not able to install geoquery package
3
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@farahqureshi5-12184
Last seen 3.9 years ago

Greetings!

i am not able to install geoquery package

17-03-07 14:52:19 (91.1 KB/s) - ‘/tmp/RtmpRyyZEo/downloaded_packages/GEOquery_2.36.0.tar.gz’ saved [13676520/13676520]

* 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
ERROR: configuration failed for package ‘XML’
* removing ‘/home/farah/R/x86_64-pc-linux-gnu-library/3.2/XML’
* 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/farah/R/x86_64-pc-linux-gnu-library/3.2/RCurl’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘GEOquery’
* removing ‘/home/farah/R/x86_64-pc-linux-gnu-library/3.2/GEOquery’

The downloaded source packages are in
    ‘/tmp/RtmpRyyZEo/downloaded_packages’
Old packages: 'boot', 'cluster', 'codetools', 'foreign', 'lattice',
  'Matrix', 'mgcv', 'nlme', 'survival'
Update all/some/none? [a/s/n]:
n
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 ‘GEOquery’ had non-zero exit status

microarrays xml RCurl libxml2 libcurl • 1.4k views
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@martin-morgan-1513
Last seen 20 days ago
United States

You need to install the 'devel' version of the libxml2 and libcurl system dependencies, using the software manager (e.g., apt, yum) on your linux system.

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can you please tell me how to do that

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You need to provide more information about your operating system. For me I have

$ lsb_release  -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 16.04.1 LTS
Release:    16.04
Codename:    xenial

nd the command (requiring system administration privileges) is

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

If you do not have sys. admin privileges it is easier -- ask your system administrator to do this for you.

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@farahqureshi5-12184
Last seen 3.9 years ago

thank u so much. it really worked

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@farahqureshi5-12184
Last seen 3.9 years ago

but m again getting an error. it is not able to download the file

getGEOSuppFiles("GSE20986")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE20nnn/GSE20986/suppl/
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE20nnn/GSE20986/suppl//GSE20986_RAW.tar'
ftp data connection made, file length 56360960 bytes
=================================================
downloaded 53.0 MB

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE20nnn/GSE20986/suppl//filelist.txt'
ftp data connection made, file length 740 bytes
==================================================
downloaded 740 bytes

Warning message:
In download.file(file.path(url, i), destfile = file.path(storedir,  :
  downloaded length 55573156 != reported length 56360960

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Post this as a different question, rather than an 'answer' to an unrelated question.

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