Say I'm developing a package called magicr to do some statistical magic and I want it to use functions from another package called fairydust which (hypothetically) exists on CRAN.
Unfortunately fairydust has just released version 2.0.0 to CRAN and completely broken the functions I was planning to use.
So I update my DESCRIPTION
Imports:
fairydust (<= 1.9.9)
And build the package and try a test install into a clean library
devtools::install_local("~path/to/magicr")
Installing magicr
Installing 1 package: fairydust
Installing package into /path/to/current/library/fairydust
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/fairydust_2.0.0.zip'
Content type 'application/zip' length 11235813 bytes (11.2 MB)
downloaded 11.2 MB
package ‘fairydust’ successfully unpacked and MD5 sums checked
* installing *source* package 'magicr' ...
** R
** inst
** tests
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'fairydust' 2.0.0 is being loaded, but <= 1.9.9 is required
ERROR: lazy loading failed for package 'magicr'
* removing 'path/to/current/library/magicr'
Error: Command failed (1)
So when resolving dependencies it simply installed the most recent version of fairydust from CRAN and then checked the version when trying to load magicr.
Is there a way to get the required version of fairydust automatically when magicr is installed without building and pointing to a custom repository (a la drat and miniCRAN).
I know that this is super old but since this was a top hit in my search: R apparently does not respect maximum versions, just >=
Source
Related
Whenever I try to install tidyverse in R v 3.6.2
I receive the following error message:
Installing package into ‘C:/Users/daeb/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependency ‘broom’
There is a binary version available but the source version is later:
binary source needs_compilation
broom 0.5.3 0.5.4 FALSE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tidyverse_1.3.0.zip'
Content type 'application/zip' length 440101 bytes (429 KB)
downloaded 429 KB
package ‘tidyverse’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\daeb\AppData\Local\Temp\RtmpuWXq4I\downloaded_packages
installing the source package ‘broom’
trying URL 'https://cran.rstudio.com/src/contrib/broom_0.5.4.tar.gz'
Content type 'application/x-gzip' length 1228129 bytes (1.2 MB)
downloaded 1.2 MB
* installing *source* package 'broom' ...
** package 'broom' 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
Fejl i loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called 'zeallot'
Kald: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Kørsel stoppet
ERROR: lazy loading failed for package 'broom'
* removing 'C:/Users/daeb/Documents/R/win-library/3.6/broom'
Warning in install.packages :
installation of package ‘broom’ had non-zero exit status
I have tried reinstalling both R and Rstudio but it does not solve the problem. I tried installing Rtools, but it does not work either. It appears I have to solve the source/binary issue with broom but I do not know how.
As #hplieninger suggests, the proximal problem is that the installation of broom is looking for the zeallot package, which isn't installed:
there is no package called 'zeallot'
You should try manually installing the zeallot package (install.packages("zeallot")) and then try installing tidyverse again.
It might also help to say "no" when R asks you whether you want to install the packages with more recent source-code versions from source rather than binary. (The worst thing that can happen is that you end up with slightly older versions of some packages.)
However it's surprising that this requirement comes up. Are you using install.packages("tidyverse")? Are you specifying something like dependencies=TRUE?
Because according to the CRAN index pages
The current version of broom (0.5.4, apparently the same version that R is trying to install for you) doesn't directly import zeallot: it Depends only on R and
Imports: backports, dplyr, generics (≥ 0.0.2), methods, nlme, purrr, reshape2, stringr, tibble, tidyr
The current version of zeallot shouldn't obviously be needed. The packages that use it are:
Reverse imports: completejourney, graphTweets, ipumsr, keras, mlflow, statsExpressions
Reverse suggests: listarrays, SDMtune, vctrs
I'm trying to install the package "circlize" and I am having trouble resolving what seems to be a simple error.
When I run:
install.packages("circlize")
It says:
Installing package into ‘*file location*/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependency ‘GlobalOptions’ is not available
There is a binary version available but the source version is later:
binary source needs_compilation
circlize 0.3.10 0.4.3 FALSE
installing the source package ‘circlize’
trying URL 'https://mirrors.sorengard.com/cran/src/contrib/circlize_0.4.3.tar.gz'
Content type 'application/x-gzip' length 2456906 bytes (2.3 MB)
downloaded 2.3 MB
* installing *source* package 'circlize' ...
** package 'circlize' successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace 'GlobalOptions' 0.0.11 is being loaded, but >= 0.0.12 is required
ERROR: lazy loading failed for package 'circlize'
* removing '*file location*/3.2/circlize'
Warning in install.packages :
running command '"*file location*/x64/R" CMD INSTALL -l "*file location*\3.2" *file location*/downloaded_packages/circlize_0.4.3.tar.gz' had status 1
Warning in install.packages :
installation of package ‘circlize’ had non-zero exit status
The downloaded source packages are in
‘*file location*\downloaded_packages’
These parts seem most relevant to me:
dependency ‘GlobalOptions’ is not available
namespace 'GlobalOptions' 0.0.11 is being loaded, but >= 0.0.12 is required
When I run sessionInfo() I see under "other attached packages": [1] GlobalOptions_0.0.11
My best guess is that I have the wrong version of GlobalOptions -- I see that GlobalOptions v0.0.13 is available here, but being new to R, I'm not sure what to do now to get the right version up and running.
I'd really appreciate if someone could tell me where I should look next. (I looked through the documentation within that link, but I'm still lost about what to do now.) Thanks!
If you have R version >=3.3.0 you should
install GlobalOptions_0.0.13 from CRAN
install.packages("GlobalOptions")
quit and restart R
re-install circlize from source as before.
If you have an older R version, update R to a more recent version first.
Question: unable to install dplyr in R... code below. Anyone offer any solutions?
I'm on a mac osx sierra and R Version 1.0.136
> install.packages("dplyr")
There is a binary version available but the source version
is later:
binary source needs_compilation
dplyr 0.5.0 0.7.0 TRUE
Do you want to install from sources the package which needs compilation?
y/n:
y
installing the source package ‘dplyr’
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.7.0.tar.gz'
Content type 'application/x-gzip' length 690938 bytes (674 KB)
==================================================
downloaded 674 KB
* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘dplyr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/dplyr’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/dplyr’
Warning in install.packages :
installation of package ‘dplyr’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/ll/6vx1dr1n5bb9zwbv1z9v53z00000gn/T/RtmpitMpQn/downloaded_packages’
> library(dplyr)
Error: package or namespace load failed for ‘dplyr’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘DBI’
Not sure why this isn't working! Tried to download manually and it didn't work either (similar/same warnings/errors)
A new dplyr version was accepted into CRAN yesterday. Usually CRAN provides packages for both Windows and OSX in binary form, but it takes up to 48 hours for CRAN to provide the compiled packages.
When you try to install a package in that time window, R asks you to either install the previous binary version or the new version from source. If you decide to install the version from source you will need to have a c++ compiler.
The easiest thing for you to do is to either install the previous binary package or wait until the latest version gets compiled at CRAN.
Checkout https://cran.r-project.org/web/packages/dplyr/index.html to see if the binaries for your OS are already available.
Update: It seems there are some issues with the latest dplyr version, and the OSX compilation seems to fail. More info here: https://cran.r-project.org/web/checks/check_results_dplyr.html. I would rather stay with 0.5.0 until those issues are ironed out.
> require("caret")
Loading required package: caret
Loading required package: lattice
Loading required package: ggplot2
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘pbkrtest’
So I found that there is lack of "pbkrtest" then I tried to reinstall it.
> install.packages("pbkrtest")
Installing package into ‘C:/Users/ADMIN/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is
later:
binary source needs_compilation
pbkrtest 0.4-2 0.4-3 FALSE
installing the source package ‘pbkrtest’
trying URL 'https://rweb.crmda.ku.edu/cran/src/contrib/pbkrtest_0.4- 3.tar.gz'
Content type 'application/x-gzip' length 164415 bytes (160 KB)
downloaded 160 KB
* installing *source* package 'pbkrtest' ...
** package 'pbkrtest' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'stats::sigma' when loading 'pbkrtest'
Error : object 'sigma' is not exported by 'namespace:stats'
ERROR: lazy loading failed for package 'pbkrtest'
* removing 'C:/Users/ADMIN/Documents/R/win-library/3.2/pbkrtest'
The downloaded source packages are in
‘C:\Users\ADMIN\AppData\Local\Temp\Rtmpk7mJT0\downloaded_packages’
Warning messages:
1: running command '"D:/R-3.2.3/bin/x64/R" CMD INSTALL -l
"C:\Users\ADMIN\Documents\R\win-library\3.2"
C:\Users\ADMIN\AppData\Local\Temp\Rtmpk7mJT0/downloaded_packages/pbkrtest_0.4- 3.tar.gz' had status 1
2: In install.packages("pbkrtest") :
installation of package ‘pbkrtest’ had non-zero exit status
It seems like that the installation keeps failing.
As a result, I couldn't use other code using caret packages.
I faced this problem as well on Windows 7. I did following steps in the sequence and it worked.
a) Make sure your R version is updated latest R release 3.2.3
b) The default sources seems to be installing Unix version. So I manually downloaded https://cran.r-project.org/web/packages/pbkrtest/index.html for windows
c) Use manually install function from R menu to install the package.
Cheers,
Ratan
Check version of R by typing version in your console.
If version is not "version.string R version 3.3.2" or later then
Install new version of R from https://cran.r-project.org/bin/windows/base/
Update R version using Tools => Global Options in RStudio.
install package using "install.packages("caret")" in your console.
do require(caret).
test using ?createDataPartition.
I am trying to install the mediation package. However, this fails due to lacking dependencies:
> install.packages("mediation")
Installing package into ‘/home/simoncolumbus/R/i686-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/mediation_4.4.4.tar.gz'
Content type 'application/x-gzip' length 1463736 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb
* installing *source* package ‘mediation’ ...
** package ‘mediation’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace ‘lattice’ 0.20-24 is already loaded, but >= 0.20.27 is required
Error : package ‘sandwich’ could not be loaded
ERROR: lazy loading failed for package ‘mediation’
* removing ‘/home/simoncolumbus/R/i686-pc-linux-gnu-library/3.0/mediation’
Warning in install.packages :
installation of package ‘mediation’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpWpmJqS/downloaded_packages’
This is somewhat surprising, because both lattice and sandwich, as well as zoo (which calls lattice) are up to date:
> installed.packages()
lattice "lattice" "/home/simoncolumbus/R/i686-pc-linux-gnu-library/3.0" "0.20-31" "recommended"
sandwich "sandwich" "/home/simoncolumbus/R/i686-pc-linux-gnu-library/3.0" "2.3-3" NA
zoo "zoo" "/home/simoncolumbus/R/i686-pc-linux-gnu-library/3.0" "1.7-12" NA
I've tried unloading the packages, updating them, installing them via the package manager - nothing seems to have an impact, though. Any suggestions?
Edit: Fixed the problem by updating to the latest available version of R; must be some incompatibility with the old version I was running that caused this.
Exit R. Delete the .Rdata file. Restart. The .Rdata file is able to hold and load packages.