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Last seen 6.2 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
