I need biomaRT but it is not installing. How do I fix this?
BiocManager::install("biomaRt")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://mirror.las.iastate.edu/CRAN
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Warning message:
package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'biomaRt'
This doesn't look like an error. The relevant part of the message is
package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'biomaRt'
Essentially, this is saying "You've already got the biomaRt package installed and it's the same version as in Bioconductor, so you don't need to do anything."
You should be able to load biomaRt with: library(biomaRt).
Related
I am trying to use package glmmTMB. When I call library(glmmTMB) this is the error message:
">library(glmmTMB)
Error: package or namespace load failed for ‘glmmTMB’ in inDL(x, as.logical(local), as.logical(now), ...):
function 'Rcpp_precious_remove' not provided by package 'Rcpp'
In addition: Warning messages:
1: package ‘glmmTMB’ was built under R version 4.0.5
2: In checkMatrixPackageVersion() :
Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.2.18
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
I have tried using install.packages('TMB', type = 'source') with no luck. Any ideas?
It's a FAQ -- search for 'Rcpp_precious_remove' not provided by package 'Rcpp'.
In short you are mixing a NEWER compilatio nof something that was built with Rcpp 1.0.7 present with an older installed version which lacks the symbol.
Fix: install.packages("Rcpp") to get the newer Rcpp. And I generally recommend regular update.packages() runs to avoid these issues.
I was trying to install ripgrep_all using cargo install ripgrep_all. It gave the following error:
% cargo install ripgrep_all
Updating crates.io index
Installing ripgrep_all v0.9.6
error: failed to compile `ripgrep_all v0.9.6`, intermediate artifacts can be found at `/tmp/cargo-install5HlOMt`
Caused by:
failed to select a version for the requirement `cachedir = "^0.1.1"`
candidate versions found which didn't match: 0.3.0, 0.2.0
location searched: crates.io index
required by package `ripgrep_all v0.9.6`
Then I searched a bit and found:
It looks like cachedir yanked version 0.1.1.
And the solution was to:
cargo install --locked ripgrep_all
I was able to install it successfully. However, During the installation it said:
% cargo install --force --locked ripgrep_all
Updating crates.io index
Installing ripgrep_all v0.9.6
warning: package `cachedir v0.1.1` in Cargo.lock is yanked in registry `crates.io`, consider running without --locked
warning: package `smallvec v1.4.0` in Cargo.lock is yanked in registry `crates.io`, consider running without --locked
It made me curious. What does Yank mean in rust world?
It means that the package has been marked as "yanked". This is usually done when the authors of have package have a very compelling reason that a certain version of a package should not be used at all, and to very strongly suggest that the package should not be used. You can ignore yanks with --force to force yanked packages to be used, but that is usually a bad idea: packages were usually yanked for a good reason.
In your case: The yanked cachedir 0.1.X version is a completely different package with a different author than the newer versions. The older versions are unmaintained and cannot be updated (since cachedir now has a different owner who publishes a different package), so the new owner of cachedir yanked the older versions. smallvec 1.4.0 has a bug where it causes Undefined Behaviour when used with zero-sized types, and that UB is bad enough that it is exceedingly unlikely that you actually want to use that version. The fix to this is to update to a later version of smallvec that doesn't have that bug.
I'm trying to include a specific version of a library in a Haskell project. The library is bed-and-breakfast (which is used for martix operations), but I need the specific version 0.4.3 which fixed a bug with the multiplication implementation.
So, my stack.yaml looks like this:
flags: {}
extra-package-dbs: []
packages:
- .
extra-deps:
- bed-and-breakfast-0.4
- base-4.6.0.1
resolver: lts-12.8
But I'm getting this error when building:
Error: While constructing the build plan, the following exceptions were encountered:
In the dependencies for bed-and-breakfast-0.4:
base-4.11.1.0 from stack configuration does not match >=4.5 && <4.7 (latest matching version
is 4.6.0.1)
needed due to realworldhaskell-0.1.0.0 -> bed-and-breakfast-0.4
Some different approaches to resolving this:
* Set 'allow-newer: true' to ignore all version constraints and build anyway.
* Consider trying 'stack solver', which uses the cabal-install solver to attempt to find some
working build configuration. This can be convenient when dealing with many complicated
constraint errors, but results may be unpredictable.
* Recommended action: try adding the following to your extra-deps
in C:\Users\info\Desktop\Projects\haskell\stack.yaml:
- base-4.6.0.1
I've done the recommended action but it didn't solve anything. I've tried using different resolvers to see if it's an issue with my GHCi version but nothings worked. What is the best way to interpret error messages like this and how should I proceed?
EDIT:
If I remove -base.4.6.0.1 and add allow-newer: true I get this:
WARNING: Ignoring out of range dependency (allow-newer enabled): base-4.11.1.0. bed-and-breakfast requires: >=4.5 && <4.7
bed-and-breakfast-0.4: configure
Progress 1/2
-- While building custom Setup.hs for package bed-and-breakfast-0.4 using:
C:\sr\setup-exe-cache\x86_64-windows\Cabal-simple_Z6RU0evB_2.2.0.1_ghc-8.4.3.exe --builddir=.stack-work\dist\7d103d30 configure --with-ghc=C:\Users\info\AppData\Local\Programs\stack\x86_64-windows\ghc-8.4.3\bin\ghc.EXE --with-g
hc-pkg=C:\Users\info\AppData\Local\Programs\stack\x86_64-windows\ghc-8.4.3\bin\ghc-pkg.EXE --user --package-db=clear --package-db=global --package-db=C:\sr\snapshots\76fd1958\pkgdb --package-db=C:\Users\info\Desktop\Projects\haskell\
.stack-work\install\8c390635\pkgdb --libdir=C:\Users\info\Desktop\Projects\haskell\.stack-work\install\8c390635\lib --bindir=C:\Users\info\Desktop\Projects\haskell\.stack-work\install\8c390635\bin --datadir=C:\Users\info\Desktop\Proj
ects\haskell\.stack-work\install\8c390635\share --libexecdir=C:\Users\info\Desktop\Projects\haskell\.stack-work\install\8c390635\libexec --sysconfdir=C:\Users\info\Desktop\Projects\haskell\.stack-work\install\8c390635\etc --docdir=C:
\Users\info\Desktop\Projects\haskell\.stack-work\install\8c390635\doc\bed-and-breakfast-0.4 --htmldir=C:\Users\info\Desktop\Projects\haskell\.stack-work\install\8c390635\doc\bed-and-breakfast-0.4 --haddockdir=C:\Users\info\Desktop\Pr
ojects\haskell\.stack-work\install\8c390635\doc\bed-and-breakfast-0.4 --dependency=array=array-0.5.2.0 --dependency=base=base-4.11.1.0 --dependency=binary=binary-0.8.5.1 --dependency=deepseq=deepseq-1.4.3.0 --dependency=template-hask
ell=template-haskell-2.13.0.0 --extra-include-dirs=C:\Users\info\AppData\Local\Programs\stack\x86_64-windows\msys2-20150512\mingw64\include --extra-lib-dirs=C:\Users\info\AppData\Local\Programs\stack\x86_64-windows\msys2-20150512\min
gw64\bin --extra-lib-dirs=C:\Users\info\AppData\Local\Programs\stack\x86_64-windows\msys2-20150512\mingw64\lib --exact-configuration
Process exited with code: ExitFailure 1
Logs have been written to: C:\Users\info\Desktop\Projects\haskell\.stack-work\logs\bed-and-breakfast-0.4.log
Configuring bed-and-breakfast-0.4...
Cabal-simple_Z6RU0evB_2.2.0.1_ghc-8.4.3.exe: The package has an impossible
version range for a dependency on an internal library: bed-and-breakfast
==0.3.2. This version range does not include the current package, and must be
removed as the current package's library will always be used.
EDIT 2:
Ok, so I'm guessing that the bed-and-breakfast library needs base 4.11.1.0 which is included in GHCi 6.10.2 (according to https://wiki.haskell.org/Base_package) so I need a resolver which matches that GHCi version. Where can I find out what resolver version that is?
Here is the constraint on the latest available bed-and-breakfast package: base (>=4.5 && <4.7), which means it will likely not even compile with GHC version higher then 7.6. Considering that there is even no LTS snapshot prior to GHC 7.8, you are out of luck with that package.
To say it in another words, the package is outdated and your choices are:
submit an issue and hope maintainer will do something about it
try to make it work with newer ghc yourself
Use a different package
I'm currently trying to use pandoc (as a Haskell module, not as a program) to convert MediaWiki text to other formats.
Let's assume this program:
import Text.Pandoc.Readers.MediaWiki
main = do print "foo"
When using runghc to run it, I get the following error message:
pandock.hs:1:8:
Could not find module `Text.Pandoc.Readers.MediaWiki'
Use -v to see a list of the files searched for.
My first assumption was that pandoc was either not installed or incorrectly installed. Therefore I reinstalled it with --force-reinstalls
$ cabal install pandoc --reinstall
[...]
In order, the following will be installed:
pandoc-1.12.3.1 (reinstall) changes: old-time-1.1.0.1 added
[...]
[32 of 55] Compiling Text.Pandoc.Readers.MediaWiki ( src/Text/Pandoc/Readers/MediaWiki.hs, dist/build/Text/Pandoc/Readers/MediaWiki.o )
[...]
Installing library in
/home/uli/.cabal/lib/x86_64-linux-ghc-7.6.3/pandoc-1.12.3.1
Installing executable(s) in /home/uli/.cabal/bin
Registering pandoc-1.12.3.1...
Installed pandoc-1.12.3.1
The output of runghc -v pandock.hs is quite long, I assume the relevant part is:
*** Chasing dependencies:
Chasing modules from: *pandock.hs
pandock.hs:1:8:
Could not find module `Text.Pandoc.Readers.MediaWiki'
Locations searched:
Text/Pandoc/Readers/MediaWiki.hs
Text/Pandoc/Readers/MediaWiki.lhs
Failed, modules loaded: none.
However, both ~/.cabal/lib/x86_64-linux-ghc-7.6.3/pandoc-1.12.3.1/Text/Pandoc/Readers/Mediawiki/MediaWiki.hi and ~/.cabal/bin/pandoc exist. How can I make GHC properly recognize the cabal-installed package?
Any help will be appreciated!
When trying to reproduce this issue on other computers, only 2 out of 5 computers had this issue. On both of them I installed cabal packages in about the same way and order.
In retrospect I assume this issue arose because of some broken packages wreaking havoc:
$ ghc-pkg check
There are problems in package feed-0.3.9.2:
dependency "xml-1.3.13-dd52b1688e97a3c6cd0aa48dba7b153e" doesn't exist
There are problems in package hxt-9.3.1.3:
dependency "network-2.4.2.2-ea77cdf1bc747bc58308fdeb52745c4d" doesn't exist
There are problems in package hspec-1.8.1.1:
dependency "QuickCheck-2.6-409fcc32c191cd6e04afdebb15869820" doesn't exist
There are problems in package quickcheck-io-0.1.0:
dependency "QuickCheck-2.6-409fcc32c191cd6e04afdebb15869820" doesn't exist
There are problems in package regex-compat-0.95.1:
dependency "regex-base-0.93.2-2023953b859e6f91efe89733d2ef5421" doesn't exist
There are problems in package regex-posix-0.95.2:
dependency "regex-base-0.93.2-2023953b859e6f91efe89733d2ef5421" doesn't exist
There are problems in package hxt-9.3.1.2:
dependency "network-2.4.2.2-ea77cdf1bc747bc58308fdeb52745c4d" doesn't exist
The following packages are broken, either because they have a problem
listed above, or because they depend on a broken package.
feed-0.3.9.2
hxt-9.3.1.3
hspec-1.8.1.1
quickcheck-io-0.1.0
regex-compat-0.95.1
regex-posix-0.95.2
hxt-9.3.1.2
MissingH-1.2.0.2
yesod-test-1.2.1
Note that neither pandoc nor yaml (I installed it after asking the question and had the exact same issues as with pandoc) are listed there.
For users also having a similar problem, please ensure:
The package is installed and you're not inside any sandbox where the package is not installed.
In the directory where you're executing the test script, ensure that there is no Text/Pandoc folder (or equivalent, depending on the package causing the problem
Run your test script with runghc -v to check if it searches the proper directory
ghc-pkg list lists your package as installed, and no packages are broken (use ghc-pkg check to check)
I solved my problem by renaming ~/.cabal and ~/.ghc. Note that I did this lacking a proper solution, I think you should only do this as a last resort.
I want to use Yesod web framework with yesod-auth-oauth, but I encountered a dependency problem while cabal-dev install:
/Users/kenta/myapp/oryza% cabal-dev install
Resolving dependencies...
cabal: cannot configure yesod-platform-1.0.2. It requires data-default ==0.4.0
For the dependency on data-default ==0.4.0 there are these packages:
data-default-0.4.0. However none of them are available.
data-default-0.4.0 was excluded because authenticate-oauth-1.3.0 requires
data-default ==0.3.*
data-default-0.4.0 was excluded because data-default-0.3.0 was selected
instead
data-default-0.4.0 was excluded because oryza-0.0.0 requires data-default
==0.3.*
I don't have any idea of what's wrong.
What I did is just inserting one line in Cabal file:
yesod-auth-oauth >= 1.0 && < 1.1
The default scaffolding works fine, which is created through yesod init.
The version information
yesod-core: 1.0.1
cabal-dev: 0.9.1 (build with Cabal 1.14.0)
cabal-install: 0.10.2
GHC: 7.0.4
OS: Mac OS X Lion
Thanks.
This looks like an overly restrictive upper bound in the authenticate-oauth package. It would be best to follow up directly with the maintainer of that package.
In general, these kinds of issues are a side-effect of following the Package Versioning Policy. Basically, it's a trade-off between having these "refuse to compile" annoyances and more insidious "can't compile" problems.
I don't remember for sure, but I think my change to the cabal file for yesod-auth-oauth fixes this.