TxDb.Hsapiens.UCSC.hg19.knownGene and EnsDb.Hsapiens.v75 can't be installed anymore
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6
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@Batool-24467
Last seen 8 months 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


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?

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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

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Entering edit mode

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


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.