Question: not able to install geoquery package
0
gravatar for farahqureshi5
2.6 years ago by
farahqureshi50 wrote:

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

ADD COMMENTlink modified 2.6 years ago by Martin Morgan ♦♦ 23k • written 2.6 years ago by farahqureshi50
Answer: noe able to install geoquery package
0
gravatar for Martin Morgan
2.6 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

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.

ADD COMMENTlink written 2.6 years ago by Martin Morgan ♦♦ 23k

can you please tell me how to do that

ADD REPLYlink written 2.6 years ago by farahqureshi50

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.

ADD REPLYlink written 2.6 years ago by Martin Morgan ♦♦ 23k
Answer: noe able to install geoquery package
0
gravatar for farahqureshi5
2.6 years ago by
farahqureshi50 wrote:

thank u so much. it really worked

ADD COMMENTlink written 2.6 years ago by farahqureshi50
Answer: noe able to install geoquery package
0
gravatar for farahqureshi5
2.6 years ago by
farahqureshi50 wrote:

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

ADD COMMENTlink written 2.6 years ago by farahqureshi50

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

ADD REPLYlink written 2.6 years ago by Martin Morgan ♦♦ 23k
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