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Question: Rhtslib - install error
0
gravatar for boboshaq
20 days ago by
boboshaq0
boboshaq0 wrote:

Hi!

I tried to install package: Rhtslib in my miniconda env, but I get error:

make[1]: Entering directory '/tmp/Rtmpmkgpv4/R.INSTALL78e3ccf441d/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/cluster/bioinfo/mbon/miniconda/3/envs/R-3.5.1/lib/R/etc/Makeconf:160: warning: ignoring old recipe for target '.c.o'
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -I.  -c -o kstring.o kstring.c
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
x86_64-conda_cos6-linux-gnu-cc -g -Wall -O2 -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>
          ^~~~~~~~
compilation terminated.
make[1]: *** [Makefile.Rhtslib:128: bgzf.o] Error 1
make[1]: Leaving directory '/tmp/Rtmpmkgpv4/R.INSTALL78e3ccf441d/Rhtslib/src/htslib-1.7'
make: *** [Makevars.common:21: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’

I using Bioconductor 3.7 (BiocInstaller 1.30.0)

What I can do, to install that package?

 
ADD COMMENTlink modified 7 days ago by Martin Morgan ♦♦ 22k • written 20 days ago by boboshaq0
0
gravatar for Martin Morgan
20 days ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Since you're using conda, are you installing Rhtslib using conda (rather than biocLite() / BiocManager::install() / install.packages())?

If you are using conda to install Rhtslib, then think this is ultimately a shortcoming of the conda recipe for Rhtslib, and a conda solution is required -- installing the appropriate conda container for libz. I don't know how to do that other than via google, which lead me to https://anaconda.org/anaconda/zlib

 

ADD COMMENTlink written 20 days ago by Martin Morgan ♦♦ 22k
0
gravatar for boboshaq
7 days ago by
boboshaq0
boboshaq0 wrote:

Hi,

I using miniconda with installed R 3.5.1. First I want to install package: methylkit:

http://bioconductor.org/packages/release/bioc/html/methylKit.html

but during installation that error will show:

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>

          ^~~~

compilation terminated.

I tried those command:

1. BiocManager::install("methylKit", version = "3.8")

result: error shown above

2. conda install -c bioconda bioconductor-methylkit

   result error:

Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
  - bioconductor-methylkit -> bioconductor-fastseg -> bioconductor-biobase[version='>=2.40.0,<2.42.0'] -> bioconductor-biocgenerics[version='>=0.26.0,<0.28.0'] -> r-base[version='>=3.5.1,<3.5.2.0a0'] -> _r-mutex[version='1.*,1.*',build=anacondar_1]
  - r-microsoftr

My installed packages are:

_r-mutex                  1.0.0                     mro_2

r-microsoftr              3.5.0.108              mro351_0

r-base - non installed

biocgenerics - non installed
biobase - non installed

htslib                    1.9                  hc238db4_4    bioconda

zlib                      1.2.11               hfbfcf68_1    anaconda

 

Why methylKit installatin script do not see zlib and htslib ?

ADD COMMENTlink written 7 days ago by boboshaq0

f you were not using conda, the standard method of installation would work or would be remedied by installing libz. You are using conda, so this is a conda error and needs to be reported to them.

The Bioconductor approach is not finding libz and headers, because they are installed in a location known to conda but not to R.

ADD REPLYlink modified 7 days ago • written 7 days ago by Martin Morgan ♦♦ 22k
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