charset[ rand() % max_index ];
+ };
+ List ret(list_elements.size());
+ std::string str(10,0);
+ for(size_t i=0; i<list_elements.size(); i++) {
+ switch(list_elements[i]) {
+ case 1:
+ ret[i] = R_NilValue;
+ break;
+ case 2:
+ std::generate_n( str.begin(), 10, randchar );
+ ret[i] = str;
+ break;
+ case 3:
+ ret[i] = rand();
+ break;
+ case 4:
+ ret[i] = static_cast<double>(rand());
+ break;
+ }
+ }
+ return ret;
+ }")
> if (nzchar(R_TESTS)) Sys.setenv(R_TESTS = R_TESTS)
>
> args <- commandArgs(T)
> if (nzchar(R_TESTS) || ((length(args) > 0) && args[1] == "check")) { # do fewer tests within R CMD check so it completes within a reasonable amount of time
+ reps <- 2
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6)
+ test_points_slow <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16) # for Character Vector, stringfish and list
+ max_size <- 1e6
+ } else {
+ reps <- 3
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6, 1e7)
+ test_points_slow <- test_points
+ max_size <- 1e7
+ }
> myfile <- tempfile()
>
> obj_size <- 0
> get_obj_size <- function() {
+ get("obj_size", envir = globalenv())
+ }
> set_obj_size <- function(x) {
+ assign("obj_size", get_obj_size() + as.numeric(object.size(x)), envir = globalenv())
+ return(get_obj_size());
+ }
> random_object_generator <- function(N, with_envs = FALSE) { # additional input: global obj_size, max_size
+ if (sample(3, 1) == 1) {
+ ret <- as.list(1:N)
+ } else if (sample(2, 1) == 1) {
+ ret <- as.pairlist(1:N)
+ } else {
+ ret <- as.pairlist(1:N)
+ setlev(ret, sample(2L^12L, 1L) - 1L)
+ setobj(ret, 1L)
+ }
+
+ for (i in 1:N) {
+ if (get_obj_size() > get("max_size", envir = globalenv())) break;
+ otype <- sample(12, size = 1)
+ z <- NULL
+ is_attribute <- ifelse(i == 1, F, sample(c(F, T), size = 1))
+ if (otype == 1) {z <- rnorm(1e4); set_obj_size(z);}
+ else if (otype == 2) { z <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (otype == 3) { z <- sample(c(T, F, NA), size = 1e4, replace = T); set_obj_size(z); }
+ else if (otype == 4) { z <- (sample(256, size = 1e4, replace = T) - 1) %>% as.raw; set_obj_size(z); }
+ else if (otype == 5) { z <- replicate(sample(1e4, size = 1), {rep(letters, length.out = sample(10, size = 1)) %>% paste(collapse = "")}); set_obj_size(z); }
+ else if (otype == 6) { z <- rep(letters, length.out = sample(1e4, size = 1)) %>% paste(collapse = ""); set_obj_size(z); }
+ else if (otype == 7) { z <- as.formula("y ~ a + b + c : d", env = globalenv()); attr(z, "blah") <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (with_envs && otype %in% c(8, 9)) { z <- function(x) {x + runif(1)} }
+ # else if(with_envs && otype %in% c(10,11)) { z <- new.env(); z$x <- random_object_generator(N, with_envs); makeActiveBinding("y", function() runif(1), z) }
+ else { z <- random_object_generator(N, with_envs) }
+ if (is_attribute) {
+ attr(ret[[i - 1]], runif(1) %>% as.character()) <- z
+ } else {
+ ret[[i]] <- z
+ }
+ }
+ return(ret)
+ }
>
> rand_strings <- function(n) {
+ s <- sample(0:100, size = n, replace = T)
+ x <- lapply(unique(s), function(si) {
+ stringfish::random_strings(sum(s == si), si, vector_mode = "normal")
+ }) %>% unlist %>% sample
+ x[sample(n, size = n/10)] <- NA
+ return(x)
+ }
>
> nested_tibble <- function() {
+ sub_tibble <- function(nr = 600, nc = 4) {
+ z <- lapply(1:nc, function(i) rand_strings(nr)) %>%
+ setNames(make.unique(paste0(sample(letters, nc), rand_strings(nc)))) %>%
+ bind_cols %>%
+ as_tibble
+ }
+ tibble(
+ col1 = rand_strings(100),
+ col2 = rand_strings(100),
+ col3 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col4 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col5 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4))
+ ) %>% setNames(make.unique(paste0(sample(letters, 5), rand_strings(5))))
+ }
>
> printCarriage <- function(x) {
+ cat(x, "\r")
+ }
>
> attributes_serialize_identical <- function(attributes, full_object) {
+ identical(serialize(attributes(full_object), NULL), serialize(attributes, NULL))
+ }
>
> attributes_identical <- function(attributes, full_object) {
+ identical(attributes, attributes(full_object))
+ }
>
> ################################################################################################
>
> qsave_rand <- function(x, file) {
+ alg <- sample(c("lz4", "zstd", "lz4hc", "zstd_stream", "uncompressed"), 1)
+ # alg <- "zstd_stream"
+ nt <- sample(5,1)
+ sc <- sample(0:15,1)
+ cl <- sample(10,1)
+ ch <- sample(c(T,F),1)
+ qsave(x, file = file, preset = "custom", algorithm = alg,
+ compress_level = cl, shuffle_control = sc, nthreads = nt, check_hash = ch)
+ }
>
> qattributes_rand <- function(file) {
+ # ar <- sample(c(T,F),1)
+ # don't use altrep to avoid serialization differences
+ # attributes_serialize_identical won't pass with ALTREP
+ ar <- FALSE
+ nt <- sample(5,1)
+ qattributes(file, use_alt_rep = ar, nthreads = nt, strict = T)
+ }
>
> ################################################################################################
>
> for (q in 1:reps) {
+ cat("Rep", q, "of", reps, "\n")
+ # String correctness
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rep(letters, length.out = tp) %>% paste(collapse = "")
+ x1 <- c(NA, "", x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("strings: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Character vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ # qs_use_alt_rep(F)
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Character Vectors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # stringfish character vectors -- require R > 3.5.0
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ x1 <- stringfish::convert_to_sf(x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Stringfish: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+ }
+
+ # Integers
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- sample(1:tp, replace = T)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Integers: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Doubles
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rnorm(tp)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Numeric: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Logical
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+
+ x1 <- sample(c(T, F, NA), replace = T, size = tp)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Logical: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ # List
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- generateList(sample(1:4, replace = T, size = tp))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("List: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.frame(str = x1,num = runif(1:1000), stringsAsFactors = F)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Data.frame test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.table(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_serialize_identical(z, x1))
+ }
+ cat("Data.table test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- tibble(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Tibble test")
+ cat("\n")
+
+ # Encoding test
+ if (Sys.info()[['sysname']] != "Windows") {
+ for (i in 1:3) {
+ x1 <- "己所不欲，勿施于人" # utf 8
+ x2 <- x1
+ Encoding(x2) <- "latin1"
+ x3 <- x1
+ Encoding(x3) <- "bytes"
+ x4 <- rep(x1, x2, length.out = 1e4) %>% paste(collapse = ";")
+ x1 <- c(x1, x2, x3, x4)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage("Encoding test")
+ } else {
+ printCarriage("(Encoding test not run on windows)")
+ }
+ cat("\n")
+
+ # complex vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ re <- rnorm(tp)
+ im <- runif(tp)
+ x1 <- complex(real = re, imaginary = im)
+ x1 <- c(NA_complex_, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Complex: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # factors
+ for (tp in test_points) {
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- factor(rep(letters, length.out = tp), levels = sample(letters), ordered = TRUE)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Factors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Random objects
+ time <- vector("numeric", length = 8)
+ for (i in 1:8) {
+ # qs_use_alt_rep(sample(c(T, F), size = 1))
+ obj_size <- 0
+ x1 <- random_object_generator(12)
+ printCarriage(sprintf("Random objects: %s bytes", object.size(x1) %>% as.numeric))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Random objects: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # nested attributes
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- as.list(1:26)
+ attr(x1[[26]], letters[26]) <- rnorm(100)
+ for (i in 25:1) {
+ attr(x1[[i]], letters[i]) <- x1[[i + 1]]
+ }
+ time[i] <- Sys.time()
+ for(j in 1:length(x1)) {
+ qsave_rand(x1[[j]], file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1[[j]]))
+ }
+ }
+ printCarriage(sprintf("Nested attributes: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # alt-rep -- should serialize the unpacked object
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- 1:max_size
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Alt rep integer: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+
+ # Environment test
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- new.env()
+ x1[["a"]] <- 1:max_size
+ x1[["b"]] <- runif(max_size)
+ x1[["c"]] <- stringfish::random_strings(1e4, vector_mode = "normal")
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z[["a"]], x1[["a"]]))
+ stopifnot(attributes_identical(z[["b"]], x1[["b"]]))
+ stopifnot(attributes_identical(z[["c"]], x1[["c"]]))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("Environment test: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- nested_tibble()
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z, x1))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("nested tibble test: %s s", signif(mean(time), 4)))
+ cat("\n")
+ }
Rep 1 of 2
strings: 0, 0.03002 s
strings: 1, 0.009603 s
strings: 2, 0.007507 s
strings: 4, 0.001152 s
strings: 8, 0.007605 s
strings: 31, 0.01061 s
strings: 33, 0.001795 s
strings: 32, 0.005755 s
strings: 255, 0.005023 s
strings: 257, 0.008942 s
strings: 256, 0.005154 s
strings: 65535, 0.01246 s
strings: 65537, 0.004623 s
strings: 65536, 0.01116 s
strings: 1e+06, 0.0111 s
Character Vectors: 0, 0.0008359 s
Character Vectors: 1, 0.003309 s
Character Vectors: 2, 0.002368 s
Character Vectors: 4, 0.003778 s
Character Vectors: 8, 0.001159 s
Character Vectors: 31, 0.0004169 s
Character Vectors: 33, 0.003439 s
Character Vectors: 32, 0.0002722 s
Character Vectors: 255, 0.002782 s
Character Vectors: 257, 0.001211 s
Character Vectors: 256, 0.005099 s
Character Vectors: 65535, 0.005992 s
Character Vectors: 65537, 0.0077 s
Character Vectors: 65536, 0.006215 s
Stringfish: 0, 0.001074 s
Stringfish: 1, 0.007044 s
Stringfish: 2, 0.0001624 s
Stringfish: 4, 0.0001747 s
Stringfish: 8, 0.002396 s
Stringfish: 31, 0.003171 s
Stringfish: 33, 0.003076 s
Stringfish: 32, 0.0004567 s
Stringfish: 255, 0.002023 s
Stringfish: 257, 0.0008605 s
Stringfish: 256, 0.003166 s
Stringfish: 65535, 0.002653 s
Stringfish: 65537, 0.005199 s
Stringfish: 65536, 0.004957 s
Integers: 0, 0.006887 s
Integers: 1, 0.001464 s
Integers: 2, 0.003595 s
Integers: 4, 0.0007495 s
Integers: 8, 0.007794 s
Integers: 31, 0.01693 s
Integers: 33, 0.00375 s
Integers: 32, 0.01152 s
Integers: 255, 0.00675 s
Integers: 257, 0.00436 s
Integers: 256, 0.005943 s
Integers: 65535, 0.01373 s
Integers: 65537, 0.003816 s
Integers: 65536, 0.00916 s
Integers: 1e+06, 0.05327 s
Numeric: 0, 0.001094 s
Numeric: 1, 0.005408 s
Numeric: 2, 0.006115 s
Numeric: 4, 0.0007989 s
Numeric: 8, 0.003113 s
Numeric: 31, 0.005278 s
Numeric: 33, 0.00801 s
Numeric: 32, 0.001482 s
Numeric: 255, 0.00753 s
Numeric: 257, 0.006523 s
Numeric: 256, 0.006103 s
Numeric: 65535, 0.007591 s
Numeric: 65537, 0.01428 s
Numeric: 65536, 0.01321 s
Numeric: 1e+06, 0.2131 s
Logical: 0, 0.01131 s
Logical: 1, 0.005397 s
Logical: 2, 0.004055 s
Logical: 4, 0.002563 s
Logical: 8, 0.00691 s
Logical: 31, 0.0047 s
Logical: 33, 0.007184 s
Logical: 32, 0.002822 s
Logical: 255, 0.00255 s
Logical: 257, 0.002524 s
Logical: 256, 0.005227 s
Logical: 65535, 0.01163 s
Logical: 65537, 0.01284 s
Logical: 65536, 0.003144 s
Logical: 1e+06, 0.02753 s
List: 0, 0.002595 s
List: 1, 0.006332 s
List: 2, 0.002796 s
List: 4, 0.007051 s
List: 8, 0.005828 s
List: 31, 0.005061 s
List: 33, 0.003982 s
List: 32, 0.00236 s
List: 255, 0.003144 s
List: 257, 0.02368 s
List: 256, 0.005819 s
List: 65535, 0.04752 s
List: 65537, 0.02165 s
List: 65536, 0.03846 s
Data.frame test
Error: attributes_serialize_identical(z, x1) is not TRUE
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.27.3
Check: tests
Result: ERROR
Running ‘correctness_testing.R’ [259s/264s]
Running ‘qattributes_testing.R’ [50s/49s]
Running ‘qsavemload_testing.R’
Running the tests in ‘tests/qattributes_testing.R’ failed.
Complete output:
> total_time <- Sys.time()
>
> suppressMessages(library(Rcpp))
> suppressMessages(library(dplyr))
> suppressMessages(library(data.table))
> suppressMessages(library(qs))
> suppressMessages(library(stringfish))
> options(warn = 1)
>
> do_gc <- function() {
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ gc(full = TRUE)
+ } else {
+ gc()
+ }
+ }
>
> # because sourceCpp uses setwd, we need absolute path to R_TESTS when run within R CMD check
> R_TESTS <- Sys.getenv("R_TESTS") # startup.Rs
> if (nzchar(R_TESTS)) {
+ R_TESTS_absolute <- normalizePath(R_TESTS)
+ Sys.setenv(R_TESTS = R_TESTS_absolute)
+ }
> sourceCpp(code="#include <Rcpp.h>
+ using namespace Rcpp;
+ // [[Rcpp::plugins(cpp11)]]
+ // [[Rcpp::export(rng=false)]]
+ CharacterVector splitstr(std::string x, std::vector<double> cuts){
+ CharacterVector ret(cuts.size() - 1);
+ for(uint64_t i=1; i<cuts.size(); i++) {
+ ret[i-1] = x.substr(std::round(cuts[i-1])-1, std::round(cuts[i])-std::round(cuts[i-1]));
+ }
+ return ret;
+ }
+ // [[Rcpp::export(rng=false)]]
+ int setlev(SEXP x, int i) {
+ return SETLEVELS(x,i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ void setobj(SEXP x, int i) {
+ return SET_OBJECT(x, i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ List generateList(std::vector<int> list_elements){
+ auto randchar = []() -> char
+ {
+ const char charset[] =
+ \"0123456789\"
+ \"ABCDEFGHIJKLMNOPQRSTUVWXYZ\"
+ \"abcdefghijklmnopqrstuvwxyz\";
+ const size_t max_index = (sizeof(charset) - 1);
+ return charset[ rand() % max_index ];
+ };
+ List ret(list_elements.size());
+ std::string str(10,0);
+ for(size_t i=0; i<list_elements.size(); i++) {
+ switch(list_elements[i]) {
+ case 1:
+ ret[i] = R_NilValue;
+ break;
+ case 2:
+ std::generate_n( str.begin(), 10, randchar );
+ ret[i] = str;
+ break;
+ case 3:
+ ret[i] = rand();
+ break;
+ case 4:
+ ret[i] = static_cast<double>(rand());
+ break;
+ }
+ }
+ return ret;
+ }")
> if (nzchar(R_TESTS)) Sys.setenv(R_TESTS = R_TESTS)
>
> args <- commandArgs(T)
> if (nzchar(R_TESTS) || ((length(args) > 0) && args[1] == "check")) { # do fewer tests within R CMD check so it completes within a reasonable amount of time
+ reps <- 2
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6)
+ test_points_slow <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16) # for Character Vector, stringfish and list
+ max_size <- 1e6
+ } else {
+ reps <- 3
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6, 1e7)
+ test_points_slow <- test_points
+ max_size <- 1e7
+ }
> myfile <- tempfile()
>
> obj_size <- 0
> get_obj_size <- function() {
+ get("obj_size", envir = globalenv())
+ }
> set_obj_size <- function(x) {
+ assign("obj_size", get_obj_size() + as.numeric(object.size(x)), envir = globalenv())
+ return(get_obj_size());
+ }
> random_object_generator <- function(N, with_envs = FALSE) { # additional input: global obj_size, max_size
+ if (sample(3, 1) == 1) {
+ ret <- as.list(1:N)
+ } else if (sample(2, 1) == 1) {
+ ret <- as.pairlist(1:N)
+ } else {
+ ret <- as.pairlist(1:N)
+ setlev(ret, sample(2L^12L, 1L) - 1L)
+ setobj(ret, 1L)
+ }
+
+ for (i in 1:N) {
+ if (get_obj_size() > get("max_size", envir = globalenv())) break;
+ otype <- sample(12, size = 1)
+ z <- NULL
+ is_attribute <- ifelse(i == 1, F, sample(c(F, T), size = 1))
+ if (otype == 1) {z <- rnorm(1e4); set_obj_size(z);}
+ else if (otype == 2) { z <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (otype == 3) { z <- sample(c(T, F, NA), size = 1e4, replace = T); set_obj_size(z); }
+ else if (otype == 4) { z <- (sample(256, size = 1e4, replace = T) - 1) %>% as.raw; set_obj_size(z); }
+ else if (otype == 5) { z <- replicate(sample(1e4, size = 1), {rep(letters, length.out = sample(10, size = 1)) %>% paste(collapse = "")}); set_obj_size(z); }
+ else if (otype == 6) { z <- rep(letters, length.out = sample(1e4, size = 1)) %>% paste(collapse = ""); set_obj_size(z); }
+ else if (otype == 7) { z <- as.formula("y ~ a + b + c : d", env = globalenv()); attr(z, "blah") <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (with_envs && otype %in% c(8, 9)) { z <- function(x) {x + runif(1)} }
+ # else if(with_envs && otype %in% c(10,11)) { z <- new.env(); z$x <- random_object_generator(N, with_envs); makeActiveBinding("y", function() runif(1), z) }
+ else { z <- random_object_generator(N, with_envs) }
+ if (is_attribute) {
+ attr(ret[[i - 1]], runif(1) %>% as.character()) <- z
+ } else {
+ ret[[i]] <- z
+ }
+ }
+ return(ret)
+ }
>
> rand_strings <- function(n) {
+ s <- sample(0:100, size = n, replace = T)
+ x <- lapply(unique(s), function(si) {
+ stringfish::random_strings(sum(s == si), si, vector_mode = "normal")
+ }) %>% unlist %>% sample
+ x[sample(n, size = n/10)] <- NA
+ return(x)
+ }
>
> nested_tibble <- function() {
+ sub_tibble <- function(nr = 600, nc = 4) {
+ z <- lapply(1:nc, function(i) rand_strings(nr)) %>%
+ setNames(make.unique(paste0(sample(letters, nc), rand_strings(nc)))) %>%
+ bind_cols %>%
+ as_tibble
+ }
+ tibble(
+ col1 = rand_strings(100),
+ col2 = rand_strings(100),
+ col3 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col4 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col5 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4))
+ ) %>% setNames(make.unique(paste0(sample(letters, 5), rand_strings(5))))
+ }
>
> printCarriage <- function(x) {
+ cat(x, "\r")
+ }
>
> attributes_serialize_identical <- function(attributes, full_object) {
+ identical(serialize(attributes(full_object), NULL), serialize(attributes, NULL))
+ }
>
> attributes_identical <- function(attributes, full_object) {
+ identical(attributes, attributes(full_object))
+ }
>
> ################################################################################################
>
> qsave_rand <- function(x, file) {
+ alg <- sample(c("lz4", "zstd", "lz4hc", "zstd_stream", "uncompressed"), 1)
+ # alg <- "zstd_stream"
+ nt <- sample(5,1)
+ sc <- sample(0:15,1)
+ cl <- sample(10,1)
+ ch <- sample(c(T,F),1)
+ qsave(x, file = file, preset = "custom", algorithm = alg,
+ compress_level = cl, shuffle_control = sc, nthreads = nt, check_hash = ch)
+ }
>
> qattributes_rand <- function(file) {
+ # ar <- sample(c(T,F),1)
+ # don't use altrep to avoid serialization differences
+ # attributes_serialize_identical won't pass with ALTREP
+ ar <- FALSE
+ nt <- sample(5,1)
+ qattributes(file, use_alt_rep = ar, nthreads = nt, strict = T)
+ }
>
> ################################################################################################
>
> for (q in 1:reps) {
+ cat("Rep", q, "of", reps, "\n")
+ # String correctness
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rep(letters, length.out = tp) %>% paste(collapse = "")
+ x1 <- c(NA, "", x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("strings: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Character vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ # qs_use_alt_rep(F)
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Character Vectors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # stringfish character vectors -- require R > 3.5.0
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ x1 <- stringfish::convert_to_sf(x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Stringfish: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+ }
+
+ # Integers
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- sample(1:tp, replace = T)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Integers: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Doubles
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rnorm(tp)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Numeric: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Logical
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+
+ x1 <- sample(c(T, F, NA), replace = T, size = tp)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Logical: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ # List
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- generateList(sample(1:4, replace = T, size = tp))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("List: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.frame(str = x1,num = runif(1:1000), stringsAsFactors = F)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Data.frame test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.table(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_serialize_identical(z, x1))
+ }
+ cat("Data.table test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- tibble(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Tibble test")
+ cat("\n")
+
+ # Encoding test
+ if (Sys.info()[['sysname']] != "Windows") {
+ for (i in 1:3) {
+ x1 <- "己所不欲，勿施于人" # utf 8
+ x2 <- x1
+ Encoding(x2) <- "latin1"
+ x3 <- x1
+ Encoding(x3) <- "bytes"
+ x4 <- rep(x1, x2, length.out = 1e4) %>% paste(collapse = ";")
+ x1 <- c(x1, x2, x3, x4)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage("Encoding test")
+ } else {
+ printCarriage("(Encoding test not run on windows)")
+ }
+ cat("\n")
+
+ # complex vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ re <- rnorm(tp)
+ im <- runif(tp)
+ x1 <- complex(real = re, imaginary = im)
+ x1 <- c(NA_complex_, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Complex: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # factors
+ for (tp in test_points) {
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- factor(rep(letters, length.out = tp), levels = sample(letters), ordered = TRUE)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Factors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Random objects
+ time <- vector("numeric", length = 8)
+ for (i in 1:8) {
+ # qs_use_alt_rep(sample(c(T, F), size = 1))
+ obj_size <- 0
+ x1 <- random_object_generator(12)
+ printCarriage(sprintf("Random objects: %s bytes", object.size(x1) %>% as.numeric))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Random objects: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # nested attributes
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- as.list(1:26)
+ attr(x1[[26]], letters[26]) <- rnorm(100)
+ for (i in 25:1) {
+ attr(x1[[i]], letters[i]) <- x1[[i + 1]]
+ }
+ time[i] <- Sys.time()
+ for(j in 1:length(x1)) {
+ qsave_rand(x1[[j]], file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1[[j]]))
+ }
+ }
+ printCarriage(sprintf("Nested attributes: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # alt-rep -- should serialize the unpacked object
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- 1:max_size
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Alt rep integer: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+
+ # Environment test
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- new.env()
+ x1[["a"]] <- 1:max_size
+ x1[["b"]] <- runif(max_size)
+ x1[["c"]] <- stringfish::random_strings(1e4, vector_mode = "normal")
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z[["a"]], x1[["a"]]))
+ stopifnot(attributes_identical(z[["b"]], x1[["b"]]))
+ stopifnot(attributes_identical(z[["c"]], x1[["c"]]))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("Environment test: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- nested_tibble()
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z, x1))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("nested tibble test: %s s", signif(mean(time), 4)))
+ cat("\n")
+ }
Rep 1 of 2
strings: 0, 0.01877 s
strings: 1, 0.00233 s
strings: 2, 0.001731 s
strings: 4, 0.001663 s
strings: 8, 0.002074 s
strings: 31, 0.002256 s
strings: 33, 0.001094 s
strings: 32, 0.0069 s
strings: 255, 0.001523 s
strings: 257, 0.006322 s
strings: 256, 0.002874 s
strings: 65535, 0.002745 s
strings: 65537, 0.002542 s
strings: 65536, 0.002555 s
strings: 1e+06, 0.005651 s
Character Vectors: 0, 0.0007025 s
Character Vectors: 1, 0.0005259 s
Character Vectors: 2, 0.0007988 s
Character Vectors: 4, 0.0005541 s
Character Vectors: 8, 0.00188 s
Character Vectors: 31, 0.00111 s
Character Vectors: 33, 0.0007223 s
Character Vectors: 32, 0.0002493 s
Character Vectors: 255, 0.0001628 s
Character Vectors: 257, 0.0004144 s
Character Vectors: 256, 0.0001899 s
Character Vectors: 65535, 0.004162 s
Character Vectors: 65537, 0.006137 s
Character Vectors: 65536, 0.005242 s
Stringfish: 0, 0.0005091 s
Stringfish: 1, 0.0004363 s
Stringfish: 2, 0.001141 s
Stringfish: 4, 0.0003858 s
Stringfish: 8, 0.0008759 s
Stringfish: 31, 0.0002047 s
Stringfish: 33, 0.001546 s
Stringfish: 32, 0.0007424 s
Stringfish: 255, 0.0004779 s
Stringfish: 257, 0.0005674 s
Stringfish: 256, 0.0005625 s
Stringfish: 65535, 0.004842 s
Stringfish: 65537, 0.004768 s
Stringfish: 65536, 0.003957 s
Integers: 0, 0.007171 s
Integers: 1, 0.003663 s
Integers: 2, 0.002543 s
Integers: 4, 0.003133 s
Integers: 8, 0.002388 s
Integers: 31, 0.001636 s
Integers: 33, 0.001823 s
Integers: 32, 0.0008195 s
Integers: 255, 0.002802 s
Integers: 257, 0.002472 s
Integers: 256, 0.0007814 s
Integers: 65535, 0.005651 s
Integers: 65537, 0.01358 s
Integers: 65536, 0.004114 s
Integers: 1e+06, 0.1235 s
Numeric: 0, 0.00308 s
Numeric: 1, 0.002168 s
Numeric: 2, 0.001306 s
Numeric: 4, 0.002583 s
Numeric: 8, 0.001827 s
Numeric: 31, 0.001171 s
Numeric: 33, 0.002374 s
Numeric: 32, 0.001065 s
Numeric: 255, 0.002766 s
Numeric: 257, 0.002006 s
Numeric: 256, 0.00285 s
Numeric: 65535, 0.008034 s
Numeric: 65537, 0.01131 s
Numeric: 65536, 0.02376 s
Numeric: 1e+06, 0.1543 s
Logical: 0, 0.00469 s
Logical: 1, 0.002046 s
Logical: 2, 0.0009995 s
Logical: 4, 0.003164 s
Logical: 8, 0.001053 s
Logical: 31, 0.003974 s
Logical: 33, 0.003265 s
Logical: 32, 0.001825 s
Logical: 255, 0.002292 s
Logical: 257, 0.001415 s
Logical: 256, 0.003399 s
Logical: 65535, 0.004209 s
Logical: 65537, 0.005805 s
Logical: 65536, 0.01047 s
Logical: 1e+06, 0.09702 s
List: 0, 0.00271 s
List: 1, 0.01169 s
List: 2, 0.00126 s
List: 4, 0.004836 s
List: 8, 0.001077 s
List: 31, 0.002509 s
List: 33, 0.002096 s
List: 32, 0.00148 s
List: 255, 0.0008624 s
List: 257, 0.001487 s
List: 256, 0.001679 s
List: 65535, 0.03178 s
List: 65537, 0.02155 s
List: 65536, 0.02548 s
Data.frame test
Error: attributes_serialize_identical(z, x1) is not TRUE
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.27.3
Check: compiled code
Result: WARN
File 'qs/libs/x64/qs.dll':
Found non-API calls to R: 'ATTRIB', 'CLOENV', 'ENCLOS', 'FRAME',
'HASHTAB', 'IS_S4_OBJECT', 'LEVELS', 'OBJECT', 'PRENV',
'Rf_allocSExp', 'SETLEVELS', 'SET_ATTRIB', 'SET_CLOENV',
'SET_ENCLOS', 'SET_FRAME', 'SET_HASHTAB', 'SET_OBJECT',
'SET_PRENV', 'SET_S4_OBJECT', 'SET_TRUELENGTH'
These entry points may be removed soon:
'SET_FRAME', 'SET_HASHTAB', 'SET_ENCLOS', 'SET_S4_OBJECT', 'FRAME', 'HASHTAB', 'IS_S4_OBJECT', 'CLOENV', 'ENCLOS', 'OBJECT', 'SET_CLOENV', 'LEVELS', 'SETLEVELS'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Flavor: r-devel-windows-x86_64
Version: 0.27.3
Check: compiled code
Result: NOTE
File ‘qs/libs/qs.so’:
Found non-API calls to R: ‘CLOENV’, ‘ENCLOS’, ‘FRAME’, ‘HASHTAB’,
‘IS_S4_OBJECT’, ‘LEVELS’, ‘OBJECT’, ‘PRENV’, ‘Rf_allocSExp’,
‘SETLEVELS’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FRAME’,
‘SET_HASHTAB’, ‘SET_PRENV’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64
Version: 0.27.3
Check: tests
Result: ERROR
Running ‘correctness_testing.R’ [189s/194s]
Running ‘qattributes_testing.R’ [39s/44s]
Running ‘qsavemload_testing.R’ [2s/2s]
Running the tests in ‘tests/qattributes_testing.R’ failed.
Complete output:
> total_time <- Sys.time()
>
> suppressMessages(library(Rcpp))
> suppressMessages(library(dplyr))
> suppressMessages(library(data.table))
> suppressMessages(library(qs))
> suppressMessages(library(stringfish))
> options(warn = 1)
>
> do_gc <- function() {
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ gc(full = TRUE)
+ } else {
+ gc()
+ }
+ }
>
> # because sourceCpp uses setwd, we need absolute path to R_TESTS when run within R CMD check
> R_TESTS <- Sys.getenv("R_TESTS") # startup.Rs
> if (nzchar(R_TESTS)) {
+ R_TESTS_absolute <- normalizePath(R_TESTS)
+ Sys.setenv(R_TESTS = R_TESTS_absolute)
+ }
> sourceCpp(code="#include <Rcpp.h>
+ using namespace Rcpp;
+ // [[Rcpp::plugins(cpp11)]]
+ // [[Rcpp::export(rng=false)]]
+ CharacterVector splitstr(std::string x, std::vector<double> cuts){
+ CharacterVector ret(cuts.size() - 1);
+ for(uint64_t i=1; i<cuts.size(); i++) {
+ ret[i-1] = x.substr(std::round(cuts[i-1])-1, std::round(cuts[i])-std::round(cuts[i-1]));
+ }
+ return ret;
+ }
+ // [[Rcpp::export(rng=false)]]
+ int setlev(SEXP x, int i) {
+ return SETLEVELS(x,i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ void setobj(SEXP x, int i) {
+ return SET_OBJECT(x, i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ List generateList(std::vector<int> list_elements){
+ auto randchar = []() -> char
+ {
+ const char charset[] =
+ \"0123456789\"
+ \"ABCDEFGHIJKLMNOPQRSTUVWXYZ\"
+ \"abcdefghijklmnopqrstuvwxyz\";
+ const size_t max_index = (sizeof(charset) - 1);
+ return charset[ rand() % max_index ];
+ };
+ List ret(list_elements.size());
+ std::string str(10,0);
+ for(size_t i=0; i<list_elements.size(); i++) {
+ switch(list_elements[i]) {
+ case 1:
+ ret[i] = R_NilValue;
+ break;
+ case 2:
+ std::generate_n( str.begin(), 10, randchar );
+ ret[i] = str;
+ break;
+ case 3:
+ ret[i] = rand();
+ break;
+ case 4:
+ ret[i] = static_cast<double>(rand());
+ break;
+ }
+ }
+ return ret;
+ }")
> if (nzchar(R_TESTS)) Sys.setenv(R_TESTS = R_TESTS)
>
> args <- commandArgs(T)
> if (nzchar(R_TESTS) || ((length(args) > 0) && args[1] == "check")) { # do fewer tests within R CMD check so it completes within a reasonable amount of time
+ reps <- 2
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6)
+ test_points_slow <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16) # for Character Vector, stringfish and list
+ max_size <- 1e6
+ } else {
+ reps <- 3
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6, 1e7)
+ test_points_slow <- test_points
+ max_size <- 1e7
+ }
> myfile <- tempfile()
>
> obj_size <- 0
> get_obj_size <- function() {
+ get("obj_size", envir = globalenv())
+ }
> set_obj_size <- function(x) {
+ assign("obj_size", get_obj_size() + as.numeric(object.size(x)), envir = globalenv())
+ return(get_obj_size());
+ }
> random_object_generator <- function(N, with_envs = FALSE) { # additional input: global obj_size, max_size
+ if (sample(3, 1) == 1) {
+ ret <- as.list(1:N)
+ } else if (sample(2, 1) == 1) {
+ ret <- as.pairlist(1:N)
+ } else {
+ ret <- as.pairlist(1:N)
+ setlev(ret, sample(2L^12L, 1L) - 1L)
+ setobj(ret, 1L)
+ }
+
+ for (i in 1:N) {
+ if (get_obj_size() > get("max_size", envir = globalenv())) break;
+ otype <- sample(12, size = 1)
+ z <- NULL
+ is_attribute <- ifelse(i == 1, F, sample(c(F, T), size = 1))
+ if (otype == 1) {z <- rnorm(1e4); set_obj_size(z);}
+ else if (otype == 2) { z <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (otype == 3) { z <- sample(c(T, F, NA), size = 1e4, replace = T); set_obj_size(z); }
+ else if (otype == 4) { z <- (sample(256, size = 1e4, replace = T) - 1) %>% as.raw; set_obj_size(z); }
+ else if (otype == 5) { z <- replicate(sample(1e4, size = 1), {rep(letters, length.out = sample(10, size = 1)) %>% paste(collapse = "")}); set_obj_size(z); }
+ else if (otype == 6) { z <- rep(letters, length.out = sample(1e4, size = 1)) %>% paste(collapse = ""); set_obj_size(z); }
+ else if (otype == 7) { z <- as.formula("y ~ a + b + c : d", env = globalenv()); attr(z, "blah") <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (with_envs && otype %in% c(8, 9)) { z <- function(x) {x + runif(1)} }
+ # else if(with_envs && otype %in% c(10,11)) { z <- new.env(); z$x <- random_object_generator(N, with_envs); makeActiveBinding("y", function() runif(1), z) }
+ else { z <- random_object_generator(N, with_envs) }
+ if (is_attribute) {
+ attr(ret[[i - 1]], runif(1) %>% as.character()) <- z
+ } else {
+ ret[[i]] <- z
+ }
+ }
+ return(ret)
+ }
>
> rand_strings <- function(n) {
+ s <- sample(0:100, size = n, replace = T)
+ x <- lapply(unique(s), function(si) {
+ stringfish::random_strings(sum(s == si), si, vector_mode = "normal")
+ }) %>% unlist %>% sample
+ x[sample(n, size = n/10)] <- NA
+ return(x)
+ }
>
> nested_tibble <- function() {
+ sub_tibble <- function(nr = 600, nc = 4) {
+ z <- lapply(1:nc, function(i) rand_strings(nr)) %>%
+ setNames(make.unique(paste0(sample(letters, nc), rand_strings(nc)))) %>%
+ bind_cols %>%
+ as_tibble
+ }
+ tibble(
+ col1 = rand_strings(100),
+ col2 = rand_strings(100),
+ col3 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col4 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col5 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4))
+ ) %>% setNames(make.unique(paste0(sample(letters, 5), rand_strings(5))))
+ }
>
> printCarriage <- function(x) {
+ cat(x, "\r")
+ }
>
> attributes_serialize_identical <- function(attributes, full_object) {
+ identical(serialize(attributes(full_object), NULL), serialize(attributes, NULL))
+ }
>
> attributes_identical <- function(attributes, full_object) {
+ identical(attributes, attributes(full_object))
+ }
>
> ################################################################################################
>
> qsave_rand <- function(x, file) {
+ alg <- sample(c("lz4", "zstd", "lz4hc", "zstd_stream", "uncompressed"), 1)
+ # alg <- "zstd_stream"
+ nt <- sample(5,1)
+ sc <- sample(0:15,1)
+ cl <- sample(10,1)
+ ch <- sample(c(T,F),1)
+ qsave(x, file = file, preset = "custom", algorithm = alg,
+ compress_level = cl, shuffle_control = sc, nthreads = nt, check_hash = ch)
+ }
>
> qattributes_rand <- function(file) {
+ # ar <- sample(c(T,F),1)
+ # don't use altrep to avoid serialization differences
+ # attributes_serialize_identical won't pass with ALTREP
+ ar <- FALSE
+ nt <- sample(5,1)
+ qattributes(file, use_alt_rep = ar, nthreads = nt, strict = T)
+ }
>
> ################################################################################################
>
> for (q in 1:reps) {
+ cat("Rep", q, "of", reps, "\n")
+ # String correctness
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rep(letters, length.out = tp) %>% paste(collapse = "")
+ x1 <- c(NA, "", x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("strings: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Character vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ # qs_use_alt_rep(F)
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Character Vectors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # stringfish character vectors -- require R > 3.5.0
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ x1 <- stringfish::convert_to_sf(x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Stringfish: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+ }
+
+ # Integers
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- sample(1:tp, replace = T)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Integers: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Doubles
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rnorm(tp)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Numeric: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Logical
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+
+ x1 <- sample(c(T, F, NA), replace = T, size = tp)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Logical: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ # List
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- generateList(sample(1:4, replace = T, size = tp))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("List: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.frame(str = x1,num = runif(1:1000), stringsAsFactors = F)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Data.frame test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.table(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_serialize_identical(z, x1))
+ }
+ cat("Data.table test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- tibble(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Tibble test")
+ cat("\n")
+
+ # Encoding test
+ if (Sys.info()[['sysname']] != "Windows") {
+ for (i in 1:3) {
+ x1 <- "己所不欲，勿施于人" # utf 8
+ x2 <- x1
+ Encoding(x2) <- "latin1"
+ x3 <- x1
+ Encoding(x3) <- "bytes"
+ x4 <- rep(x1, x2, length.out = 1e4) %>% paste(collapse = ";")
+ x1 <- c(x1, x2, x3, x4)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage("Encoding test")
+ } else {
+ printCarriage("(Encoding test not run on windows)")
+ }
+ cat("\n")
+
+ # complex vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ re <- rnorm(tp)
+ im <- runif(tp)
+ x1 <- complex(real = re, imaginary = im)
+ x1 <- c(NA_complex_, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Complex: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # factors
+ for (tp in test_points) {
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- factor(rep(letters, length.out = tp), levels = sample(letters), ordered = TRUE)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Factors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Random objects
+ time <- vector("numeric", length = 8)
+ for (i in 1:8) {
+ # qs_use_alt_rep(sample(c(T, F), size = 1))
+ obj_size <- 0
+ x1 <- random_object_generator(12)
+ printCarriage(sprintf("Random objects: %s bytes", object.size(x1) %>% as.numeric))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Random objects: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # nested attributes
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- as.list(1:26)
+ attr(x1[[26]], letters[26]) <- rnorm(100)
+ for (i in 25:1) {
+ attr(x1[[i]], letters[i]) <- x1[[i + 1]]
+ }
+ time[i] <- Sys.time()
+ for(j in 1:length(x1)) {
+ qsave_rand(x1[[j]], file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1[[j]]))
+ }
+ }
+ printCarriage(sprintf("Nested attributes: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # alt-rep -- should serialize the unpacked object
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- 1:max_size
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Alt rep integer: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+
+ # Environment test
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- new.env()
+ x1[["a"]] <- 1:max_size
+ x1[["b"]] <- runif(max_size)
+ x1[["c"]] <- stringfish::random_strings(1e4, vector_mode = "normal")
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z[["a"]], x1[["a"]]))
+ stopifnot(attributes_identical(z[["b"]], x1[["b"]]))
+ stopifnot(attributes_identical(z[["c"]], x1[["c"]]))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("Environment test: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- nested_tibble()
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z, x1))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("nested tibble test: %s s", signif(mean(time), 4)))
+ cat("\n")
+ }
Rep 1 of 2
strings: 0, 0.009266 s
strings: 1, 0.002223 s
strings: 2, 0.007671 s
strings: 4, 0.00265 s
strings: 8, 0.007241 s
strings: 31, 0.005385 s
strings: 33, 0.004859 s
strings: 32, 0.006556 s
strings: 255, 0.009068 s
strings: 257, 0.002912 s
strings: 256, 0.006309 s
strings: 65535, 0.004612 s
strings: 65537, 0.004343 s
strings: 65536, 0.005225 s
strings: 1e+06, 0.005279 s
Character Vectors: 0, 0.0007679 s
Character Vectors: 1, 0.005265 s
Character Vectors: 2, 0.001912 s
Character Vectors: 4, 0.005302 s
Character Vectors: 8, 0.002699 s
Character Vectors: 31, 0.002589 s
Character Vectors: 33, 0.002123 s
Character Vectors: 32, 0.00557 s
Character Vectors: 255, 0.002804 s
Character Vectors: 257, 0.0004973 s
Character Vectors: 256, 0.004507 s
Character Vectors: 65535, 0.003491 s
Character Vectors: 65537, 0.003233 s
Character Vectors: 65536, 0.006017 s
Stringfish: 0, 0.002958 s
Stringfish: 1, 0.002406 s
Stringfish: 2, 0.002227 s
Stringfish: 4, 0.002035 s
Stringfish: 8, 0.001661 s
Stringfish: 31, 0.0002929 s
Stringfish: 33, 0.004649 s
Stringfish: 32, 0.0006292 s
Stringfish: 255, 0.0002771 s
Stringfish: 257, 0.001251 s
Stringfish: 256, 0.002665 s
Stringfish: 65535, 0.003706 s
Stringfish: 65537, 0.002324 s
Stringfish: 65536, 0.006042 s
Integers: 0, 0.02357 s
Integers: 1, 0.01597 s
Integers: 2, 0.004495 s
Integers: 4, 0.004973 s
Integers: 8, 0.004492 s
Integers: 31, 0.008321 s
Integers: 33, 0.002936 s
Integers: 32, 0.01706 s
Integers: 255, 0.003017 s
Integers: 257, 0.001349 s
Integers: 256, 0.003095 s
Integers: 65535, 0.01793 s
Integers: 65537, 0.014 s
Integers: 65536, 0.007182 s
Integers: 1e+06, 0.04113 s
Numeric: 0, 0.01579 s
Numeric: 1, 0.0007196 s
Numeric: 2, 0.002466 s
Numeric: 4, 0.006141 s
Numeric: 8, 0.002724 s
Numeric: 31, 0.007196 s
Numeric: 33, 0.003422 s
Numeric: 32, 0.002835 s
Numeric: 255, 0.001236 s
Numeric: 257, 0.006217 s
Numeric: 256, 0.005832 s
Numeric: 65535, 0.00266 s
Numeric: 65537, 0.02158 s
Numeric: 65536, 0.01703 s
Numeric: 1e+06, 0.07503 s
Logical: 0, 0.006371 s
Logical: 1, 0.03009 s
Logical: 2, 0.01412 s
Logical: 4, 0.001675 s
Logical: 8, 0.003439 s
Logical: 31, 0.008325 s
Logical: 33, 0.05828 s
Logical: 32, 0.04441 s
Logical: 255, 0.03292 s
Logical: 257, 0.008382 s
Logical: 256, 0.007674 s
Logical: 65535, 0.007509 s
Logical: 65537, 0.0198 s
Logical: 65536, 0.007301 s
Logical: 1e+06, 0.01145 s
List: 0, 0.006958 s
List: 1, 0.0006555 s
List: 2, 0.01578 s
List: 4, 0.0007408 s
List: 8, 0.02397 s
List: 31, 0.0005113 s
List: 33, 0.008809 s
List: 32, 0.0007137 s
List: 255, 0.003401 s
List: 257, 0.008428 s
List: 256, 0.0007162 s
List: 65535, 0.03993 s
List: 65537, 0.02159 s
List: 65536, 0.03678 s
Data.frame test
Error: attributes_serialize_identical(z, x1) is not TRUE
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.27.3
Check: compiled code
Result: NOTE
File 'qs/libs/x64/qs.dll':
Found non-API calls to R: 'CLOENV', 'ENCLOS', 'FRAME', 'HASHTAB',
'IS_S4_OBJECT', 'LEVELS', 'OBJECT', 'PRENV', 'Rf_allocSExp',
'SETLEVELS', 'SET_CLOENV', 'SET_ENCLOS', 'SET_FRAME',
'SET_HASHTAB', 'SET_PRENV', 'SET_S4_OBJECT', 'SET_TRUELENGTH'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Flavor: r-release-windows-x86_64
Version: 0.27.3
Check: tests
Result: ERROR
Running 'correctness_testing.R' [157s]
Running 'qattributes_testing.R' [33s]
Running 'qsavemload_testing.R' [2s]
Running the tests in 'tests/qattributes_testing.R' failed.
Complete output:
> total_time <- Sys.time()
>
> suppressMessages(library(Rcpp))
> suppressMessages(library(dplyr))
> suppressMessages(library(data.table))
> suppressMessages(library(qs))
> suppressMessages(library(stringfish))
> options(warn = 1)
>
> do_gc <- function() {
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ gc(full = TRUE)
+ } else {
+ gc()
+ }
+ }
>
> # because sourceCpp uses setwd, we need absolute path to R_TESTS when run within R CMD check
> R_TESTS <- Sys.getenv("R_TESTS") # startup.Rs
> if (nzchar(R_TESTS)) {
+ R_TESTS_absolute <- normalizePath(R_TESTS)
+ Sys.setenv(R_TESTS = R_TESTS_absolute)
+ }
> sourceCpp(code="#include <Rcpp.h>
+ using namespace Rcpp;
+ // [[Rcpp::plugins(cpp11)]]
+ // [[Rcpp::export(rng=false)]]
+ CharacterVector splitstr(std::string x, std::vector<double> cuts){
+ CharacterVector ret(cuts.size() - 1);
+ for(uint64_t i=1; i<cuts.size(); i++) {
+ ret[i-1] = x.substr(std::round(cuts[i-1])-1, std::round(cuts[i])-std::round(cuts[i-1]));
+ }
+ return ret;
+ }
+ // [[Rcpp::export(rng=false)]]
+ int setlev(SEXP x, int i) {
+ return SETLEVELS(x,i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ void setobj(SEXP x, int i) {
+ return SET_OBJECT(x, i);
+ }
+ // [[Rcpp::export(rng=false)]]
+ List generateList(std::vector<int> list_elements){
+ auto randchar = []() -> char
+ {
+ const char charset[] =
+ \"0123456789\"
+ \"ABCDEFGHIJKLMNOPQRSTUVWXYZ\"
+ \"abcdefghijklmnopqrstuvwxyz\";
+ const size_t max_index = (sizeof(charset) - 1);
+ return charset[ rand() % max_index ];
+ };
+ List ret(list_elements.size());
+ std::string str(10,0);
+ for(size_t i=0; i<list_elements.size(); i++) {
+ switch(list_elements[i]) {
+ case 1:
+ ret[i] = R_NilValue;
+ break;
+ case 2:
+ std::generate_n( str.begin(), 10, randchar );
+ ret[i] = str;
+ break;
+ case 3:
+ ret[i] = rand();
+ break;
+ case 4:
+ ret[i] = static_cast<double>(rand());
+ break;
+ }
+ }
+ return ret;
+ }")
> if (nzchar(R_TESTS)) Sys.setenv(R_TESTS = R_TESTS)
>
> args <- commandArgs(T)
> if (nzchar(R_TESTS) || ((length(args) > 0) && args[1] == "check")) { # do fewer tests within R CMD check so it completes within a reasonable amount of time
+ reps <- 2
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6)
+ test_points_slow <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16) # for Character Vector, stringfish and list
+ max_size <- 1e6
+ } else {
+ reps <- 3
+ test_points <- c(0, 1, 2, 4, 8, 2^5 - 1, 2^5 + 1, 2^5, 2^8 - 1, 2^8 + 1, 2^8, 2^16 - 1, 2^16 + 1, 2^16, 1e6, 1e7)
+ test_points_slow <- test_points
+ max_size <- 1e7
+ }
> myfile <- tempfile()
>
> obj_size <- 0
> get_obj_size <- function() {
+ get("obj_size", envir = globalenv())
+ }
> set_obj_size <- function(x) {
+ assign("obj_size", get_obj_size() + as.numeric(object.size(x)), envir = globalenv())
+ return(get_obj_size());
+ }
> random_object_generator <- function(N, with_envs = FALSE) { # additional input: global obj_size, max_size
+ if (sample(3, 1) == 1) {
+ ret <- as.list(1:N)
+ } else if (sample(2, 1) == 1) {
+ ret <- as.pairlist(1:N)
+ } else {
+ ret <- as.pairlist(1:N)
+ setlev(ret, sample(2L^12L, 1L) - 1L)
+ setobj(ret, 1L)
+ }
+
+ for (i in 1:N) {
+ if (get_obj_size() > get("max_size", envir = globalenv())) break;
+ otype <- sample(12, size = 1)
+ z <- NULL
+ is_attribute <- ifelse(i == 1, F, sample(c(F, T), size = 1))
+ if (otype == 1) {z <- rnorm(1e4); set_obj_size(z);}
+ else if (otype == 2) { z <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (otype == 3) { z <- sample(c(T, F, NA), size = 1e4, replace = T); set_obj_size(z); }
+ else if (otype == 4) { z <- (sample(256, size = 1e4, replace = T) - 1) %>% as.raw; set_obj_size(z); }
+ else if (otype == 5) { z <- replicate(sample(1e4, size = 1), {rep(letters, length.out = sample(10, size = 1)) %>% paste(collapse = "")}); set_obj_size(z); }
+ else if (otype == 6) { z <- rep(letters, length.out = sample(1e4, size = 1)) %>% paste(collapse = ""); set_obj_size(z); }
+ else if (otype == 7) { z <- as.formula("y ~ a + b + c : d", env = globalenv()); attr(z, "blah") <- sample(1e4) - 5e2; set_obj_size(z); }
+ else if (with_envs && otype %in% c(8, 9)) { z <- function(x) {x + runif(1)} }
+ # else if(with_envs && otype %in% c(10,11)) { z <- new.env(); z$x <- random_object_generator(N, with_envs); makeActiveBinding("y", function() runif(1), z) }
+ else { z <- random_object_generator(N, with_envs) }
+ if (is_attribute) {
+ attr(ret[[i - 1]], runif(1) %>% as.character()) <- z
+ } else {
+ ret[[i]] <- z
+ }
+ }
+ return(ret)
+ }
>
> rand_strings <- function(n) {
+ s <- sample(0:100, size = n, replace = T)
+ x <- lapply(unique(s), function(si) {
+ stringfish::random_strings(sum(s == si), si, vector_mode = "normal")
+ }) %>% unlist %>% sample
+ x[sample(n, size = n/10)] <- NA
+ return(x)
+ }
>
> nested_tibble <- function() {
+ sub_tibble <- function(nr = 600, nc = 4) {
+ z <- lapply(1:nc, function(i) rand_strings(nr)) %>%
+ setNames(make.unique(paste0(sample(letters, nc), rand_strings(nc)))) %>%
+ bind_cols %>%
+ as_tibble
+ }
+ tibble(
+ col1 = rand_strings(100),
+ col2 = rand_strings(100),
+ col3 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col4 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4)),
+ col5 = lapply(1:100, function(i) sub_tibble(nr = 600, nc = 4))
+ ) %>% setNames(make.unique(paste0(sample(letters, 5), rand_strings(5))))
+ }
>
> printCarriage <- function(x) {
+ cat(x, "\r")
+ }
>
> attributes_serialize_identical <- function(attributes, full_object) {
+ identical(serialize(attributes(full_object), NULL), serialize(attributes, NULL))
+ }
>
> attributes_identical <- function(attributes, full_object) {
+ identical(attributes, attributes(full_object))
+ }
>
> ################################################################################################
>
> qsave_rand <- function(x, file) {
+ alg <- sample(c("lz4", "zstd", "lz4hc", "zstd_stream", "uncompressed"), 1)
+ # alg <- "zstd_stream"
+ nt <- sample(5,1)
+ sc <- sample(0:15,1)
+ cl <- sample(10,1)
+ ch <- sample(c(T,F),1)
+ qsave(x, file = file, preset = "custom", algorithm = alg,
+ compress_level = cl, shuffle_control = sc, nthreads = nt, check_hash = ch)
+ }
>
> qattributes_rand <- function(file) {
+ # ar <- sample(c(T,F),1)
+ # don't use altrep to avoid serialization differences
+ # attributes_serialize_identical won't pass with ALTREP
+ ar <- FALSE
+ nt <- sample(5,1)
+ qattributes(file, use_alt_rep = ar, nthreads = nt, strict = T)
+ }
>
> ################################################################################################
>
> for (q in 1:reps) {
+ cat("Rep", q, "of", reps, "\n")
+ # String correctness
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rep(letters, length.out = tp) %>% paste(collapse = "")
+ x1 <- c(NA, "", x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("strings: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Character vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ # qs_use_alt_rep(F)
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Character Vectors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # stringfish character vectors -- require R > 3.5.0
+ if (utils::compareVersion(as.character(getRversion()), "3.5.0") != -1) {
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- rep(as.raw(sample(255)), length.out = tp*10) %>% rawToChar
+ cuts <- sample(tp*10, tp + 1) %>% sort %>% as.numeric
+ x1 <- splitstr(x1, cuts)
+ x1 <- c(NA, "", x1)
+ x1 <- stringfish::convert_to_sf(x1)
+ qsave_rand(x1, file = myfile)
+ time[i] <- Sys.time()
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Stringfish: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+ }
+
+ # Integers
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- sample(1:tp, replace = T)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Integers: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Doubles
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ x1 <- rnorm(tp)
+ x1 <- c(NA, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Numeric: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Logical
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+
+ x1 <- sample(c(T, F, NA), replace = T, size = tp)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Logical: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ # List
+ time <- vector("numeric", length = 3)
+ for (tp in test_points_slow) {
+ for (i in 1:3) {
+ x1 <- generateList(sample(1:4, replace = T, size = tp))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("List: %s, %s s",tp, signif(mean(time),4)))
+ }
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.frame(str = x1,num = runif(1:1000), stringsAsFactors = F)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Data.frame test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- data.table(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_serialize_identical(z, x1))
+ }
+ cat("Data.table test")
+ cat("\n")
+
+ for (i in 1:3) {
+ x1 <- rep( replicate(1000, { rep(letters, length.out = 2^7 + sample(10, size = 1)) %>% paste(collapse = "") }), length.out = 1e6 )
+ x1 <- tibble(str = x1,num = runif(1:1e6))
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ cat("Tibble test")
+ cat("\n")
+
+ # Encoding test
+ if (Sys.info()[['sysname']] != "Windows") {
+ for (i in 1:3) {
+ x1 <- "己所不欲，勿施于人" # utf 8
+ x2 <- x1
+ Encoding(x2) <- "latin1"
+ x3 <- x1
+ Encoding(x3) <- "bytes"
+ x4 <- rep(x1, x2, length.out = 1e4) %>% paste(collapse = ";")
+ x1 <- c(x1, x2, x3, x4)
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage("Encoding test")
+ } else {
+ printCarriage("(Encoding test not run on windows)")
+ }
+ cat("\n")
+
+ # complex vectors
+ time <- vector("numeric", length = 3)
+ for (tp in test_points) {
+ for (i in 1:3) {
+ re <- rnorm(tp)
+ im <- runif(tp)
+ x1 <- complex(real = re, imaginary = im)
+ x1 <- c(NA_complex_, x1)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Complex: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # factors
+ for (tp in test_points) {
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- factor(rep(letters, length.out = tp), levels = sample(letters), ordered = TRUE)
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Factors: %s, %s s",tp, signif(mean(time), 4)))
+ }
+ cat("\n")
+
+ # Random objects
+ time <- vector("numeric", length = 8)
+ for (i in 1:8) {
+ # qs_use_alt_rep(sample(c(T, F), size = 1))
+ obj_size <- 0
+ x1 <- random_object_generator(12)
+ printCarriage(sprintf("Random objects: %s bytes", object.size(x1) %>% as.numeric))
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Random objects: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # nested attributes
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- as.list(1:26)
+ attr(x1[[26]], letters[26]) <- rnorm(100)
+ for (i in 25:1) {
+ attr(x1[[i]], letters[i]) <- x1[[i + 1]]
+ }
+ time[i] <- Sys.time()
+ for(j in 1:length(x1)) {
+ qsave_rand(x1[[j]], file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1[[j]]))
+ }
+ }
+ printCarriage(sprintf("Nested attributes: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ # alt-rep -- should serialize the unpacked object
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- 1:max_size
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ stopifnot(attributes_identical(z, x1))
+ }
+ printCarriage(sprintf("Alt rep integer: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+
+ # Environment test
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- new.env()
+ x1[["a"]] <- 1:max_size
+ x1[["b"]] <- runif(max_size)
+ x1[["c"]] <- stringfish::random_strings(1e4, vector_mode = "normal")
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z[["a"]], x1[["a"]]))
+ stopifnot(attributes_identical(z[["b"]], x1[["b"]]))
+ stopifnot(attributes_identical(z[["c"]], x1[["c"]]))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("Environment test: %s s", signif(mean(time), 4)))
+ cat("\n")
+
+ time <- vector("numeric", length = 3)
+ for (i in 1:3) {
+ x1 <- nested_tibble()
+ time[i] <- Sys.time()
+ qsave_rand(x1, file = myfile)
+ z <- qattributes_rand(file = myfile)
+ stopifnot(attributes_identical(z, x1))
+ time[i] <- Sys.time() - time[i]
+ do_gc()
+ }
+ printCarriage(sprintf("nested tibble test: %s s", signif(mean(time), 4)))
+ cat("\n")
+ }
Rep 1 of 2
strings: 0, 0.008173 s
strings: 1, 0.005753 s
strings: 2, 0.004758 s
strings: 4, 0.004785 s
strings: 8, 0.01057 s
strings: 31, 0.002491 s
strings: 33, 0.01816 s
strings: 32, 0.002198 s
strings: 255, 0.001604 s
strings: 257, 0.003438 s
strings: 256, 0.001623 s
strings: 65535, 0.006239 s
strings: 65537, 0.005004 s
strings: 65536, 0.004663 s
strings: 1e+06, 0.008224 s
Character Vectors: 0, 0.00164 s
Character Vectors: 1, 0.0002183 s
Character Vectors: 2, 0.0006637 s
Character Vectors: 4, 0.000895 s
Character Vectors: 8, 0.0007137 s
Character Vectors: 31, 0.0001673 s
Character Vectors: 33, 0.0006073 s
Character Vectors: 32, 0.0007986 s
Character Vectors: 255, 0.001033 s
Character Vectors: 257, 0.001895 s
Character Vectors: 256, 0.001336 s
Character Vectors: 65535, 0.002715 s
Character Vectors: 65537, 0.003256 s
Character Vectors: 65536, 0.003826 s
Stringfish: 0, 0.0004973 s
Stringfish: 1, 0.00164 s
Stringfish: 2, 0.001381 s
Stringfish: 4, 0.0001317 s
Stringfish: 8, 0.001391 s
Stringfish: 31, 0.0009197 s
Stringfish: 33, 0.001339 s
Stringfish: 32, 0.0002203 s
Stringfish: 255, 0.0003281 s
Stringfish: 257, 0.0005397 s
Stringfish: 256, 0.001648 s
Stringfish: 65535, 0.002172 s
Stringfish: 65537, 0.003244 s
Stringfish: 65536, 0.003985 s
Integers: 0, 0.008876 s
Integers: 1, 0.002755 s
Integers: 2, 0.001289 s
Integers: 4, 0.003056 s
Integers: 8, 0.00556 s
Integers: 31, 0.003457 s
Integers: 33, 0.001644 s
Integers: 32, 0.00168 s
Integers: 255, 0.005613 s
Integers: 257, 0.001885 s
Integers: 256, 0.002546 s
Integers: 65535, 0.005419 s
Integers: 65537, 0.005231 s
Integers: 65536, 0.0109 s
Integers: 1e+06, 0.01414 s
Numeric: 0, 0.003568 s
Numeric: 1, 0.00333 s
Numeric: 2, 0.001723 s
Numeric: 4, 0.003801 s
Numeric: 8, 0.002167 s
Numeric: 31, 0.003432 s
Numeric: 33, 0.001896 s
Numeric: 32, 0.00352 s
Numeric: 255, 0.005581 s
Numeric: 257, 0.001446 s
Numeric: 256, 0.003614 s
Numeric: 65535, 0.01812 s
Numeric: 65537, 0.01551 s
Numeric: 65536, 0.006931 s
Numeric: 1e+06, 0.06755 s
Logical: 0, 0.008955 s
Logical: 1, 0.005273 s
Logical: 2, 0.001814 s
Logical: 4, 0.00233 s
Logical: 8, 0.001888 s
Logical: 31, 0.0007984 s
Logical: 33, 0.002666 s
Logical: 32, 0.002696 s
Logical: 255, 0.002578 s
Logical: 257, 0.00295 s
Logical: 256, 0.001301 s
Logical: 65535, 0.02363 s
Logical: 65537, 0.007436 s
Logical: 65536, 0.001939 s
Logical: 1e+06, 0.03294 s
List: 0, 0.005019 s
List: 1, 0.002342 s
List: 2, 0.0008224 s
List: 4, 0.002841 s
List: 8, 0.00343 s
List: 31, 0.002859 s
List: 33, 0.0006824 s
List: 32, 0.01522 s
List: 255, 0.001475 s
List: 257, 0.003035 s
List: 256, 0.001278 s
List: 65535, 0.01992 s
List: 65537, 0.01499 s
List: 65536, 0.0126 s
Data.frame test
Error: attributes_serialize_identical(z, x1) is not TRUE
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.27.3
Check: installed package size
Result: NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
doc 1.1Mb
libs 7.8Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: NOTE: 8, OK: 5
Version: 0.1.6
Check: compiled code
Result: NOTE
File ‘qs2/libs/qs2.so’:
Found non-API calls to R: ‘ATTRIB’, ‘SET_ATTRIB’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.6
Check: compiled code
Result: NOTE
File 'qs2/libs/x64/qs2.dll':
Found non-API calls to R: 'ATTRIB', 'SET_ATTRIB'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Flavor: r-devel-windows-x86_64
Version: 0.1.6
Check: installed package size
Result: NOTE
installed size is 8.8Mb
sub-directories of 1Mb or more:
libs 8.6Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.1.6
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 3, OK: 10
Version: 0.3.5
Check: installed package size
Result: NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
data 1.1Mb
libs 4.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.3.5
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.3.5
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘pwalign’
Flavor: r-oldrel-macos-x86_64
Current CRAN status: NOTE: 8, OK: 5
Version: 0.17.0
Check: compiled code
Result: NOTE
File ‘stringfish/libs/stringfish.so’:
Found non-API call to R: ‘ATTRIB’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.17.0
Check: compiled code
Result: NOTE
File 'stringfish/libs/x64/stringfish.dll':
Found non-API call to R: 'ATTRIB'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Flavor: r-devel-windows-x86_64
Version: 0.17.0
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64