Installing GEOQuery failed with conda
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261092095 ▴ 10
@261092095-16052
Last seen 2.9 years ago

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 • 619 views
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@james-w-macdonald-5106
Last seen 12 hours ago
United States

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.

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1
Entering edit mode
@martin-morgan-1513
Last seen 15 days ago
United States

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
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