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.
Related
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).
I'm following this tutorial here and have also looked into Rocket's official guide of setting up a web server.
I've set as default the nightly builds. But I get the following error:
error: failed to select a version for the requirement `ring = "^0.11.0"`
candidate versions found which didn't match: 0.16.11, 0.16.10, 0.16.9, ...
location searched: crates.io index
required by package `cookie v0.9.1`
... which is depended on by `rocket v0.3.6`
... which is depended on by `my-project`
Obviously there's some mismatch with the dependencies, but since ring is something required by the framework itself, I'm not sure how to debug this... furthermore, I'm using the latest versions of cargo and rust:
cargo 1.43.0-nightly (... 2020-02-18)
rustc 1.43.0-nightly (... 2020-02-21)
ring v0.11.0 was yanked from crates.io (see this issue for some background). Since some versions rocket depended on versions of ring that were yanked, those versions of rocket will no longer work.
Upgrading to rocket v0.4.0 (or the latest v0.4.2) should solve this issue.
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
When I attempt to install the criterion package I get the following error message: error: #error Unsupported OS/architecture/compiler!. I believe the fix is here: Restore support for 32 bit Intel CPUs . However how do I install that fix?
As I can tell from http://hackage.haskell.org/package/criterion-1.1.4.0/src/cbits/cycles.c, v1.1.4.0 includes the fix you linked to.
To use that version or a later one, add a lower bound to your dependency on criterion:
build-depends:
...
, criterion >= 1.1.4.0
...
https://travis-ci.org/Fresheyeball/fbatch
Preprocessing library monad-parallel-0.5...
Control/Monad/Parallel.hs:67:8:
Could not find module `Control.Monad.Identity'
It is a member of the hidden package `mtl-2.2.1'.
Perhaps you need to add `mtl' to the build-depends in your .cabal file.
Use -v to see a list of the files searched for.
cabal: Error: some packages failed to install:
monad-parallel-0.5 failed during the building phase. The exception was:
ExitFailure 1
I am new to haskell, and just can't seem to get past this. I've tinkered with my .cabal file all I can, and the sub dependency fails on Travis every time.
Please help.
If a build fails while resolving a dependency, it's worth having a look a what version of that package gets installed. Normally, cabal should default to the most recent possible, which if well-maintained should install fine. Older versions do of course often mean trouble, if some dependency of theirs has now a newer, incompatible version installed.
In your case, cabal tried to install the somewhat ancient monad-parallel-0.5, which imports a module that doesn't exist in transformers (namely Control.Monad.Identity). The more recent version 0.7.1.2 does not try this and thus builds successfully. You can force such a recent install by giving a lower bound to the dependency in your .cabal file, in this case monad-parallel >= 0.7.