Question: Issue installing RNA-seq workflow
0
gravatar for pavan-bioconductor
24 days 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 24 days 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 24 days ago by pavan-bioconductor0
Answer: C: Issue installing RNA-seq workflow
0
gravatar for Martin Morgan
24 days 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 24 days 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 23 days 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 23 days ago • written 23 days ago by Martin Morgan ♦♦ 23k
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