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Question: Bioconductor installing pakage error, R 3.4.2, Ubuntu 17.10
2
gravatar for martyferr90
15 months ago by
martyferr9020
martyferr9020 wrote:

Hi all, I have a situation. I'm trying to install Bioconductor pakages, but I receive only errors. I use R version 3.4.2 on Ubuntu 17.10. For the installation of Bioconductor pakages i type:

source("https://bioconductor.org/biocLite.R")
biocLite()

but i receive these erroros

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘IRanges’, ‘AnnotationDbi’
also installing the dependencies ‘BiocGenerics’, ‘S4Vectors’

provo con l'URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocGenerics_0.24.0.tar.gz'
Content type 'application/x-gzip' length 43393 bytes (42 KB)
==================================================
downloaded 42 KB

provo con l'URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/S4Vectors_0.16.0.tar.gz'
Content type 'application/x-gzip' length 432152 bytes (422 KB)
==================================================
downloaded 422 KB

provo con l'URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/IRanges_2.12.0.tar.gz'
Content type 'application/x-gzip' length 485066 bytes (473 KB)
==================================================
downloaded 473 KB

provo con l'URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/AnnotationDbi_1.40.0.tar.gz'
Content type 'application/x-gzip' length 4336842 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Error : identical(as.call(parse(text = old_code)[[1L]]), body[[7L]][[3L]]) is not TRUE
Error in apply_hotfix73465(getGeneric("cbind")) :
  hotfix failed for generic function cbind()
Error : unable to load R code in package ‘BiocGenerics’
ERROR: lazy loading failed for package ‘BiocGenerics’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.4/BiocGenerics’
ERROR: dependency ‘BiocGenerics’ is not available for package ‘S4Vectors’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.4/S4Vectors’
ERROR: dependencies ‘BiocGenerics’, ‘S4Vectors’ are not available for package ‘IRanges’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.4/IRanges’
ERROR: dependencies ‘BiocGenerics’, ‘IRanges’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’
* removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.4/AnnotationDbi’

The downloaded source packages are in
    ‘/tmp/RtmpsCYUVP/downloaded_packages’
installation path not writeable, unable to update packages: mgcv
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BiocGenerics’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘S4Vectors’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IRanges’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status

How can I resolve this?

ADD COMMENTlink modified 15 months ago • written 15 months ago by martyferr9020
Answer: Bioconductor installing pakage error, R 3.4.2, Ubuntu 17.10
0
gravatar for Martin Morgan
15 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

See C: Problem installing BiocGenerics where a solution is to install the patched version of R. But it is still interesting to understand what the particular features of your setup-are that trigger this. A diagnostic step is provided C: Problem installing BiocGenerics; it would be very helpful to provide some additional information about your particular setup, including how you installed R, whether you see the problem (simplified as biocLite("BiocGenerics")) when running an R session with no additional packages attached -- R --vanilla from the command line, the output of sessionInfo(), and whatever other diagnostics that might be helpful to understand the problem.

ADD COMMENTlink written 15 months ago by Martin Morgan ♦♦ 22k
Answer: Bioconductor installing pakage error, R 3.4.2, Ubuntu 17.10
0
gravatar for martyferr90
15 months ago by
martyferr9020
martyferr9020 wrote:

I tryed to install the R-patched but I have some problem with the installation. First of all I type:

sudo tar zxvf R-patched.tar.gz

then

cd R-patched/

then sudo ./configure

and then

sudo make

but I receive an error

make: *** No specified target and no makefile found. Stop.

How can I resolve?

ADD COMMENTlink written 15 months ago by martyferr9020

I usually build 'out-of-source'. Also best practice is to reserve use of sudo for the essential steps

tar zxvf R-patched.tar.gz
mkdir R-3-4-2-patched
cd R-3-4-2-patched
../R-patched/configure
make -j

R-3-4-2/bin/R should be executable;

sudo make install

if you want to install as root, though actually I don't usually do that but instead modify my shell PATH to include the location of the bin.

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 22k

I used your guideline, but i receive the same error. This is the last row of configure procedure

configure: error: --with-readline=yes (default) and headers/libs are not available

IS there a way to resolve this?

ADD REPLYlink written 15 months ago by martyferr9020

You can either install readline ,I think

sudo apt-get install readline-common

or configure R not to use readline

../R-patched/configure --with-readline=no

The former is the better solution, although the package (readline-common) is only a guess.

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 22k

I tried to install readlines, but i already have it

eadline-common is already the newest version (7.0-0ubuntu2).

So I tried to configure R with your tip, but

configure: error: --with-x=yes (default) and X11 headers/libs are not available
ADD REPLYlink written 15 months ago by martyferr9020

It is the same story, a missing system library, to be installed via apt-get or to configure R without. A different route through this is to install R itself via apt, following relevant instructions here https://cran.r-project.org/bin/linux/ and installing the -devel flavor. This will also install the dependencies. Then build your own R

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 22k
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