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Questions tagged [rhdf5]

35 questions
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How can I specify a package version for bio conductor package in Travis?

I am trying to use travis for my R package. The check are fine for R 3.4, results are here For R 3.3, Travis is KO because Travis install the package rhdf5 but it's not the correct version. Results are here I have in my description file, the…
Maaehj
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How to read and extract a attribute data from HE5 (HDF5) dataset in R

The dataset contains following groups with different attribute data. How can i extract and plot the attribute number 8 with latitude longitude using the packages 'rhdf5','rgdal' and 'raster'? 8 /HDFEOS/GRIDS/ColumnAmountNO2/Data Fields …
Dipu
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Get column names of objects inside HDF5 object with R

I have created a dummy HDF5 object as libray(rhdf5) handle = h5createFile("rhd5file.h5") df_A <- data.frame(height = rnorm(20,55,3), index = c(1:20)) df_B <- data.frame(age = rnorm(10,30,5), address = sample(letters,size= 10,replace =…
Haroon Lone
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Writing R data.table object to hdf5 file

I have R data.table which I tried to write as h5 file using rhdf5 package. This gives me a warning h5writeAttribute.default(Attr[[i]], h5obj, name = names(Attr)[i]) : No function found to write attribute of class 'externalptr'. Attribute…
user8401743
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R: error while reading .h5 files from R using rdhf5 package

I am new to hdf5 files. Trying to read some sample files from the below URL.. https://support.hdfgroup.org/ftp/HDF5/examples/files/exbyapi/ while trying to reading one of the .h5 files in R environment library(rhdf5) h5ls("h5ex_d_sofloat.h5") I am…
himanshu tripathi
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Modify, remove or add data to hdf5 files with R

I have a hdf5 file with several attributes, each attribute is either a matrix or an array. I would like to modify some of the attributes by adding or removing a column to the matrix. How can this be done? I have tried with the rhdf5 library in R but…
Herman Toothrot
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How to avoid printing / showing messages

this question has been asked before but non of the answers is working for me. I am using the library rhdf5 from bioconductor.org to read HDF5 files: source("http://bioconductor.org/biocLite.R"); biocLite("rhdf5"); library(rhdf5); When I use the…
MAB
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rhdf5 library in R: reading in file with h5ls

I want to read in an hdf5 file in R, but I can't seem to get it to work. The error I'm getting is: h<-h5ls(tsdatabase_path) Error in H5Fopen(file, "H5F_ACC_RDONLY") : HDF5. File accessability. Unable to open file. where h5ls is a method in…
Froblinkin
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How to read HDF5 files in R without the memory error?

Goal Read the data component of a hdf5 file in R. Problem I am using rhdf5 to read hdf5 files in R. Out of 75 files, it successfully read 61 files. But it throws an error about memory for the rest of the files. Although, some of these files are…
umair durrani
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Is it possible to write a boolean to an hdf5 file in R that Python will recognise as an 8 bit enum

I want to be able to save an R TRUE/FALSE value in HDF5 such that when reading the file into Python and checking the data type is Boolean the test will pass. At the moment I can't do this. If I use: library(rhdf5) h5file =…
Dave_L
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Issue Converting HDF5 into raster format

I am trying to convert my h5 daily files into a raster format. I converted into raster format. When I extracted my area of interest. I could not extract my area of interest from the raster image Kindly anyone guides me on how to solve this issue.…
Muhammad Usman Liaqat
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1 answer

Space efficient data store for list of list of lists. Elements are integers, and size of all lists varies in length

Say my data looks like this thisList = [ [[13, 43, 21, 4], [33, 2, 111, 33332, 23, 43, 2, 2], [232, 2], [23, 11]] , [[21, 2233, 2], [2, 3, 2,1, 32, 22], [3]], [[3]], [[23, 12], [55, 3]], .... ] What is the most…
SantoshGupta7
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Can't write hdf5 file: Error in H5Dcreate

When I am trying to write a dgcMatrix of 30 000x80 000 using rhdf5 in Rstudio: h5writeDataset(as.matrix(dge_cut), file, 'rawcounts') I am getting the error: Error in H5Dcreate(loc$H5Identifier, dataset, tid, sid, dcpl = dcpl) : HDF5. Dataset.…
Nikita Vlasenko
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How to use coordinate origin to project raster from h5 file in R?

I would like to project a data.frame from an h5 file into a projected raster. The h5 file I am using is a snow-water equivalent grid for the Sierra-Nevada, California, and the origin for the coordinates is in one of the sub-levels of the file. I…
MNewco
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How can I reproduce CRAN errors for debian platform ?

I must correct some errors in my package antaresProcessing. I want to reproduce these errors before. Here, you can see CRAN Checks I don't have debian OS. I tried rhub, you can see that the results are ok I tried to execute these functions, all…
Maaehj
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