`TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed anymore
0
6
Entering edit mode
Batool ▴ 370
@Batool-24467
Last seen 3.2 years ago

I think there is a problem with TxDb.Hsapiens.UCSC.hg19.knownGene and EnsDb.Hsapiens.v75. I'm struggling to install all of these packages as they pause at byte-compile and prepare package for lazy loading. Can anyone try to re-install them in their local machine because am not the only one who is having the problem, please? They used to work fine until a week ago!

As usual, I install the packages by:

BiocManager::install(c("Homo.sapiens", "EnsDb.Hsapiens.v75", "TxDb.Hsapiens.UCSC.hg19.knownGene"))

I also tried installing them individually:

BiocManager::install("EnsDb.Hsapiens.v75")
BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")

It pauses at :

* installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

sessionInfo( )

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3

I'm not using RStudio. I'd be grateful if someone can try to replicate the error, please?

EnsDb.Hsapiens.v75 TxDb.Hsapiens.UCSC.hg19.knownGene • 1.3k views
ADD COMMENT
0
Entering edit mode

When you say they pause at byte-compile, for how long do they pause? E.g. do they pause forever or longer than usual?

Also you say these packages worked fine until a week ago. What has changed on your system since last week? E.g. did you upgrade your OS to macOS Big Sur? I'm curious to know why you are re-installing them if they were working fine.

Any additional information you can provide that could give us a clue of what's going on?

Thanks

ADD REPLY
6
Entering edit mode

Thank you Hervé Pagès for your reply and Happy New Year!

Regarding why am I re-installed the packages, long story short, I have a project in Rmarkdown which I was working on it for the last six months. The project (under version control ) uses different packages from bioconductor. I took a week break from the project at the end of December, then came back to it. At the time I came back to it, I didn't upgrade to Big Sur, was using macOS Catalina.

The first problem I encountered was When I tried to load ggiob, using library (ggbio), my console will show this message:

Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

then, the console will stuck forever, even after pressing Ctrl + C unless restarted again. So, I tried to clear the cache and remove ggbio from RFrameworks and re-install it again but the same problem occurred. So, I removed RStudio, R, all packages and re-install them but the same problem occurred (this time also had a problem installing TxDb.Hsapiens.UCSC.hg19.knownGene). I tried to solve the problem myself for a few days and googled to look if anyone having the same problem, found this forum, so I posted for the first time my two questions (regarding ggbio and TxDb.Hsapiens.UCSC.hg19.knownGene).

I tried it on my Sister's Mac but unfriendly I encountered the same problem. Please note my sister's mac doesn't have R, so installed R and then just installed ggbio and TxDb.Hsapiens.UCSC.hg19.knownGene from R without RStudio but had a problem with both packages and this is the sessionInfo() from my sister's Mac:

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.0.3

Then. I upgraded to macOS Big Sur and tried again to install R and the packages but no luck.

To replicate the problem: Just install R and then run:

BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene") but it will reach

* installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

and I left it for 18 hours but it never continues, it only pause indefinitely.

Then, you can also try (as I mentioned in a different question):

BiocManager::install(`ggbio`)
library(ggbio)

Please note that ggbio is installed fine but once it's loaded with library(ggbio), it shows:

Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2

and the console then stuck forever. All this without using RStudio and I don't recall changes in my local machine that might affect the installation this much.

To summarise, I re-installed the packages because of the problem I was having with ggbio. Thank you again for your patience.

ADD REPLY

Login before adding your answer.

Traffic: 714 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6