Question: Installing GEOQuery failed with conda
1
gravatar for 261092095
15 months ago by
26109209510
26109209510 wrote:

I rented a server, using ananconda, when I installed the GEOquery package, I made a mistake and asked for help. (it was installed and used, but it failed after restarting.)

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R;
  see http://bioconductor.org/install
> biocLite('GEOquery')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘GEOquery’
also installing the dependency ‘xml2’

trying URL 'https://cran.rstudio.com/src/contrib/xml2_1.2.0.tar.gz'
Content type 'application/x-gzip' length 251614 bytes (245 KB)
==================================================
downloaded 245 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GEOquery_2.46.15.tar.gz'
Content type 'application/x-gzip' length 13717934 bytes (13.1 MB)
==================================================
downloaded 13.1 MB

* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/u1366/R/x86_64-pc-linux-gnu-library/3.4/xml2’
ERROR: dependency ‘xml2’ is not available for package ‘GEOquery’
* removing ‘/home/u1366/R/x86_64-pc-linux-gnu-library/3.4/GEOquery’

The downloaded source packages are in
	‘/tmp/Rtmpzitb47/downloaded_packages’
installation path not writeable, unable to update packages: annotate, bit, bit64,
  blockmodeling, caTools, cluster, data.table, edgeR, evaluate, fastcluster, foreign,
  Formula, futile.options, GenomicAlignments, GenomicFeatures, glue, Hmisc, hms,
  htmlTable, htmlwidgets, lambda.r, lattice, maftools, matrixStats, mvtnorm, nlme,
  openssl, pcaPP, pillar, pkgmaker, purrr, Rcpp, RcppArmadillo, rjson, robustbase, rrcov,
  RSQLite, scales, shape, slam, stringi, SummarizedExperiment, utf8, VariantAnnotation,
  WGCNA, withr, XML, yaml, zoo
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘xml2’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GEOquery’ had non-zero exit status

$ conda list
# packages in environment at /home/u1366/anaconda3:

libxcb                    1.12                          1
libxml2                   2.9.8                h422b904_3    conda-forge...
libxslt                   1.1.29                        5    conda-forge
....
r-xml2                    1.2.0                    r341_0    conda-forge
 

geoquery anaconda libxml2 • 371 views
ADD COMMENTlink modified 15 months ago by Martin Morgan ♦♦ 24k • written 15 months ago by 26109209510
Answer: Installing GEOQuery failed with conda
1
gravatar for James W. MacDonald
15 months ago by
United States
James W. MacDonald51k wrote:

Did you see this part?

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)

You need the libxml2 headers to install xml2, and there are some helpful ways to install listed, depending on the distro you are using.

ADD COMMENTlink written 15 months ago by James W. MacDonald51k
Answer: Installing GEOQuery failed with conda
1
gravatar for Martin Morgan
15 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

I think that this is basically a variant of C: Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH, where mixing conda and R installation mechanisms fails when there are system libraries in non-standard locations (see also this conda issue). You would instead like to say

conda install bioconductor-geoquery
ADD COMMENTlink written 15 months ago by Martin Morgan ♦♦ 24k
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