unable to install GenomeInfoDbData package

farha · July 18, 2023, 3:21pm

BiocManager::install("GenomeInfoDbData")

it gives me this error : "there is no package called ‘GenomeInfoDbData’"

Gabor · July 18, 2023, 3:37pm

What's your R version? What's your BiocManager version?

You can also give pak a try:

source("https://pak.r-lib.org/install.R")
pak::pkg_install("GenomeInfoDbData")

farha · July 18, 2023, 3:50pm

i tried ur code abd gives me this error
" Failed to build GenomeInfoDbData 1.2.10
Error:
! error in pak subprocess
Caused by error in stop_task_build(state, worker):
! Failed to build source package 'GenomeInfoDbData'
Full installation output"

R version (4.3.1)
BioManager version (1.30.21)

Gabor · July 18, 2023, 4:16pm

What is your OS?

Also, is there more output after

Full installation output

?

farha · July 18, 2023, 4:20pm

am on Windows

"Type .Last.error to see the more details."

Gabor · July 18, 2023, 6:23pm

So did you type in .Last.error to see more?

Do you have a virus scanner? Can you install other Bioconductor (annotation) packages? Can you go to the web page of the package at Bioconductor - GenomeInfoDbData and then can you download and install it manually?

farha · July 18, 2023, 7:13pm

i type .Last.error and get that ".Last.error
Error in loadNamespace(x) : there is no package called ‘rstudioapi’"
then I installed ‘rstudioapi this package and tried to re-install GenomeInfoDbData , it gave me the same error after I type .Last.error ".Last.error
<callr_error/rlib_error_3_0/rlib_error/error>
Error:
! error in pak subprocess
Caused by error in stop_task_build(state, worker):
! Failed to build source package 'GenomeInfoDbData'
Full installation output:

Backtrace:

pak::pkg_install("GenomeInfoDbData")
pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
err$throw(res$error)

Subprocess backtrace:

base::withCallingHandlers(cli_message = function(msg) { …
get("pkg_install_do_plan", asNamespace("pak"))(...)
proposal$install()
pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
base::withCallingHandlers({ …
pkgdepends:::handle_events(state, events)
pkgdepends:::handle_event(state, i)
pkgdepends:::stop_task(state, worker)
pkgdepends:::stop_task_build(state, worker)
base::throw(new_pkg_build_error("Failed to build source package {pkg}", …
| base::signalCondition(cond)
global (function (e) …"

I was having virus scanner but I uninstall it
this error in the first place because of installing clusterProfiler package and then call it by library() , then it gives me this error " there is no package called ‘GenomeInfoDbData"

Gabor · July 18, 2023, 7:49pm

Can you install other Bioconductor (annotation) packages? Can you go to the web page of the package at Bioconductor - GenomeInfoDbData and then can you download and install it manually?

farha · July 19, 2023, 1:33pm

i tried to install it manually "install.packages("C:\Users\compu\AppData\Local\R\win-library\4.3\GenomeInfoDbData_1.2.10.tar.gz", repos = NULL, type = "source")"

and gives me this error "Installing package into ‘C:/Users/compu/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
Warning in install.packages :
installation of package ‘C:/Users/compu/AppData/Local/R/win-library/4.3/GenomeInfoDbData_1.2.10.tar.gz’ had non-zero exit status"

yes, I can install other Bioconductor packages.
is GenomeInfoDbData require any prior dependencies or prior packages?

Gabor · July 19, 2023, 3:49pm

I don't think so. Can you please show all output? E.g. this is my output:

❯ install.packages("GenomeInfoDbData", repos = "https://bioconductor.org/packages/3.17/data/annotation")
Installing package into ‘/Users/gaborcsardi/Library/R/arm64/4.3/library’
(as ‘lib’ is unspecified)
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GenomeInfoDbData_1.2.10.tar.gz'
Content type 'application/x-gzip' length 12026674 bytes (11.5 MB)
==================================================
downloaded 11.5 MB

* installing *source* package ‘GenomeInfoDbData’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)

The downloaded source packages are in
	‘/private/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T/Rtmpey96pI/downloaded_packages’

farha · July 19, 2023, 4:01pm

install.packages("C:\Users\compu\AppData\Local\R\win-library\4.3\GenomeInfoDbData_1.2.10.tar.gz", repos = NULL, type = "source")
Installing package into ‘C:/Users/compu/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
Warning in install.packages :
installation of package ‘C:/Users/compu/AppData/Local/R/win-library/4.3/GenomeInfoDbData_1.2.10.tar.gz’ had non-zero exit status

install.packages("GenomeInfoDbData", repos = "Bioconductor - 3.17 AnnotationData Packages")
Installing package into ‘C:/Users/compu/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GenomeInfoDbData_1.2.10.tar.gz'
Content type 'application/x-gzip' length 12026674 bytes (11.5 MB)
downloaded 11.5 MB

Warning in install.packages :
installation of package ‘GenomeInfoDbData’ had non-zero exit status

The downloaded source packages are in
‘C:\Users\compu\AppData\Local\Temp\RtmpKYREXm\downloaded_packages’

Gabor · July 19, 2023, 5:05pm

So you don't have a part that says

* installing *source* package ‘GenomeInfoDbData’ ...

???

Is this an IDE? Can you show the output of

sessionInfo()

?

farha · July 19, 2023, 5:58pm

yes, i do not have this part

this is Rstudio

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: Africa/Cairo
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocManager_1.30.21

loaded via a namespace (and not attached):
[1] crayon_1.5.2 vctrs_0.6.3 httr_1.4.6 cli_3.6.1 rlang_1.1.1
[6] DBI_1.1.3 png_0.1-8 bit_4.0.5 S4Vectors_0.38.1 RCurl_1.98-1.12
[11] pak_0.5.1 stats4_4.3.1 Biobase_2.60.0 bitops_1.0-7 fastmap_1.1.1
[16] IRanges_2.34.1 memoise_2.0.1 compiler_4.3.1 RSQLite_2.3.1 blob_1.2.4
[21] XVector_0.40.0 rstudioapi_0.15.0 R6_2.5.1 tools_4.3.1 bit64_4.0.5
[26] zlibbioc_1.46.0 BiocGenerics_0.46.0 cachem_1.0.8

Gabor · July 19, 2023, 7:18pm

Can you please try running the installation from a terminal instead of RStudio, so see if you can get at least the installation output?

farha · July 21, 2023, 6:44pm

how can I install it from the terminal?

AlexisW · July 25, 2023, 12:02am

open the Start menu, and search "Command Prompt". This opens a terminal. In there, type R and [Enter], this should open the terminal version of R. Check the version number, it's possible that the version opened is not the latest (i.e. older than 4.3.1).

To quit, you can use q(), and answer n [Enter] when asked to save session.

If the version opening by default is not 4.3.1, you can directly look for it with its full path, in a fresh terminal, try:

"C:\Program Files\R\R-4.3.1\bin\R.exe"

(the path might be slightly different on your computer)

When the correct version of R is open, you can run the same command as previously to install.

farha · July 25, 2023, 6:23pm

thank u it works for me

system · August 15, 2023, 6:24pm

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.