Installation ERROR: configuration failed for package ‘Rhdf5lib’

[sorenwacker]

I am trying to install xcms locally with BiocManager::install("xcms"). The installation process stops with the following output:

...
checking if zlib is wanted... yes
checking for inflateEnd in -lz... no
checking zlib.h usability... no
checking zlib.h presence... no
checking for zlib.h... no
checking zlib in /usr... failed
configure: error: either specify a valid zlib installation with --with-zlib=DIR or disable zlib usage with --without-zlib
ERROR: configuration failed for package ‘Rhdf5lib’

[sneumann]

Hi, which operating system / distribution is that ? The error indicates that you need the developer files for zlib, On Ubuntu that's apt install zlib1g-dev, on Redhat it'll be different. Yours, Steffen

[sorenwacker]

It is Ubuntu 18.04 and sudo apt-get install zlib1g-dev returns:

> zlib1g-dev is already the newest version (1:1.2.11.dfsg-0ubuntu2).
> 0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.

R is installed in an anaconda environment. I also tried installing zlib in that environment with conda install -c anaconda zlib. But the error message remains.

[jorainer]

Could you please provide the output of sessionInfo(). Also, it seems that Rhdf5lib is the culprit, please try to install it directly with BiocManager::install("Rhdf5lib").

[sorenwacker]

R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS/LAPACK: /home/swacker/miniconda3/envs/py3/lib/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] 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] compiler_3.5.1

I tried installing Rhdf5lib on its own and it gave the same error message.

[MikeHala]

Hello,

I have similar problem

conda install -c anaconda zlib All requested packages already installed. packages in environment at /exports/igmm/eddie/bioinfsvice/mhalache/anaconda/envs/scEyeMap: zlib 1.2.11 h7b6447c_3 anaconda

BiocManager::install("Rhdf5lib") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'Rhdf5lib' trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rhdf5lib_1.6.0.tar.gz' ..... checking if zlib is wanted... yes checking for inflateEnd in -lz... no checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking zlib in /usr... failed configure: error: either specify a valid zlib installation with --with-zlib=DIR or disable zlib usage with --without-zlib ERROR: configuration failed for package ‘Rhdf5lib’

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: Scientific Linux 7.5 (Nitrogen) Matrix products: default BLAS/LAPACK: /gpfs/igmmfs01/eddie/bioinfsvice/mhalache/anaconda/envs/scEyeMap/lib/R/lib/libRblas.so locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.6.0

Thanks, Mike

[sneumann]

I think those errors should be reported to https://github.com/grimbough/Rhdf5lib Yours, Steffen

[grimbough]

There's an open issue for this error at https://github.com/grimbough/Rhdf5lib/issues/21