Question: Issue installing RNA-seq workflow
0
gravatar for pavan-bioconductor
4 months ago by
pavan-bioconductor0 wrote:

Hi, Bioconductor and R noob here. While trying to install RNA-seq workflow I ran into several warning messages. Not sure how this will affect functionality down the road. I would appreciate suggestions on how to proceed forward.

Here are the warning messages:

> warnings()
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘Rhtslib’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘Rsamtools’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘GenomicAlignments’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘ShortRead’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘rtracklayer’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘BSgenome’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘GenomicFeatures’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘VariantAnnotation’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘OrganismDbi’ had non-zero exit status
10: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘ensembldb’ had non-zero exit status
11: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘EDASeq’ had non-zero exit status
12: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘biovizBase’ had non-zero exit status
13: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘RUVSeq’ had non-zero exit status
14: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘ggbio’ had non-zero exit status
15: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘Gviz’ had non-zero exit status
16: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘ReportingTools’ had non-zero exit status
17: In install.packages(pkgs = doing, lib = lib, repos = repos,  ... :
  installation of package ‘rnaseqGene’ had non-zero exit status
----
> traceback()
No traceback available
ADD COMMENTlink written 4 months ago by pavan-bioconductor0

I am on Mac OS High Sierra 10.13.6 and R version 3.6.0 (2019-04-26).

ADD REPLYlink written 4 months ago by pavan-bioconductor0
Answer: C: Issue installing RNA-seq workflow
0
gravatar for Martin Morgan
4 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

These warnings need to be addressed. Tackle the first one first, as it is likely to have triggered subsequent problems. Try installing just Rhtslib

BiocManager::install("Rhtslib")

Probably you want getOption("pkgType") to return "mac.binary.el-capitan" installation, rather than "source"; this assumes that you've installed R from CRAN.

ADD COMMENTlink written 4 months ago by Martin Morgan ♦♦ 23k

Hi, Thanks for the reply. I am on High Sierra OS 10.13.6 and R version 3.6.0 (2019-04-26) installed from CRAN. I tried the method you suggested and still getting following error message:

> BiocManager::install("Rhtslib")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
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 "/usr/local/Cellar/r/3.6.0_3/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
Makefile.Rhtslib:130: warning: overriding commands for target `.c.o'
/usr/local/Cellar/r/3.6.0_3/lib/R/etc/Makeconf:167: warning: ignoring old commands for target `.c.o'
clang -g -Wall -O2 -fpic -I.  -c -o kfunc.o kfunc.c
clang -g -Wall -O2 -fpic -I.  -c -o knetfile.o knetfile.c
clang -g -Wall -O2 -fpic -I.  -c -o kstring.o kstring.c
clang -g -Wall -O2 -fpic -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -g -Wall -O2 -fpic -I.  -c -o bgzf.o bgzf.c
clang -g -Wall -O2 -fpic -I.  -c -o errmod.o errmod.c
clang -g -Wall -O2 -fpic -I.  -c -o faidx.o faidx.c
clang -g -Wall -O2 -fpic -I.  -c -o hfile.o hfile.c
clang -g -Wall -O2 -fpic -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
clang -g -Wall -O2 -fpic -I.  -c -o hts.o hts.c
clang -g -Wall -O2 -fpic -I.  -c -o hts_os.o hts_os.c
clang -g -Wall -O2 -fpic -I.  -c -o md5.o md5.c
clang -g -Wall -O2 -fpic -I.  -c -o multipart.o multipart.c
clang -g -Wall -O2 -fpic -I.  -c -o probaln.o probaln.c
clang -g -Wall -O2 -fpic -I.  -c -o realn.o realn.c
clang -g -Wall -O2 -fpic -I.  -c -o regidx.o regidx.c
clang -g -Wall -O2 -fpic -I.  -c -o sam.o sam.c
clang -g -Wall -O2 -fpic -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -g -Wall -O2 -fpic -I.  -c -o vcf_sweep.o vcf_sweep.c
clang -g -Wall -O2 -fpic -I.  -c -o tbx.o tbx.c
clang -g -Wall -O2 -fpic -I.  -c -o textutils.o textutils.c
clang -g -Wall -O2 -fpic -I.  -c -o thread_pool.o thread_pool.c
clang -g -Wall -O2 -fpic -I.  -c -o vcf.o vcf.c
clang -g -Wall -O2 -fpic -I.  -c -o vcfutils.o vcfutils.c
clang -g -Wall -O2 -fpic -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -g -Wall -O2 -fpic -I.  -c -o cram/cram_decode.o cram/cram_decode.c
clang -g -Wall -O2 -fpic -I.  -c -o cram/cram_encode.o cram/cram_encode.c
clang -g -Wall -O2 -fpic -I.  -c -o cram/cram_external.o cram/cram_external.c
clang -g -Wall -O2 -fpic -I.  -c -o cram/cram_index.o cram/cram_index.c
clang -g -Wall -O2 -fpic -I.  -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found
#include <lzma.h>
         ^~~~~~~~
1 error generated.
make[1]: *** [cram/cram_io.o] Error 1
make: *** [htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/usr/local/lib/R/3.6/site-library/Rhtslib’

The downloaded source packages are in
    ‘/private/var/folders/l7/frxc0f_9639fjgg9g0mc7hz4cxv3nh/T/Rtmptcq3fi/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘Rhtslib’ had non-zero exit status

Upon trying this a second time I got following error message:

> install.packages("Rhtslib")
Installing package into ‘/usr/local/lib/R/3.6/site-library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘Rhtslib’ is not available (for R version 3.6.0)
ADD REPLYlink written 4 months ago by pavan-bioconductor0

How did you install R?

Use the first approach, but set the package installation type first

options(pkgType = "mac.binary.el-capitan")
BiocManager::install("Rhtslib")

Format any code in your post to the support site by selecting the code, and thne pressing the icon with the 0's and 1's in the editor.

ADD REPLYlink modified 4 months ago • written 4 months ago by Martin Morgan ♦♦ 23k

Hi,

I am trying to install a similar package in the AWS R environment. I am getting the same error as above. I also tried your suggestions but that didn't work as well. Can you help me resolve this issue?

Warning message in install.packages(pkgs = doing, lib = lib, repos = repos, ...): “installation of package ‘Rhtslib’ had non-zero exit status”Updating HTML index of packages in '.Library' Making 'packages.html' ... done

ADD REPLYlink written 11 weeks ago by sselvar0

It seems like your linux-based AWS environment needs something like lzma-dev system dependency to be installed, using apt get or similar depending on the operating system.

ADD REPLYlink written 11 weeks ago by Martin Morgan ♦♦ 23k
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