Bioconductor installing pakage error, R 3.4.2, Ubuntu 17.10
2
2
Entering edit mode
martyferr90 ▴ 20
@martyferr90-14371
Last seen 6.2 years ago

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?

bioconductor biocinstaller package installation • 3.3k views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 4 weeks ago
United States

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 COMMENT
0
Entering edit mode
martyferr90 ▴ 20
@martyferr90-14371
Last seen 6.2 years ago

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 750 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6