I have tried to install hdf5 via BiocManager::install() using ubuntu 18.04. I think I need this package to read .h5 file. Info on my R is here:

$ R
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

Here is an error I got.

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
1: package ‘hdf5’ is not available (for R version 3.5.1) 
2:  install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : 
  installation of package ‘curl’ had non-zero exit status

Here is what I tried.

$ sudo dpkg -i libcurl4-openssl-dev_7.58.0-2ubuntu3.8_amd64.deb
$ export PKG_CONFIG_PATH=/usr/lib/pkgconfig

Now I think libcurl.pc file is located in the PATH(/usr/lib/pkgconfig) as shown here:

/usr/lib/pkgconfig$ ls
ibus-table.pc  libR.pc  libcurl.pc

Also I tried to update some packages shown here:

$ conda install -c r r-curl
$ conda install -c conda-forge/label/cf202003 r-hdf5r
$ conda install -c conda-forge libcurl

All process seemed to go successfully so I have the latest version for these packages.

I did not try the following command because I dont know what I should put in the ... part.

R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

I know many people are facing the same error and I have checked them, but I cannot still fix my error. Please kindly give me some advice.

There's a lot going on here and I'm not really sure where to start. This is just a collection of thoughts, what order you might want to look at them is up to you.

You're using a pretty old version of R, and in Bioconductor packages are tied to version of R, so I'd recommend updating to the latest R. We're currently on R-3.6.3 and R-4.0.0 will be out in a few weeks.

There's no package called hdf5, which is why you get the package ‘hdf5’ is not available (for R version 3.5.1) error. You need to get the name correct, otherwise nothing will be installed.

There's a package called rhdf5 in Bioconductor and hdf5r in CRAN. This is the place to ask for help with Bioconductor packages, but not for CRAN packages.

If you're using R installed via conda then I recommend installing the packages with conda too, rather than using install.packages() or BiocManager::install()

The same applies for installing system libraries like libcurl. It looks like you've done that in your last set of instructions.