Installation of biocLite packages dependencies

[Hasche89]

Hi, I recently started using R on Ubuntu 12.04. I am using R 3.2.3. Is there a R command that automatically downloads and installs dependencies along with the intended package; say- Biobase. Kindly help.

[Laurent]

 

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Biobase")

Same procedure for all Bioconductor packages.

[Hasnahana Chetia]

@Laurent Do this command also perform concurrent installation of all the dependencies of Biobase?

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Ms. Hasnahana Chetia

Research Scholar,

Bioengineering Research Laboratory,

Dept. of Biosciences and Bioengineering ,

Indian Institute of Technology Guwahati, Assam-39

[Hasnahana Chetia]

I got the following message-
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status

Did the package install properly? if not how can I correct this?

[Laurent Gatto]

On 15 Feb 2016 04:07, "Hasnahana Chetia" <hasc...@gmail.com> wrote:
>
> @Laurent Do this command also perform concurrent installation of all the dependencies of Biobase?

Try it out and you will see for yourself that it does so.

[Hasnahana Chetia]

Well, it did for Biobase. Doing the same for GenomicFeatures gave the foll. warning messages-

1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status

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[Laurent]

On Monday, 15 February 2016 08:06:40 UTC, Hasche89 wrote:

Well, it did for Biobase. Doing the same for GenomicFeatures gave the foll. warning messages-

So you answered your question - well done.

1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status

On Mon, Feb 15, 2016 at 12:31 PM, Laurent Gatto <lauren...@gmail.com> wrote:

On 15 Feb 2016 04:07, "Hasnahana Chetia" <hasc...@gmail.com> wrote:
>
> @Laurent Do this command also perform concurrent installation of all the dependencies of Biobase?

Try it out and you will see for yourself that it does so.

> On Sun, Feb 14, 2016 at 8:19 PM, Laurent <lauren...@gmail.com> wrote:
>>
>>  
>>
>> ## try http:// if https:// URLs are not supported
>> source("https://bioconductor.org/biocLite.R")
>> biocLite("Biobase")
>>
>> Same procedure for all Bioconductor packages.
>>

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[Hasnahana Chetia]

To all who has the same problem as mine,

The non-zero exit status error occurred due to lack of libxml and libcurl. Install these with "sudo apt-get" which will solve the problem. GL.

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Ms. Hasnahana Chetia

Research Scholar,

Bioengineering Research Laboratory,

Dept. of Biosciences and Bioengineering ,

Indian Institute of Technology Guwahati, Assam-39

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