GeneDMRs is an R package to detect the differentially methylated regions based on genes, gene body, CpG islands and gene body interacted with CpG island features.
installing source package ‘ggtree’ ...
using staged installation
R
inst
byte-compile and prepare package for lazy loading
Error in get(x, envir = ns, inherits = FALSE) :
object 'rect_to_poly' not found
Error: unable to load R code in package ‘ggtree’
Execution halted
ERROR: lazy loading failed for package ‘ggtree’
removing ‘/home/juaguila/R/x86_64-pc-linux-gnu-library/4.3/ggtree’
ERROR: dependency ‘ggtree’ is not available for package ‘enrichplot’
removing ‘/home/juaguila/R/x86_64-pc-linux-gnu-library/4.3/enrichplot’
ERROR: dependency ‘enrichplot’ is not available for package ‘clusterProfiler’
The downloaded source packages are in
‘/tmp/RtmpuCZWpL/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/local/lib/R/site-library
packages:
bbmle, bdsmatrix, BH, cli, coda, data.table, fastcluster, filelock, glue, locfit,
matrixStats, R.oo, Rcpp, RCurl, readr, rlang, vroom, WGCNA, yaml
Old packages: 'systemfonts', 'textshaping'
Update all/some/none? [a/s/n]:
a
...
...
The downloaded source packages are in
‘/tmp/RtmpuCZWpL/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as or greater than current; use force = TRUE to
re-install: 'devtools' 'corrplot' 'dplyr' 'ffbase' 'genomation' 'pheatmap' 'plotrix' 'qqman'
'RCircos' 'VennDiagram' 'org.Mm.eg.db'
2: In install.packages(...) :
installation of package ‘ggtree’ had non-zero exit status
3: In install.packages(...) :
installation of package ‘enrichplot’ had non-zero exit status
4: In install.packages(...) :
installation of package ‘clusterProfiler’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘systemfonts’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘textshaping’ had non-zero exit status
Then I try installing ggtree and it fails too;
BiocManager::install("ggtree")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'ggtree'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/ggtree_3.8.2.tar.gz'
Content type 'application/gzip' length 360923 bytes (352 KB)
downloaded 352 KB
installing source package ‘ggtree’ ...
using staged installation
R
inst
byte-compile and prepare package for lazy loading
Error in get(x, envir = ns, inherits = FALSE) :
object 'rect_to_poly' not found
Error: unable to load R code in package ‘ggtree’
Execution halted
ERROR: lazy loading failed for package ‘ggtree’
The downloaded source packages are in
‘/tmp/RtmpuCZWpL/downloaded_packages’
Warning messages:
1: In install.packages(...) :
installation of package ‘ggtree’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘systemfonts’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘textshaping’ had non-zero exit status
Hi, I am trying to install the software in Linux using Rstudio and it keeps on failing and I can't install it.
I tried to install the dependencies and it fails:
The downloaded source packages are in ‘/tmp/RtmpuCZWpL/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/local/lib/R/site-library packages: bbmle, bdsmatrix, BH, cli, coda, data.table, fastcluster, filelock, glue, locfit, matrixStats, R.oo, Rcpp, RCurl, readr, rlang, vroom, WGCNA, yaml Old packages: 'systemfonts', 'textshaping' Update all/some/none? [a/s/n]: a
... ... The downloaded source packages are in ‘/tmp/RtmpuCZWpL/downloaded_packages’ Warning messages: 1: package(s) not installed when version(s) same as or greater than current; use
force = TRUEto re-install: 'devtools' 'corrplot' 'dplyr' 'ffbase' 'genomation' 'pheatmap' 'plotrix' 'qqman' 'RCircos' 'VennDiagram' 'org.Mm.eg.db' 2: In install.packages(...) : installation of package ‘ggtree’ had non-zero exit status 3: In install.packages(...) : installation of package ‘enrichplot’ had non-zero exit status 4: In install.packages(...) : installation of package ‘clusterProfiler’ had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘systemfonts’ had non-zero exit status 6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘textshaping’ had non-zero exit statusThen I try installing ggtree and it fails too;
The downloaded source packages are in ‘/tmp/RtmpuCZWpL/downloaded_packages’ Installation paths not writeable, unable to update packages path: /usr/local/lib/R/site-library packages: bbmle, bdsmatrix, BH, cli, coda, data.table, fastcluster, filelock, glue, locfit, matrixStats, R.oo, Rcpp, RCurl, readr, rlang, vroom, WGCNA, yaml Old packages: 'systemfonts', 'textshaping' Update all/some/none? [a/s/n]: a
ERROR: configuration failed for package ‘textshaping’
The downloaded source packages are in ‘/tmp/RtmpuCZWpL/downloaded_packages’ Warning messages: 1: In install.packages(...) : installation of package ‘ggtree’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘systemfonts’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘textshaping’ had non-zero exit status