diff --git a/vignettes/practical_tips.Rmd b/vignettes/practical_tips.Rmd index 35f2632..f03a350 100644 --- a/vignettes/practical_tips.Rmd +++ b/vignettes/practical_tips.Rmd @@ -301,7 +301,7 @@ gather_tmp_h5 <- function(output_file, input) { } ``` -Finally we need to create a wrapper function that brings our split and gather functions together. Like the `simple_writer()` function we created earlier, this takes the name of an output file and the list of datasets to be written as input. We can also provide a `BiocParallelParam` instance from `r Biocpkg("BiocParallel")` to trial writing the temporary file in parallel. If the `BPPARAM` argument isn't provided then they will be written in serial. +Finally we need to create a wrapper function that brings our split and gather functions together. Like the `simple_writer()` function we created earlier, this takes the name of an output file and the list of datasets to be written as input. We can also provide a `BiocParallelParam` instance from `r BiocStyle::Biocpkg("BiocParallel")` to trial writing the temporary file in parallel. If the `BPPARAM` argument isn't provided then they will be written in serial. ```{r, define-split-gather} split_and_gather <- function(output_file, input_dsets, BPPARAM = NULL) { diff --git a/vignettes/rhdf5.Rmd b/vignettes/rhdf5.Rmd index e4dceaf..3bdfd49 100644 --- a/vignettes/rhdf5.Rmd +++ b/vignettes/rhdf5.Rmd @@ -32,9 +32,9 @@ interface. On the other hand it provides high level convenience functions on **R** level to make a usage of HDF5 files more easy. #Installation of the HDF5 package -To install the `r Biocpkg("rhdf5")` package, you need a current version +To install the `r BiocStyle::Biocpkg("rhdf5")` package, you need a current version (>3.5.0) of **R** (www.r-project.org). After installing **R** you can -run the following commands from the **R** command shell to install `r Biocpkg("rhdf5")`. +run the following commands from the **R** command shell to install `r BiocStyle::Biocpkg("rhdf5")`. ```{r installation,eval=FALSE} install.packages("BiocManager") @@ -149,7 +149,7 @@ h5closeAll() ``` \subsection{Writing and reading with subsetting, chunking and compression} -The `r Biocpkg("rhdf5")` package provides two ways of subsetting. One can +The `r BiocStyle::Biocpkg("rhdf5")` package provides two ways of subsetting. One can specify the submatrix with the **R**-style index lists or with the HDF5 style hyperslabs. Note, that the two next examples below show two alternative ways for reading and writing the exact same @@ -314,7 +314,7 @@ file.size("myhdf5file.h5") **R** does not support a native datatype for 64-bit integers. All integers in **R** are 32-bit integers. When reading 64-bit integers from a HDF5-file, you -may run into troubles. `r Biocpkg("rhdf5")` is able to deal with 64-bit integers, but +may run into troubles. `r BiocStyle::Biocpkg("rhdf5")` is able to deal with 64-bit integers, but you still should pay attention. As an example, we create an HDF5 file that contains 64-bit integers. @@ -354,11 +354,11 @@ storage.mode(D64b) `bit64conversion='bit64'` is the recommended way of coercing. It represents the 64-bit integers as objects of class *integer64* as -defined in the package `r CRANpkg("bit64")`. Make sure that you have installed -`r CRANpkg("bit64")`. +defined in the package `r BiocStyle::CRANpkg("bit64")`. Make sure that you have installed +`r BiocStyle::CRANpkg("bit64")`. *The datatype *integer64* is not part of base **R**, but defined in an external package. This can produce unexpected behaviour when -working with the data.* When choosing this option the package `r CRANpkg("bit64")` +working with the data.* When choosing this option the package `r BiocStyle::CRANpkg("bit64")` will be loaded. ```{r bit64integer4} diff --git a/vignettes/rhdf5_cloud_reading.Rmd b/vignettes/rhdf5_cloud_reading.Rmd index 47046c1..d4f7b20 100644 --- a/vignettes/rhdf5_cloud_reading.Rmd +++ b/vignettes/rhdf5_cloud_reading.Rmd @@ -16,7 +16,7 @@ vignette: | knitr::opts_chunk$set(echo = TRUE) ``` -The `r Biocpkg("rhdf5")` provides limited support for read-only access to HDF5 files stored in Amazon S3 buckets. This is implemented via the [HDF5 S3 Virtual File Driver](https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS) and allows access to HDF5 files hosted in both public and private S3 buckets. +The `r BiocStyle::Biocpkg("rhdf5")` provides limited support for read-only access to HDF5 files stored in Amazon S3 buckets. This is implemented via the [HDF5 S3 Virtual File Driver](https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS) and allows access to HDF5 files hosted in both public and private S3 buckets. Currently only the functions `h5ls()`, `h5dump()` and `h5read()` are supported.