Problem installing R packages that depends from OpenSSL library in rocker/rstudio #124

gmgall · 2015-05-11T20:09:50Z

I'm using the rocker/rstudio image to generate isolated containers for my RStudio Server users. Almost everything works like a charm. Thank you for your time putting together this image.

The only problem I had was installing some R packages that depends from OpenSSL library. Like the devtools package, for example. Installing from RStudio or R I get the following messages:

[...]
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for library containing inflate... -lz
checking for library containing SSL_library_init... no
configure: error: in `/tmp/Rtmp2TqUu3/R.INSTALL4b5366585/git2r':
configure: error: OpenSSL library required
See `config.log' for more details
ERROR: configuration failed for package ‘git2r’
* removing ‘/usr/local/lib/R/site-library/git2r’
Warning in install.packages :
  installation of package ‘git2r’ had non-zero exit status
ERROR: dependency ‘git2r’ is not available for package ‘devtools’
* removing ‘/usr/local/lib/R/site-library/devtools’
Warning in install.packages :
  installation of package ‘devtools’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpPphf5x/downloaded_packages’

When I try to install it in a running container, here is what I get:

# apt-get install libssl-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libssl-dev : Depends: libssl1.0.0 (= 1.0.1k-3) but 1.0.2a-1 is to be installed
              Recommends: libssl-doc but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

Other R packages dependencies I was able to install discovering what package provides it and installing it via apt-get. libssl-dev was the only problem for now.

Strangely enough the package appears as installed:

# dpkg --get-selections | grep ssl
libssl0.9.8                 install
libssl1.0.0:amd64               install
openssl                     install

Any idea on what might be happening? Thanks in advance.

The text was updated successfully, but these errors were encountered:

eddelbuettel · 2015-05-11T20:29:55Z

Try this

 apt-get install libssl-dev/unstable

or you could install the git2r .deb binary from my ad-hoc PPA on launchpad.

cboettig · 2015-05-11T20:54:33Z

Thanks, I've also just pushed a fix for this. (Due to some apt-pinning the
dependencies can be a bit of a moving target at the moment, though we hope
to have a fix in the works with the next R release).

Also, I know the rocker/hadleyverse image is a deal heavier than
rocker/rstudio (ugh latex), but just for future reference it should always
have these things working out of the box.

On Mon, May 11, 2015 at 1:29 PM Dirk Eddelbuettel notifications@github.com
wrote:

Try this

apt-get install libssl-dev/unstable

or you could install the git2r .deb binary from my ad-hoc PPA on launchap
https://launchpad.net/%7Eedd/+archive/ubuntu/misc/+packages

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#124 (comment).

gmgall · 2015-05-11T22:19:51Z

The installation of the devtools R package finished without errors after installing libssl-dev/unstable as suggested by @eddelbuettel above. Thank you!

Is this the preferred method of solving unmet dependencies in rocker/rstudio? I'm asking because I installed other system dependencies to R packages (like libgdal-dev to rgdal) that seems to be working fine. Maybe I'll go through this type of problem again in the future when updating/installing R packages.

eddelbuettel · 2015-05-11T22:35:20Z

We would prefer to reply on just one flavor, but sometimes our hands are tied. I'd consider the fix you had to do as "temporary" but it all depends...

The (upstream Debian) package repository changes all the time as well so these things can be a tad fluid.

kmezhoud · 2015-05-20T06:23:24Z

Thanks!

eddelbuettel · 2015-05-20T11:13:36Z

As this was open for a few days: In the meantime I had two nightlies fail (following a string of seven successful builds) which was followed by a so-far-unbroken run of five working builds.

So as I indicated: there can be errors if you automate things.

RobertHagan · 2015-05-23T02:47:35Z

Thanks.. apt-get install libssl-dev/unstable works for me.

gmgall · 2015-06-02T19:37:31Z

The problem now happens with the libgdal-dev package.

# apt-get install libgdal-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libgdal-dev : Depends: libpq-dev but it is not going to be installed
               Depends: libsqlite3-dev but it is not going to be installed
               Depends: libspatialite-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

# apt-get install libgdal-dev/unstable
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Selected version '1.10.1+dfsg-8+b6' (Debian:unstable [amd64]) for 'libgdal-dev'
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libgdal-dev : Depends: libgdal1h (= 1.10.1+dfsg-8+b6) but it is not going to be installed
               Depends: libpq-dev but it is not going to be installed
               Depends: libsqlite3-dev but it is not going to be installed
               Depends: libspatialite-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

I install it as a dependency of the rgdal R package.

cboettig · 2015-06-02T19:47:11Z

Please install from the 'unstable' repos for all apt-get stuff for now:
apt-get install -t unstable libgdal-dev. Apologies for this -- we're
exploring a better solution for the next R release.

Also note that libgdal-dev is available on the rocker/ropensci image (which
is admittedly much heavier than rocker/rstudio).

On Tue, Jun 2, 2015 at 12:37 PM Guilherme Gall notifications@github.com
wrote:

The problem now happens with the libgdal-dev package.

apt-get install libgdal-dev

Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
libgdal-dev : Depends: libpq-dev but it is not going to be installed
Depends: libsqlite3-dev but it is not going to be installed
Depends: libspatialite-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

apt-get install libgdal-dev/unstable

Reading package lists... Done
Building dependency tree
Reading state information... Done
Selected version '1.10.1+dfsg-8+b6' (Debian:unstable [amd64]) for 'libgdal-dev'
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
libgdal-dev : Depends: libgdal1h (= 1.10.1+dfsg-8+b6) but it is not going to be installed
Depends: libpq-dev but it is not going to be installed
Depends: libsqlite3-dev but it is not going to be installed
Depends: libspatialite-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

I install it as a dependency of the rgdal R package.

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#124 (comment).

gmgall · 2015-06-02T21:05:22Z

Installing from unstable seems to work and I was able to install and load the rgdal R package. Thank you!

geneorama · 2015-07-21T19:59:51Z

I had the same error, but for me just installing libssl-dev did the trick on Ubuntu

anthony01 · 2015-07-25T18:02:56Z

Thank you very much for your comment, Gene Leynes! (The only receipt that helped me to solve same problem).

Houd1ny · 2016-07-10T23:18:15Z

How to fix? I got errors

from apt-get install libssl-dev/unstable
E: Release 'unstable' for 'libssl-dev' was not found\

from apt-get install -t unstable libgdal-dev
E: The value 'unstable' is invalid for APT::Default-Release as such a release is not available in the sources

eddelbuettel · 2016-07-10T23:54:45Z

Did you run apt-get update first?

Houd1ny · 2016-07-11T00:04:40Z

I had some problem with packages. Fixed them. Thank you!

sanjusebastian · 2016-07-20T05:49:08Z

@Houd1ny May I know, what did you do to fix it? I am getting the same error

eddelbuettel · 2016-09-07T11:27:09Z

@jwdkesel You are abusing a help forum for a completely different project. Please subscribe to the r-sig-debian mailing list (so that you can post) and post your question there. Thank you.

I will delete your post as it bears no relation to what either the Rocker project is about, besides being lost in some Debian configuration issue -- for this thread is not the right forum.

eddelbuettel · 2016-09-07T11:28:44Z

@cboettig Shall we close (and maybe lock?) this issue? It is from May of last year, and all versions etc have increased. The general trick of pinning still applies, but I think we also explain that somewhere else.

cboettig · 2016-09-07T16:40:36Z

Sure

On Wed, Sep 7, 2016, 4:28 AM Dirk Eddelbuettel notifications@github.com
wrote:

@cboettig https://github.com/cboettig Shall we close (and maybe lock?)
this issue? It is from May of last year, and all versions etc have
increased. The general trick of pinning still applies, but I think we also
explain that somewhere else.

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eddelbuettel · 2016-12-07T12:14:46Z

This isn't a yum-based system so you're in the wrong forum.

atongsa · 2018-05-06T12:38:34Z

ubuntu 18.04 LTS

sudo apt update
sudo apt install libssl-dev

davisidarta · 2019-03-21T14:39:18Z

I know this thread is closed. However, I still have the same errors as people who have commented above, even with the most up to date versions of rocker/rstudio and apt-get. I'm using Ubuntu 18.04 on a cloud server.

I also got the errors from

apt-get install libssl-dev/unstable
E: Release 'unstable' for 'libssl-dev' was not found\

from apt-get install -t unstable libgdal-dev
E: The value 'unstable' is invalid for APT::Default-Release as such a release is not available in the sources

I will be really glad if someone can provide further information on how to solve this for the rocker/rstudio image

Thanks a lot!

cboettig · 2019-03-21T15:36:25Z

@davisidarta please run apt update && apt install libssl-dev.

The error is telling you to please do not add a /unstable or -t unstable to your commands on the rocker/rstudio image, there is no unstable apt repository on that image.

HTH

arunintia00167 · 2019-03-26T22:08:30Z

Hi Guys,
I am getting a following error:
ERROR: dependency ‘inlinedocs’ is not available for package ‘Maaslin’

removing ‘/home/alakshmanan/R/x86_64-pc-linux-gnu-library/3.5/Maaslin’
Warning message:
In install.packages("https://bitbucket.org/biobakery/maaslin/downloads/Maaslin_0.0.5.tar.gz", :
installation of package ‘/tmp/RtmpWhjSMb/downloaded_packages/Maaslin_0.0.5.tar.gz’ had non-zero exit status

AkshayAnurag · 2019-10-17T10:42:27Z

For version of RStudio 1.2.5001

just install:

sudo apt-get install libssl-dev

fedemolina · 2019-12-29T20:16:12Z

For version of RStudio 1.2.5001

just install:

sudo apt-get install libssl-dev

This works for me

eddelbuettel closed this as completed Sep 7, 2016

AdamSpannbauer mentioned this issue Oct 25, 2018

create Dockerfile AdamSpannbauer/codeclimate-R#2

Closed

geneorama mentioned this issue Jan 24, 2019

Fix AppVeyor missing dependency (openssl) Chicago/RSocrata#160

Open

greymonroe mentioned this issue Sep 10, 2019

Package to CRAN International-Soil-Radiocarbon-Database/ISRaD#190

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Problem installing R packages that depends from OpenSSL library in rocker/rstudio #124

Problem installing R packages that depends from OpenSSL library in rocker/rstudio #124

gmgall commented May 11, 2015

eddelbuettel commented May 11, 2015

cboettig commented May 11, 2015

gmgall commented May 11, 2015

eddelbuettel commented May 11, 2015

kmezhoud commented May 20, 2015

eddelbuettel commented May 20, 2015

RobertHagan commented May 23, 2015

gmgall commented Jun 2, 2015

cboettig commented Jun 2, 2015

apt-get install libgdal-dev

apt-get install libgdal-dev/unstable

gmgall commented Jun 2, 2015

geneorama commented Jul 21, 2015

anthony01 commented Jul 25, 2015

Houd1ny commented Jul 10, 2016

eddelbuettel commented Jul 10, 2016

Houd1ny commented Jul 11, 2016 •

edited

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sanjusebastian commented Jul 20, 2016

eddelbuettel commented Sep 7, 2016

eddelbuettel commented Sep 7, 2016

cboettig commented Sep 7, 2016

eddelbuettel commented Dec 7, 2016

atongsa commented May 6, 2018

davisidarta commented Mar 21, 2019

cboettig commented Mar 21, 2019

arunintia00167 commented Mar 26, 2019

AkshayAnurag commented Oct 17, 2019

fedemolina commented Dec 29, 2019

Problem installing R packages that depends from OpenSSL library in rocker/rstudio #124

Problem installing R packages that depends from OpenSSL library in rocker/rstudio #124

Comments

gmgall commented May 11, 2015

eddelbuettel commented May 11, 2015

cboettig commented May 11, 2015

gmgall commented May 11, 2015

eddelbuettel commented May 11, 2015

kmezhoud commented May 20, 2015

eddelbuettel commented May 20, 2015

RobertHagan commented May 23, 2015

gmgall commented Jun 2, 2015

cboettig commented Jun 2, 2015

apt-get install libgdal-dev

apt-get install libgdal-dev/unstable

gmgall commented Jun 2, 2015

geneorama commented Jul 21, 2015

anthony01 commented Jul 25, 2015

Houd1ny commented Jul 10, 2016

eddelbuettel commented Jul 10, 2016

Houd1ny commented Jul 11, 2016 • edited Loading

sanjusebastian commented Jul 20, 2016

eddelbuettel commented Sep 7, 2016

eddelbuettel commented Sep 7, 2016

cboettig commented Sep 7, 2016

eddelbuettel commented Dec 7, 2016

atongsa commented May 6, 2018

davisidarta commented Mar 21, 2019

cboettig commented Mar 21, 2019

arunintia00167 commented Mar 26, 2019

AkshayAnurag commented Oct 17, 2019

fedemolina commented Dec 29, 2019

Houd1ny commented Jul 11, 2016 •

edited

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