I am using R studio on Mac OS and I want to use caret package for some data analysis. However, caret depends on rlang package and when I try to load caret package I get this error -
> library(caret)
Error: package or namespace load failed for ‘caret’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘rlang’ 0.2.2 is already loaded, but >= 0.3.0.1 is required
In addition: Warning message:
package ‘caret’ was built under R version 3.4.4
I removed the rlang package from the UI and tried installing it again but I am facing below issue -
> install.packages("rlang")
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/rlang_0.3.0.1.tgz'
Content type 'application/x-gzip' length 1074663 bytes (1.0 MB)
==================================================
downloaded 1.0 MB
The downloaded binary packages are in
/var/folders/kh/9lkdq11x3sv56717v0700p_r_16f9p/T//RtmplrCvGX/downloaded_packages
> library(rlang)
Error in value[[3L]](cond) :
Package ‘rlang’ version 0.2.2 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘rlang’ is imported by ‘tidyr’, ‘purrr’, ‘ggplot2’, ‘plotly’, ‘dplyr’, ‘tibble’, ‘pillar’ so cannot be unloaded
In addition: Warning message:
package ‘rlang’ was built under R version 3.4.4
Here is my sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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
other attached packages:
[1] dummies_1.5.6 ISLR_1.2 mltools_0.3.5 data.table_1.10.4-3 ggplot2_3.0.0.9000 lattice_0.20-35
loaded via a namespace (and not attached):
[1] reshape2_1.4.3 purrr_0.2.4 colorspace_1.3-2 htmltools_0.3.6 viridisLite_0.3.0 yaml_2.1.16 plotly_4.8.0
[8] rlang_0.3.0.1 ModelMetrics_1.2.2 pillar_1.1.0 glue_1.2.0 withr_2.1.2 bindrcpp_0.2 foreach_1.4.4
[15] bindr_0.1 plyr_1.8.4 stringr_1.2.0 munsell_0.5.0 gtable_0.2.0 htmlwidgets_1.2 devtools_1.13.4
[22] codetools_0.2-15 memoise_1.1.0 curl_3.1 Rcpp_0.12.18 scales_1.0.0 jsonlite_1.5 digest_0.6.16
[29] stringi_1.1.6 dplyr_0.7.4 grid_3.4.3 tools_3.4.3 magrittr_1.5 lazyeval_0.2.1 tibble_1.4.2
[36] tidyr_0.7.2 pkgconfig_2.0.1 Matrix_1.2-12 assertthat_0.2.0 httr_1.3.1 iterators_1.0.10 R6_2.2.2
[43] nlme_3.1-131 compiler_3.4.3 git2r_0.21.0
Maybe try this -- Remove rlang, shutdown and restart R, and then reinstall `rlang'.
If you still want to install a specific version of rlang,
1) Go to https://cran.r-project.org/src/contrib/Archive/rlang/
2) Get URL to the specific version you need. (On Chrome, Right click- Copy URL, etc)
3) Start R, install.packages("[URL]", repo=NULL, type="source")
e.g install.packages("https://cran.r-project.org/src/contrib/Archive/rlang/rlang_0.2.2.tar.gz", repo=NULL, type="source")
Related
I tried to loading DESeq2 on R:
library(DESeq2)
The Error showed is:
Loading required package: GenomicRanges
Error: package or namespace load failed for ‘GenomicRanges’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
object 'vI' not found
Error: package ‘GenomicRanges’ could not be loaded
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomeInfoDb_1.22.1 IRanges_2.21.8 S4Vectors_0.25.15
[4] BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] rstudioapi_0.11 zlibbioc_1.32.0 R6_2.4.1
[4] fansi_0.4.1 tools_3.6.3 pkgbuild_1.0.6
[7] cli_2.0.2 withr_2.1.2 remotes_2.1.1
[10] assertthat_0.2.1 rprojroot_1.3-2 crayon_1.3.4
[13] processx_3.4.2 GenomeInfoDbData_1.2.2 BiocManager_1.30.10
[16] callr_3.4.3 bitops_1.0-6 ps_1.3.2
[19] RCurl_1.98-1.1 curl_4.3 glue_1.4.0
[22] compiler_3.6.3 backports_1.1.6 prettyunits_1.1.1
I blocked since 2 days. All the problem start for "S4Vectors" package. I solved it. I update the R. I donwloaded and manually put in the library r folder the "XVector" version ‘0.27.2’ as required from GenomicRanges.
I need to use DESeq2 to normalize my cont data. I open to use also something different from r
At the end, I fixed the problem uninstalled and re-installed all the R library from my PC keeping the same OS and R version. I continue to ignore the real identity of the problem.
I resolved this problem simply by removing the "GenomicRanges" and "IRange" packages and installing "GenomicRanges" again.
To remove these packages I used .libPaths() to find the library path and removed GenomicRanges" and "IRange" folders.
Im building an R package and when testing the package using devtools::check() I get an error when the test reaches the installation phase, saying:
Error: .onLoad failed in loadNamespace() for 'pillar', details:
call: utils::packageVersion("vctrs")
error: there is no package called 'vctrs'
Execution halted
ERROR: lazy loading failed for package
Neither pillar nor vctrs are mentioned in my description file, so they must be dependents of some other package that I depend on. Both pillar and vctrs are installed and I've also tried reinstalling them. They are stored in the the first .libPath entry. I tried installing pillar from github as was suggested by mfox9 here, but this failed for me, giving this error:
> devtools::install_github("r-lib/pillar")
Downloading GitHub repo r-lib/pillar#master
√ checking for file 'C:\Users\DESCRIPTION' (337ms)
- preparing 'pillar': (664ms)
√ checking DESCRIPTION meta-information ...
- installing the package to process help pages
- checking for LF line-endings in source and make files and shell scripts (8.5s)
- checking for empty or unneeded directories
- building 'pillar_1.4.2.9001.tar.gz'
Installing package into ‘Z:/’
(as ‘lib’ is unspecified)
The filename, directory name, or volume label syntax is incorrect.
Error: Failed to install 'pillar' from GitHub:
(converted from warning) installation of package ‘C:/Users/Temp/RtmpgjFfZl/file32586b634e28/pillar_1.4.2.9001.tar.gz’ had non-zero exit status
(note: z:/ is my correct R library address)
Can someone please help?
´´´
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 15063)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pillar_1.4.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 rstudioapi_0.10 magrittr_1.5 usethis_1.5.1
[5] devtools_2.2.0 pkgload_1.0.2 R6_2.4.0 rlang_0.4.0
[9] tools_3.6.1 pkgbuild_1.0.5 DT_0.8 packrat_0.5.0
[13] sessioninfo_1.1.1 cli_1.1.0 withr_2.1.2 remotes_2.1.0
[17] htmltools_0.3.6 ellipsis_0.2.0.1 assertthat_0.2.1 digest_0.6.20
[21] rprojroot_1.3-2 crayon_1.3.4 processx_3.4.1 callr_3.3.1
[25] fs_1.3.1 htmlwidgets_1.3 ps_1.3.0 curl_4.0
[29] testthat_2.2.1 glue_1.3.1 memoise_1.1.0 compiler_3.6.1
[33] desc_1.2.0 backports_1.1.4 prettyunits_1.0.2
´´´
I am trying to install packages in a fresh install of R in Visual Studio 2017. Some packages will install, but several give me the same error. An example is the 'rvest' package. When I try install.packages("rvest")
install.packages("rvest")
Installing package into ‘C:/Users/Sean/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rvest 0.3.2 0.3.3 FALSE
installing the source package ‘rvest’
trying URL 'https://mran.microsoft.com/snapshot/2019-04-15/src/contrib/rvest_0.3.3.tar.gz'
Content type 'application/octet-stream' length 1631059 bytes (1.6 MB)
downloaded 1.6 MB
In R CMD INSTALL
The downloaded source packages are in
‘C:\Users\Sean\AppData\Local\Temp\RtmpmuXBs1\downloaded_packages’
Warning message:
In utils::install.packages(...) :
installation of package ‘rvest’ had non-zero exit status
This happens also in 'rcmdcheck':
> install.packages("rcmdcheck")
Installing package into ‘C:/Users/Sean/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rcmdcheck 1.3.1 1.3.2 FALSE
installing the source package ‘rcmdcheck’
trying URL 'https://mran.microsoft.com/snapshot/2019-04-15/src/contrib/rcmdcheck_1.3.2.tar.gz'
Content type 'application/octet-stream' length 1408582 bytes (1.3 MB)
downloaded 1.3 MB
In R CMD INSTALL
The downloaded source packages are in
‘C:\Users\Sean\AppData\Local\Temp\RtmpmuXBs1\downloaded_packages’
Warning message:
In utils::install.packages(...) :
installation of package ‘rcmdcheck’ had non-zero exit status
My sessionInfo() shows:
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] FSVRegimeDetection_0.0.0.9000 aTSA_3.1.2 autoimage_2.0 FSVPreselection_0.0.0.9000 FSVTradingRules_0.0.0.9000 FinancialInstrument_1.3.1 quantmod_0.4-14
[8] FSVIndicators_0.0.0.9000 dlm_1.1-5 PerformanceAnalytics_1.5.2 TTR_0.23-4 FSVPositionSizing_0.0.0.9000 FSVDataCheck_0.0.0.9000 xts_0.11-2
[15] zoo_1.8-5 FSVLibraryUtilities_0.0.0.9000 roxygen2_6.1.1 usethis_1.5.0 devtools_2.0.2 ldhmm_0.4.5 RevoUtils_11.0.3
[22] RevoUtilsMath_11.0.0
loaded via a namespace (and not attached):
[1] ecd_0.9.1 pkgload_1.0.2 bit64_0.9-7 moments_0.14 assertthat_0.2.1 rtvs_1.0.0.0 RcppFaddeeva_0.1.0 blob_1.1.1 yaml_2.2.0 remotes_2.0.4
[11] sessioninfo_1.1.1 numDeriv_2016.8-1 pillar_1.3.1 RSQLite_2.1.1 backports_1.1.4 lattice_0.20-38 glue_1.3.1 quadprog_1.5-5 digest_0.6.18 colorspace_1.4-1
[21] plyr_1.8.4 pkgconfig_2.0.2 purrr_0.3.2 xtable_1.8-3 scales_1.0.0 processx_3.3.0 tibble_2.1.1 gmp_0.5-13.5 ggplot2_3.1.1 withr_2.1.2
[31] lazyeval_0.2.2 Rmpfr_0.7-2 cli_1.1.0 magrittr_1.5 crayon_1.3.4 memoise_1.1.0 ps_1.3.0 fs_1.2.7 gsl_2.1-6 xml2_1.2.0
[41] pkgbuild_1.0.3 tools_3.5.3 prettyunits_1.0.2 stringr_1.4.0 munsell_0.5.0 stabledist_0.7-1 FSVBackTest_0.0.0.9000 callr_3.2.0 compiler_3.5.3 rlang_0.3.4
[51] grid_3.5.3 rstudioapi_0.10 testthat_2.0.1 gtable_0.3.0 curl_3.3 DBI_1.0.0 polynom_1.4-0 R6_2.4.0 gridExtra_2.3 knitr_1.22
[61] dplyr_0.8.0.1 optimx_2018-7.10 bit_1.1-14 commonmark_1.7 rprojroot_1.3-2 desc_1.2.0 stringi_1.4.3 parallel_3.5.3 Rcpp_1.0.1 tidyselect_0.2.5
[71] xfun_0.6
Any help tracking down the source of this issue would be greatly appreciated!
I was able to get these packages to load using
type = "binary"
argument in the install.packages() method call. Ie:
install.packages("rvest", type = "binary")
You can try to install the github version of the package using devtools, as below:
install.packages("devtools")
devtools::install_github("tidyverse/rvest")
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 trying to install the quantstrat package in R. I already installed the other packages necessary for quantstrat, below is my session info.
sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252 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
other attached packages:
[1] blotter_0.12.4 PerformanceAnalytics_1.5.1 FinancialInstrument_1.2.0 foreach_1.4.3 quantmod_0.4-11
[6] TTR_0.23-2 devtools_1.13.4 xts_0.10-0 zoo_1.8-0 lubridate_1.7.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 rstudioapi_0.7 knitr_1.17 magrittr_1.5 lattice_0.20-35 R6_2.2.2 quadprog_1.5-5 stringr_1.2.0
[9] httr_1.3.1 tools_3.4.2 grid_3.4.2 git2r_0.19.0 withr_2.1.0 iterators_1.0.8 yaml_2.1.14 digest_0.6.12
[17] codetools_0.2-15 curl_3.0 memoise_1.1.0 stringi_1.1.5 compiler_3.4.2 boot_1.3-20
when I run the install packages this is what I get:
install.packages("quantstrat", repos="https://github.com/braverock/quantstrat.git")
Installing package into ‘C:/Users/augus/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
unable to access index for repository https://github.com/braverock/quantstrat.git/src/contrib:
cannot open URL 'https://github.com/braverock/quantstrat.git/src/contrib/PACKAGES'
Warning in install.packages :
package ‘quantstrat’ is not available (for R version 3.4.2)
Warning in install.packages :
unable to access index for repository https://github.com/braverock/quantstrat.git/bin/windows/contrib/3.4:
cannot open URL 'https://github.com/braverock/quantstrat.git/bin/windows/contrib/3.4/PACKAGES'
I have also tried to download a previous version and install it, but with no success, I got it from the followin link:
http://download.r-forge.r-project.org/bin/windows/contrib/3.2/quantstrat_0.9.1739.zip
install.packages("C:/Users/augus/Dropbox/Trading/R/quantstrat_0.9.17392.zip", repos = NULL)
Installing package into ‘C:/Users/augus/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open compressed file 'quantstrat/DESCRIPTION', probable reason 'No such file or directory'
Error in install.packages : cannot open the connection
Does someone know what I am doing wrong?
Thanks
Augusto
As noted in the comments above, for completeness here is an answer.
The most straightforward way to install the latest version of quantstrat is via github with devtools (the version of quantstrat on R-forge is now out of date):
library(devtools)
install_github("braverock/quantstrat")