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License: Other
This project forked from novartis/hdf5r
License: Other
Use pkdown to create package documentation.
Getting a warning message at the end of the check that 'cleanup' is deprecated
R CMD build .;docker run --cap-add SYS_PTRACE -v "$(pwd):/mnt" f023928cf1d8 /bin/bash -c "cd /mnt; Rdevel CMD check *.tar.gz;cat /mnt/hdf5r.Rcheck/00install.out"
convert.c:2324:58: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
if((ll_ptr[i] > MAX_INT_DOUBLE_PREC || ll_ptr[i] < MIN_INT_DOUBLE_PREC) && ll_ptr[i] != NA_INTEGER64 ) {
./convert.h:31:35: note: expanded from macro 'MIN_INT_DOUBLE_PREC'
#define MIN_INT_DOUBLE_PREC (-1LL << 53)
We should check the NOTE for Non-FOSS package license.
Is there a reason why the Apache license is used or could be also use BSD_2_clause + file LICENSE?
On appveyor, a note is mentioned that R_RegisterRoutines is called.
Ensure that the note is removed.
H5ls.c: In function ‘H5Dget_info’:
H5ls.c:78:73: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
dims_char_written += sprintf(dataset_info->dims + dims_char_written, "%" PRIu64, dims[i]);
^
H5ls.c:88:84: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
maxdims_char_written += sprintf(dataset_info->maxdims + maxdims_char_written, "%" PRIu64, maxdims[i]);
When accessing dimensions using a logical vector, it is not appropriately translated to a numeric vector
Currently in read and write operations, various R6 objects are being created. This R6 object creation takes a few milliseconds. On large read and writes, this isn't a problem. On small read/writes, the performance overhead is quite substantial.
Solution: Avoid the creation of R6 objects and do the necessary bookkeeping internally.
Reading entire dataset using [] (instead of [,]) for 2-dimensional objects should also work, like in matrix(1:9, nrow = 3)[]
It can happen that a user wants to close all relevant open HDF5 IDs. A function to simplify this process is missing.
How to set up dataset with specified maximum dimensions, only using set_extent?
Copied from the h5 Makefile:
check-asan-gcc: $(PKG_NAME)_$(PKG_VERSION).tar.gz
@boot2docker up
$(shell boot2docker shellinit)
@docker run -v "$(CURRENT_DIR):/mnt" mannau/r-devel-san /bin/bash -c \
"cd /mnt; apt-get update; apt-get clean; apt-get install -y libhdf5-dev; \
R -e \"install.packages(c('Rcpp', 'testthat', 'roxygen2', 'highlight', 'zoo', 'microbenchmark'))\"; \
R CMD check $(PKG_NAME)_$(PKG_VERSION).tar.gz; \
cat /mnt/h5.Rcheck/00install.out"
check-valgrind: $(PKG_NAME)_$(PKG_VERSION).tar.gz
@rm -rf $(CHECKPATH)
$(R) CMD check --no-clean --use-valgrind $(PKG_NAME)_$(PKG_VERSION).tar.gz
insert check before expand f <- function() dset2[10:11, 9] <- matrix(rep(0, 2*9), nrow = 2)
No Support for on-the-fly group creation / Recursive group creation ? e.g. file[["testgroup/testset"]] <- 1:10 without existing testgroup
Reading and writing of data-frames has a bug when a reshuffle is needed
some common_functions seem to be assigned to some classes where they can't always give a result
Windows test cases fail
Want functionality to see all open files and reuse R6 objects related to an open file
Long usage lines do not get broken at the end of the line appropriately
H5Class_overview
is currently not working since inst/manual/function_overview.html
is missing:
> H5Class_overview()
Error in browseURL(system.file("manual/function_overview.html", package = "hdf5r"), :
'url' must be a non-empty character string
We should either:
inst/manual/function_overview.html
H5Class_overview
and all references to itProvide options to specify dimension (if maxdim is needed, should specify a space).
Currently, the evaluate_arguments function that is a helper function for subset reading and assignment is relatively slow and should be improved
The readme could be more informative
At several places it is out of date or pointing to an incorrect repo
This should work without setting chunk size: dset1 <- createDataSet(file, "testmat_1", testmat_n, space = dspace)
In R, the dimensions of each dataset are always written in reverse order (to accomodate the fact that In R the first dimension changes fastest, but in C and hdf5, the last dimension changes fastest).
When printing dataset dimensions using ls, the hdf5 ordering is written out, not the reverse order
Implement test cases DataSet-Select-Elem/DataSet-Select-Hyperslab needs refactoring of H5D$read functions (separate dataspace from read).
When accessing an array with
dset[, c(2,1)]
it results in an error. The underlying reason is that a hyperslab with a negative stride is internally requested, which is not supported by HDF5. The stride-length has to always be non-negative.
Fix windows build for the following use cases:
devtools::install_github(hhoeflin/hdf5r)
Need to check that the built-in browser based help is working properly
Need to go through the manual and check for any issues.
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