Hi all, I have a problem when trying to install Rhtslib package on my computer. Apparently, the installer is unable to find the zlib.h header file. I have zlib installed and an independent installation of htslib is able to find a suitable header to use and works fine. Also, I'm able to locate the header file on my computer via the find command.

The command used to install Rhtslib is:

BiocManager::install(c("Rhtslib"))

Which results in the following output:

Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'Rhtslib'
trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rhtslib_1.16.1.tar.gz'
Content type 'application/x-gzip' length 1470655 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/home/juanenciso/anaconda3/envs/r_bioconductor/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/tmp/RtmpHYcN5n/R.INSTALL40d18c442c9/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:130: warning: overriding recipe for target '.c.o'
/home/juanenciso/anaconda3/envs/r_bioconductor/lib/R/etc/Makeconf:168: warning: ignoring old recipe for target '.c.o'
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -fpic -I.  -c -o kfunc.o kfunc.c
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -fpic -I.  -c -o knetfile.o knetfile.c
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -fpic -I.  -c -o kstring.o kstring.c
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -fpic -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -fpic -I.  -c -o bgzf.o bgzf.c
In file included from bgzf.c:39:0:
htslib/bgzf.h:35:10: fatal error: zlib.h: No such file or directory
#include <zlib.h>
               ^~~~~~~~

I'm attaching my session information:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Manjaro Linux

Matrix products: default
BLAS/LAPACK: /home/juanenciso/anaconda3/envs/r_bioconductor/lib/R/lib/libRblas.so

locale:
[1] LC_CTYPE=en_GB.utf8        LC_NUMERIC=C              
[3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.utf8     
[5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.utf8    
[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] BiocManager_1.30.4 compiler_3.6.1     tools_3.6.1

Can you install the Rhtslib package via conda and use the pre-built version on bioconda?

Hi,

This looks like the same problem as here https://support.bioconductor.org/p/112599/ or https://support.bioconductor.org/p/114457/ A fix is in the way (in Rhtslib 1.16.2). Rhtslib 1.16.2 should become available via BiocManager::install() in the next 24h or so.

Best,

H.