I'm running R v3.2.0 with RStudio as well. The machine I'm running on has no internet access and therefore I'm having to download and install packages locally. I am trying to install ggplot2 which requires lots of dependecies (with their own dependencies) to be downloaded and installed. I have arrived at the point where most of them have been installed. However, I still get the following when I try:
> install.packages("~/R_packages/ggplot2_2.0.0.tar.gz", repos = NULL, type = "source")
Installing package into ‘/u01/app/oracle/product/12.1.0.2/dbhome_1/R/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No protocol specified
Warning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/u01/app/oracle/product/12.1.0.2/dbhome_1/R/library/scales/libs/scales.so':
/u01/app/oracle/product/12.1.0.2/dbhome_1/R/library/scales/libs/scales.so: invalid ELF header
ERROR: lazy loading failed for package ‘ggplot2’
* removing ‘/u01/app/oracle/product/12.1.0.2/dbhome_1/R/library/ggplot2’
Warning in install.packages :
installation of package ‘/home/oracle/R_packages/ggplot2_2.0.0.tar.gz’ had non-zero exit status
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Has anyone got any ideas why this is happening?
Edit:
Oracle Distribution of R version 3.2.0 (--)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Oracle Linux Server 6.7
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 LC_ADDRESS=en_US.UTF-8
[10] LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_0.4.2 stringi_0.4-1 nnet_7.3-9 randomForest_4.6-10 ROracle_1.2-1
[6] DBI_0.3.1 rpart_4.1-9 ORCH_2.5.1 ORCHstats_2.5.1 ORCHcore_2.5.1
[11] rJava_0.9-7 OREstats_1.5 MASS_7.3-40 OREbase_1.5 OREcommon_1.5
loaded via a namespace (and not attached):
[1] Rcpp_0.12.2 png_0.1-7 assertthat_0.1 R6_2.0.1 grid_3.2.0 OREembed_1.5 magrittr_1.5
[8] tools_3.2.0 parallel_3.2.0
Edit 2:
library(ggplot2)
No protocol specified
Attaching package: ‘ggplot2’
The following object is masked from ‘package:randomForest’:
margin
Warning message:
In fun(libname, pkgname) : couldn't connect to display ":0"
Related
I'm currently trying to use readFastq with the ShortRead library. I have specified the version of Bioconductor I need (3.14) in order to run it in R version 4.1 (which is the one I'm currently using). I keep getting an error message saying:
> library(ShortRead)
Error in library(Shortread) : there is no package called 'ShortRead'
and also:
ln: failed to create symbolic link 'libhts.so.2': Operation not supported
make: *** [Makevars:28: populate-usrlib-dir] Error 1
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/Rhtslib’
ERROR: dependency ‘Rhtslib’ is not available for package ‘Rsamtools’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/Rsamtools’
ERROR: dependency ‘Rsamtools’ is not available for package ‘GenomicAlignments’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/GenomicAlignments’
ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’, ‘Rhtslib’ are not available for package ‘ShortRead’
* removing ‘/home/jovyan/work/__dag_config__/R/libs/ShortRead’
and
ERROR: configuration failed for package ‘textshaping’
* removing ‘/opt/conda/envs/r/lib/R/library/textshaping’
* restoring previous ‘/opt/conda/envs/r/lib/R/library/textshaping’
* installing *source* package ‘ragg’ ...
** package ‘ragg’ successfully unpacked and MD5 sums checked
** using staged installation
and lastly
ERROR: configuration failed for package ‘ragg’
* removing ‘/opt/conda/envs/r/lib/R/library/ragg’
* restoring previous ‘/opt/conda/envs/r/lib/R/library/ragg’
The downloaded source packages are in
‘/tmp/RtmpgByRyT/downloaded_packages’
I would really appreciate som help with troubleshooting this or a "smarter" way to convert fastq.gz files to fasta files
The commands I've run so far are:
#Installing ShortRead package containing the readFastq function
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version="3.14")
BiocManager::install("GenomeInfoDbData")
BiocManager::install("GenomeInfoDb")
BiocManager::install("ShortRead")
#Loading the library
library(ShortRead)
Some extra session information:
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS/LAPACK: /opt/conda/envs/r/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.19
loaded via a namespace (and not attached):
[1] compiler_4.1.1 fastmap_1.1.0 cli_3.4.1 htmltools_0.5.3 tools_4.1.1
[6] rstudioapi_0.14 yaml_2.3.6 rmarkdown_2.17 knitr_1.40 xfun_0.34
[11] digest_0.6.30 rlang_1.0.6 evaluate_0.17
I do not understand why it won't install. I would it expect it to work when I have made sure to use the correct version
I am trying to install the R package mapview on Ubuntu but I get the error:
ERROR: lazy loading failed for package ‘mapview’
I have tried installing both the CRAN version of mapview and the development version, ie, by:
remotes::install_github("r-spatial/mapview")
In either case, I always get variations of the same message:
> install.packages("mapview")
Installing package into ‘/home/<my user name>/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/mapview_2.10.0.tar.gz'
Content type 'application/x-gzip' length 1683417 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘mapview’ ...
** package ‘mapview’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
corrupted size vs. prev_size
Aborted (core dumped)
ERROR: lazy loading failed for package ‘mapview’
* removing ‘/home/<my username>/R/x86_64-pc-linux-gnu-library/4.1/mapview’
Warning in install.packages :
installation of package ‘mapview’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpKtQmnI/downloaded_packages’
If I try the development version, it asks me to update other packages (eg, raster) but then the same problem occurs for that package.
Other postings have suggested that the error can be fixed by restarting the R session. I have not found this to be the case.
My Session Info is:
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C LC_TIME=en_NZ.UTF-8
[4] LC_COLLATE=en_NZ.UTF-8 LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_NZ.UTF-8
[7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 magrittr_2.0.1 usethis_2.1.3 devtools_2.4.3 pkgload_1.2.4
[6] R6_2.5.1 rlang_0.4.12 fastmap_1.1.0 tools_4.1.2 pkgbuild_1.2.1
[11] sessioninfo_1.2.2 cli_3.1.0 withr_2.4.3 ellipsis_0.3.2 remotes_2.4.2
[16] rprojroot_2.0.2 lifecycle_1.0.1 crayon_1.4.2 processx_3.5.2 purrr_0.3.4
[21] callr_3.7.0 fs_1.5.1 ps_1.6.0 testthat_3.1.1 curl_4.3.2
[26] memoise_2.0.1 glue_1.6.0 cachem_1.0.6 compiler_4.1.2 desc_1.4.0
[31] prettyunits_1.1.1
I can't reproduce your error, but you could solve it by installing R with Conda and then the package with https://anaconda.org/conda-forge/r-mapview
Whenever I try to install any packages in R I now get this error. This didn't used to happen and is new within the last month and seems to be ubiquitous across all packages I try to install.
I am using R studio but the error occurred when I tried to use just R alone, as well. Currently trying to install rscopus package but the error occurs with most all packages I have tried to install.
Thanks.
Console:
installing the source package ‘rscopus’
trying URL 'https://cran.rstudio.com/src/contrib/rscopus_0.6.3.tar.gz'
Content type 'application/x-gzip' length 40422 bytes (39 KB)
==================================================
downloaded 39 KB
Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
unknown timezone 'zone/tz/2018i.1.0/zoneinfo/America/New_York'
* installing *source* package ‘rscopus’ ...
** package ‘rscopus’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error : object ‘as_tibble’ is not exported by 'namespace:dplyr'
ERROR: lazy loading failed for package ‘rscopus’
* removing
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rscopus’
Warning in install.packages :
installation of package ‘rscopus’ had non-zero exit status
The downloaded source packages are in ‘/private/var/folders/wz/p_wg38vx11vcp94hhcw5dv_w0000gn/T/RtmpaJeH3b/downloaded_packages’
Sessioninfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS 10.14.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tibble_1.3.4 DescTools_0.99.21 dplyr_0.5.0 car_2.1-4
loaded via a namespace (and not attached):
[1] Rcpp_0.12.11 magrittr_1.5 splines_3.3.2 MASS_7.3-45 lattice_0.20-34
[6] R6_2.2.0 rlang_0.1.6 minqa_1.2.4 tools_3.3.2 nnet_7.3-12
[11] parallel_3.3.2 pbkrtest_0.4-6 grid_3.3.2 nlme_3.1-128 mgcv_1.8-15
[16] quantreg_5.29 DBI_0.5-1 MatrixModels_0.4-1 lme4_1.1-12 assertthat_0.1
[21] manipulate_1.0.1 Matrix_1.2-7.1 nloptr_1.0.4 boot_1.3-18 expm_0.999-2
[26] mvtnorm_1.0-6 SparseM_1.74 foreign_0.8-67
For anyone else with similar issues, I updated to the newest version of R and it seemed to solve the problem.
Thinking back to the origin of the problem, it coincided with updated to OS X Mojave.
I'm trying to install this package on a brand new setup of my Laptop W10/64, downloaded brand new RStudio 1.1.419 (as of today 1/28/2018), didn't do anything to profiles.
After running install.packages('tidyverse') I see a lot of dependencies errors like below, how to take care of them in one shot ? I assume should be some dependencies helper in install? Or there is other way to download 1G of R packages to have them all? Or should I have take of these missing brooms one by one? I did my home work and see so many thing about installation problems, assume this is OK for free version.
Warning in install.packages :
installation of package ‘callr’ had non-zero exit status
ERROR: dependencies 'rlang', 'utf8' are not available for package 'pillar'
* removing 'C:/Users/Lap10/Documents/R/win-library/3.2/pillar'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-32~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Lap10\Documents\R\win-library\3.2" C:\Users\Lap10\AppData\Local\Temp\Rtmp8g3UW7/downloaded_packages/pillar_1.1.0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘pillar’ had non-zero exit status
ERROR: dependencies 'rlang', 'tidyselect' are not available for package 'dbplyr'
* removing 'C:/Users/Lap10/Documents/R/win-library/3.2/dbplyr'
Warning in install.packages :
After going on missing packages I have this:
install.packages('rlang')
Installing package into ‘C:/Users/Lap10/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘rlang’
These will not be installed
library(rlang)
Error in inDL(x, as.logical(local), as.logical(now), ...) :
unable to load shared object 'C:/Users/Lap10/Documents/R/win-library/3.2/rlang/libs/x64/rlang.dll':
LoadLibrary failure: The specified procedure could not be found.
session info:
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_0.5.0
loaded via a namespace (and not attached):
[1] magrittr_1.5 R6_2.2.2 assertthat_0.2.0 DBI_0.7 tools_3.2.2 tibble_1.3.0
[7] Rcpp_0.12.10
>
Trying to install package "caret" on R 3.1.0 (Ubuntu 14.04.01 LTS) and running into a build error.
> install.packages('caret')
[...]
* installing *source* package ‘BradleyTerry2’ ...
** package ‘BradleyTerry2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : object ‘brglm’ is not exported by 'namespace:brglm'
ERROR: lazy loading failed for package ‘BradleyTerry2’
* removing ‘/home/br00t/R/x86_64-pc-linux-gnu-library/3.1/BradleyTerry2’
Warning in install.packages :
installation of package ‘BradleyTerry2’ had non-zero exit status
ERROR: dependency ‘BradleyTerry2’ is not available for package ‘caret’
* removing ‘/home/br00t/R/x86_64-pc-linux-gnu-library/3.1/caret’
Warning in install.packages :
installation of package ‘caret’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp7pWmvr/downloaded_packages’
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sp_1.0-16
loaded via a namespace (and not attached):
[1] grid_3.1.0 lattice_0.20-29 tools_3.1.0
Wasn't able to find anything helpful on the interwebs. Not sure if this is an issue with the BradleyTerry2 package or brglm... help?
Thanks,
br00t
If you are running a version of the brglm package greater than 0.5-9, uninstall and install brglm package version 0.5-9
I was able to get over the issue too by installing the dependencies. You may want to select your answer as the right one.