[BioC] bioc package installation problem

[Dan Tenenbaum]

On Tue, Apr 9, 2013 at 12:34 PM, carol white <wht_crl at yahoo.com> wrote:
> Thanks Dan.
>
> I have Ubuntu. which one should I install?
>
>  sudo apt-get install libxml2-dev libcurl-dev
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Package libcurl-dev is a virtual package provided by:
>   libcurl4-openssl-dev 7.22.0-3ubuntu4
>   libcurl4-nss-dev 7.22.0-3ubuntu4
>   libcurl4-gnutls-dev 7.22.0-3ubuntu4

Our Linux build machine has all three installed, so:

sudo apt-get install libxml2-dev libcurl4-openssl-dev libcurl4-nss-dev
libcurl4-gnutls-dev

Dan


> You should explicitly select one to install.
>
> E: Package 'libcurl-dev' has no installation candidate
>
> ________________________________
> From: Dan Tenenbaum <dtenenba at fhcrc.org>
> To: carol white <wht_crl at yahoo.com>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Sent: Tuesday, April 9, 2013 9:07 PM
> Subject: Re: [BioC] bioc package installation problem
>
> On Tue, Apr 9, 2013 at 12:03 PM, carol white <wht_crl at yahoo.com> wrote:
>> Hi,
>> I can't install ShortRead package. Is it because biocLite doesn't install
>> automatically the dependencies and I have to install them before ShortRead?
>>
>>
>> Best,
>>
>> Carol
>>
>> --------------------------------------------------------------------------
>>
>> source("http://bioconductor.org/biocLite.R")
>> BiocInstaller version 1.2.1, ?biocLite for help
>>>  biocLite("ShortRead")
>> BioC_mirror: 'http://www.bioconductor.org'
>> Using R version 2.14, BiocInstaller version 1.2.1.
>> Installing package(s) 'ShortRead'
>> also installing the dependencies ‘RCurl’, ‘XML’, ‘rtracklayer’,
>> ‘Rsamtools’
>>
>> trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.1.tar.gz'
>> Content type 'application/x-gzip' length 870915 bytes (850 Kb)
>> opened URL
>> ==================================================
>> downloaded 850 Kb
>>
>> trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.96-1.1.tar.gz'
>> Content type 'application/x-gzip' length 1578308 bytes (1.5 Mb)
>> opened URL
>> ==================================================
>> downloaded 1.5 Mb
>>
>> trying URL
>> 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/rtracklayer_1.14.4.tar.gz'
>> Content type 'application/x-gzip' length 1606020 bytes (1.5 Mb)
>> opened URL
>> ==================================================
>> downloaded 1.5 Mb
>>
>> trying URL
>> 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsamtools_1.6.3.tar.gz'
>> Content type 'application/x-gzip' length 2088820 bytes (2.0 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.0 Mb
>>
>> trying URL
>> 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ShortRead_1.12.4.tar.gz'
>> Content type 'application/x-gzip' length 2104718 bytes (2.0 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.0 Mb
>>
>> * installing *source* package ‘RCurl’ ...
>> ** package ‘RCurl’ successfully unpacked and MD5 sums checked
>> checking for curl-config... no
>> Cannot find curl-config
>> ERROR: configuration failed for package ‘RCurl’
>> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/RCurl’
>> * installing *source* package ‘XML’ ...
>> ** package ‘XML’ successfully unpacked and MD5 sums checked
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking how to run the C preprocessor... gcc -E
>> checking for sed... /bin/sed
>> checking for pkg-config... /usr/bin/pkg-config
>> checking for xml2-config... no
>> Cannot find xml2-config
>
>
> This means you need libcurl/libxml2 on your system. I'm not sure which linux
> distribution you are running but on Ubuntu the command to install this
> is:
>
> sudo apt-get insgtall libxml2-dev libcurl-dev
>
>
> Dan
>
>
>> ERROR: configuration failed for package ‘XML’
>> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/XML’
>> ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package
>> ‘rtracklayer’
>> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/rtracklayer’
>> ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’
>> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
>> ERROR: dependency ‘Rsamtools’ is not available for package ‘ShortRead’
>> * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/2.14/ShortRead’
>>
>> The downloaded packages are in
>>    ‘/tmp/Rtmpn9i2Os/downloaded_packages’
>> Warning messages:
>> 1: In install.packages(pkgs = pkgs, repos = repos, ...) :
>>  installation of package ‘RCurl’ had non-zero exit status
>> 2: In install.packages(pkgs = pkgs, repos = repos, ...) :
>>  installation of package ‘XML’ had non-zero exit status
>> 3: In install.packages(pkgs = pkgs, repos = repos, ...) :
>>  installation of package ‘rtracklayer’ had non-zero exit status
>> 4: In install.packages(pkgs = pkgs, repos = repos, ...) :
>>  installation of package ‘Rsamtools’ had non-zero exit status
>> 5: In install.packages(pkgs = pkgs, repos = repos, ...) :
>>  installation of package ‘ShortRead’ had non-zero exit status
>>        [[alternative HTML version deleted]]
>>
>>
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>
>