I've been trying to install DESeq2 for differential expression analysis. Unfortunately, installation keeps failing because the dependencies can not be installed. The culprit is the XVector package, that is required for one of DESeq2's dependencies. This is the error:

# Installing
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("DESeq2")

# Error
fatal error: zlib.h: No such file or directory
   16 | #include <zlib.h>
      |          ^~~~~~~~
compilation terminated.
make: *** [/usr/local/lib/R/etc/Makeconf:172: io_utils.o] Error 1
ERROR: compilation failed for package ‘XVector’
* removing ‘/usr/local/lib/R/site-library/XVector

Due to this zlib.h file that is not found, the installation fails. I'm working in rstudio hosted from a docker container based on the rocker/rstudio:4.0.5 (newer versions like 4.1.1 throw the same error). Installing zlib by running sudo apt-get install zlib1g in the docker container does not solve the problem, as zlib1g is already installed with the newest version.

I found that the error occurs even for an unaltered R 4.0.5, find the sessionInfo below.

> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C              LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.15 compiler_4.0.5      tools_4.0.5

Has anyone found a way to deal with zlib.h issues?

Due to this zlib.h file that is not found, the installation fails. I'm working in rstudio hosted from a docker container based on the rocker/rstudio:4.0.5 (newer versions like 4.1.1 throw the same error). Installing zlib by running sudo apt-get install zlib1g in the docker container does not solve the problem, as zlib1g is already installed with the newest version.

If you are extending a rocker/rstudio image you should install the development version of some libraries (only they contain the header files which are needed to build the R-packages) and two additional libraries:

  apt-get install -y \
    libxml2 \
    libxt6 \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    libpcre3-dev \
    libicu-dev \
    libjpeg-dev \
    libpng-dev \
    libxml2-dev \
    libglpk-dev

You're not showing how you're installing packages. I hope you're using BiocManager::install() which is the only safe way to install Bioconductor packages.

Using R 4.0.5 means BiocManager::install() will pick up Bioconductor 3.12, which is old and no longer supported. The current version is BioC 3.14 and requires R 4.1.2.

If you're into Docker containers, why not use the container that we provide? https://bioconductor.org/help/docker/

H.