I'm the maintainer for the package 'rase' (link).
I haven't changed the code at all since Nov 9, 2015, when the package could load without problems. However, I have received emails asking about the following problem when loading the package:
> library(rase)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘Biostrings’
Error: package or namespace load failed for ‘rase’
I tried then to do it in my own computer, and I received the same message. Between the last time I loaded the package successfully (Nov 2015) and now, I upgraded R to v 3.2.3. Naively, I reinstalled v3.2.2, but the same error appears. I have checked rase code (git here) thoroughly, but no changes have been made and there is no reference whatsoever to 'Biostrings' (or any function within). 'rase' dependencies and imports do not include 'Biostrings'.
Any help would be much appreciated as I don't know why this is happening (I'm a novice when creating packages). I guess I could install 'Biostrings', but I don't want to make a seemingly unnecessary dependency.
Here is my sessionInfo:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)
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] ape_3.4 data.table_1.9.6
loaded via a namespace (and not attached):
[1] quadprog_1.5-5 lattice_0.20-33 mvtnorm_1.0-3 msm_1.6
[5] MASS_7.3-43 chron_2.3-47 grid_3.2.2 nnls_1.4
[9] nlme_3.1-121 magrittr_1.5 Matrix_1.2-2 splines_3.2.2
[13] tools_3.2.2 igraph_1.0.1 maps_3.0.2 parallel_3.2.2
[17] numDeriv_2014.2-1 survival_2.38-3 mnormt_1.5-3 clusterGeneration_1.3.4
[21] animation_2.4 expm_0.999-0
Biostrings is a BioConductor package which you install following the instructions on this page:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
If you add BioC as a known repository on your system, it will be installable via install.packages() too. Eg this would do
r <- getOption("repos")
r["CRAN"] <- "http://cran.rstudio.com"
r["BioCsoft"] <- "http://www.bioconductor.org/packages/release/bioc"
options(repos = r)
in your .Rprofile or Rprofile.site.
Related
I am creating the interactive tutorials for R for presentation using "learnr" package. For code checking, I need the package "gradethis". When I try to install this package by
"
remotes::install_github("rstudio-education/gradethis")
"
it gives the error message:
.
.
.
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘learnr’ 0.10.1 is being loaded, but >= 0.10.1.9007 is required
ERROR: lazy loading failed for package ‘gradethis’
─ removing ‘/private/var/folders/r2/3nmkgqc51q54tmhxl00tsk2908fpk9/T/RtmpaPONJB/Rinst15003850258d/gradethis’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'gradethis' from GitHub:
.
.
.
The error message shows "‘learnr’ 0.10.1 is being loaded, but >= 0.10.1.9007 is required", however on CRAN, 0.10.1 is the latest version:
https://cran.r-project.org/web/packages/learnr/index.html
Can anyone help for this case? Many thanks.
The following show sessionInfo()
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
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
loaded via a namespace (and not attached):
[1] compiler_3.5.1 rjson_0.2.20 plyr_1.8.6
[4] markdown_1.1 htmltools_0.5.1.9000 tools_3.5.1
[7] base64enc_0.1-3 yaml_2.2.1 Rcpp_1.0.6
[10] rmarkdown_2.6 knitr_1.31 xfun_0.20
[13] digest_0.6.27 tutorial_0.4.3 rlang_0.4.10.9000
[16] evaluate_0.14
Since gradethis is still in a developmental/experimental phase, it is currently only available through GitHub at rstudio/gradethis. gradethis currently requires the developmental version of learnr which is also not yet on CRAN.
Installing both packages from their GitHub repositories will likely resolve your issues:
# install.packages("remotes") # require {remotes}
remotes::install_github("rstudio/learnr")
remotes::install_github("rstudio/gradethis")
Edit: The gradethis repository is now hosted under the rstudio GitHub organization.
Reproduced the error (macOS Big Sur 11.1 / Rstudio 1.3.1093 / R version 4.0.3) and solved the issue by uninstalling learnr with remove.packages("learnr") then installing gradethis with dependencies (including the required version of learnr) using remotes::install_github("rstudio-education/gradethis").
If you get a warning that "Skipping install of 'gradethis' from a github remote, the SHA1 has not changed since last install", use the command remotes::install_github("rstudio-education/gradethis", force = TRUE)
Successfully installing the packages requires the ability to compile from source (instructions for macOS Big Sur: https://stackoverflow.com/a/65334247/12957340)
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 am running an Rscript using crontab. In that Rscript command, I am trying to load googlesheets package using library(googlesheets). Note, I have already installed googlesheets package is already installed.
I am getting this error:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/sparavas/R/x86_64-pc-linux-gnu-library/3.2/purrr/libs/purrr.so':
/home/sparavas/R/x86_64-pc-linux-gnu-library/3.2/purrr/libs/purrr.so: ELF file OS ABI invalid
In addition: Warning message:
package 'googlesheets' was built under R version 3.2.3
Error: package or namespace load failed for 'googlesheets'
Execution halted
When I run the same script from terminal, I am not getting this error. This errors comes only when ran through crontab.
I also tried to get below sessionInfo (if this might help to detect the problem) :
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] methods stats graphics grDevices utils datasets base
other attached packages:
[1] devtools_1.11.1 reshape2_1.4.1 DIVER_0.1.1 hash_2.2.6
[5] dplyr_0.4.3
loaded via a namespace (and not attached):
[1] Rcpp_0.12.1 digest_0.6.8 withr_1.0.1 assertthat_0.1 R6_2.1.0
[6] plyr_1.8.2 DBI_0.3.1 magrittr_1.5 stringi_0.4-1 tools_3.2.0
[11] stringr_1.0.0 parallel_3.2.0 memoise_1.0.0
I also tried reinstalling packages purrr, dplyr, googlesheets. Please suggest what I am missing.
Also what does:
ELF file OS ABI invalid
mean?
I created an R package and loaded it to github (microdadosBrasil). When I try to install the package (as a user would) I get the following error:
devtools::install_github("lucasmation/microdadosBrasil")
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘stringi’
I tried solving this by adding stringi to the package dependencies
In DESCRIPTION in included:
Imports:
stringi
I also included the package import at NAMESPACE
import(stringi)
But, even then I get the same installation error.
To be hones I'm not even aware of any explicit function in my package that uses the stringi package.
If I install stringi before then the microdadosBrasil installation works:
install.packages('stringi')
devtools::install_github("lucasmation/microdadosBrasil")
This is the session information when error occurs (before pre-installing stringi)
sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.1.3
The problem is due to dependencies of packages because one package calls file in another package and so on (like recursion). So first try to install all dependencies of the package then definitely this package will work.
I would like to install the package GeoXp, but R doesn't let me...see the error below...
>install.packages("GeoXp")
...
configure: using libpng dynamic linkage
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’
* removing ‘/home/****/R/x86_64-pc-linux-gnu-library/3.0/rgl’
Warning in install.packages :
installation of package ‘rgl’ had non-zero exit status
ERROR: dependency ‘rgl’ is not available for package ‘GeoXp’
* removing ‘/home/******/R/x86_64-pc-linux-gnu-library/3.0/GeoXp’
Warning in install.packages :
installation of package ‘GeoXp’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpAbblyJ/downloaded_packages’
> library("GeoXp")
Error in library("GeoXp") : there is no package called ‘GeoXp’
Well, there seems to be a problem with the dependencies...but installing rgl does not work either...
Here my session info:
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] spacetime_1.1-3 sp_1.0-17
loaded via a namespace (and not attached):
[1] grid_3.0.2 intervals_0.15.0 lattice_0.20-29
tools_3.0.2 xts_0.9-7 zoo_1.7-11
What can I do?
GeoXp has a dependency on rgl, tries to install that first, but fails there. rgl needs to have the X11 development libraries, as well as the (open source) OpenGL development and run-time libraries (mesa). For Ubuntu, you need to install the system packages libgl1-mesa-dev and libglu1-mesa-dev first (with apt-get or sth similar), then install in R package rgl, then GeoXp.
I think the problem is that you have to install X library and gl
Ops, sorry #Pascal, I did not see your comment.