You need to install -dev package for zlib1g - it is named zlib1g-dev:

sudo apt-get install zlib1g-dev

and it will install zlib.pc file for pkg-config along with zlib.h header.

I'd ensure that this was seen by R, and that the header for libz (typically, installing the '-dev' version of the library) are available. · As a next step, if from the command line and with the unpacked source tarball available you try to install the package · > download.packages("ShortRead", ".", repos = BiocInstaller::biocinstallRepos()) · > quit() · $ tar xzf ShortRead_*gz · $ cd ShortRead · ShortRead$ R CMD INSTALL . · and then look for config.log you'll see something like · configure:2897: checking for gzeof in -lz · configure:2922: gcc -o conftest -g -O2 conftest.c -lz >&5 · configure:2922: $? = 0 · configure:2931: result: yes · except that you won't get that result, and there'll be a conftest.c file and perhaps informative messages. I'd also look on the mailing list / support site for whatever 'conda' manager you're using for similar messages.

I recently faced this issue, And this is fixed so I can answer this question.

If you are building cross compiler Define host and path to library using CPPFLAGS and LDFLAGS.

example:

CopyCPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib" ./configure --prefix=$PREFIX --host=$TARGET

If you are not building cross compiler. Then either specify the path (to library and header files) or install zlib devel package.

I believe that the problem lies with the configuration of autotools in r-base>3.4.1b2, but I'm not competent to fix that. The plus side is that, although configure can't find zlib during the pre-installation, zlib is actually present in any Conda environment with r-base and can be linked during the actual installation. I filed an issue at Conda-Forge, but until and unless the issue is resolved in r-base, I made a fork of ShortRead which skips the check. It works for me with r-base=3.5.1.

tldr: remotes::install_github("brendanf/ShortRead")

You need to install the development packages, usually called foo-devel or similar. Or you might be trying to build for the wrong architecture.

You are missing zlib.h header file, on Linux install it via:

sudo apt-get install libz-dev

As a matter of fact, the module presents as zlib1g-dev in the apt repo, so this is the up-to-date call (Feb 2019):

sudo apt install zlib1g-dev

On Fedora: sudo dnf install zlib-devel (in older versions: sudo dnf install libz-devel).

This will provide the development support files for a library implementing the deflate compression method found in gzip and PKZIP.

If you've already zlib library, make sure you're compiling your code sources with -lz. See: How to fix undefined references to inflate/deflate functions?.

The configure option --prefix is used to tell the configure script (and the resulting makefiles) where to put the programs which will be installed. It does not tell where to get header-files and libraries.

To tell the configure script where to get files, you may have to adjust these variables:

• CPPFLAGS (for directories containing header-files)
• LDFLAGS (for directories containing libraries)
• LIBS (for the actual library names)

You can pass those values on the command-line to configure, e.g.,

myheader=$HOME/junk/include
mylibs=$HOME/junk/lib
./configure CPPFLAGS="-I$myheader" LDFLAGS="-L$mylibs"

Following up on the clarification (which should have been incorporated into the question)

when I try to build the files in dropbear by running

#!/bin/bash ./configure --prefix=$HOME/Hi3536_SDK_V2.0.4.0/dropbear --with-zlib=$HOME/Hi3536_SDK_V2.0.4.0/zlib/include --host=arm CC=arm-hisiv400-linux-gcc

but it seems that it's unable to local the path to zlib

You can see the problem by looking at the source for the configure script:

# Check if zlib is needed
AC_ARG_WITH(zlib,
    [  --with-zlib=PATH        Use zlib in PATH],
    [
        # option is given
        if test -d "$withval/lib"; then
            LDFLAGS="-L${withval}/lib ${LDFLAGS}"
        else
            LDFLAGS="-L${withval} ${LDFLAGS}"
        fi
        if test -d "$withval/include"; then
            CPPFLAGS="-I${withval}/include ${CPPFLAGS}"
        else
            CPPFLAGS="-I${withval} ${CPPFLAGS}"
        fi
    ]
)

That is, it expects the option value to be the pathname of a directory which contains both the include and lib subdirectories (or a directory containing the files expected to be in those subdirectories). The comment shows that the given value was the pathname of the include (sub)directory. The following compile/link check will fail:

AC_CHECK_LIB(z, deflate, , AC_MSG_ERROR([*** zlib missing - install first or check config.log ***]))

The likely fix: change that option to

--with-zlib=$HOME/Hi3536_SDK_V2.0.4.0/zlib

I solved this problem by installing zlib development files:

# Debian-based
sudo apt install libz-dev

# Fedora-based
sudo dnf install zlib-devel

This is related to the last error you've got:

configure: error: *** zlib.h missing - please install first or check config.log ***

The warnings you've got would get solved by this also. However, if you have it installed, maybe try reinstalling or updating it.

• Bonus: One way to find required development shared libraries on your system is to ask your package manager what package provides a specific file. For example, dnf provides on Fedora could help you in these situations:

  $ sudo dnf provides /usr/include/zlib.h
  ...
  
  zlib-devel-1.2.11-30.fc35.x86_64 : Header files and libraries for Zlib development
  Repo        : @System
  Matched from:
  Filename    : /usr/include/zlib.h
  
  ...
  

Found the solution thanks to this answer.

You appear to be compiling something from source. You may find this is unneccessary, as the thing you need may be already built and packaged in binary form.

sudo apt install zlib1g

If, however, you're building some other piece of software that requires zlib, then:

sudo apt install zlib1g-dev

Which will install the development headers required by your other software.