Install DESeq2 problem for macbook pro M1 Max
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0
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Victor • 0
@d87ca81c
Last seen 2.8 years ago
France

Hi, i have problem for DESeq2 install. I have change PC (windows) for new macbook pro (chip M1 Max). I have not problem bioconductor install. My results : in put

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.14")

out put

> if (!require("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install(version = "3.14")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)

in put

BiocManager::install("DESeq2")
library("DESeq2")

out put


> BiocManager::install("DESeq2")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'DESeq2'
also installing the dependencies ‘AnnotationDbi’, ‘annotate’, ‘genefilter’, ‘geneplotter’, ‘RcppArmadillo’

Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘genefilter’ ‘DESeq2’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.1/RcppArmadillo_0.10.8.1.0.tgz'
Content type 'application/x-gzip' length 1728276 bytes (1.6 MB)
==================================================
downloaded 1.6 MB


The downloaded binary packages are in
    /var/folders/2h/43w_ny0s7zj2hjdp5tn1bjjh0000gn/T//Rtmp5e9i3r/downloaded_packages
installing the source packages ‘AnnotationDbi’, ‘annotate’, ‘genefilter’, ‘geneplotter’, ‘DESeq2’

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.2.tar.gz'
Content type 'application/x-gzip' length 4330396 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/annotate_1.72.0.tar.gz'
Content type 'application/x-gzip' length 1723060 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/genefilter_1.76.0.tar.gz'
Content type 'application/x-gzip' length 807639 bytes (788 KB)
==================================================
downloaded 788 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/geneplotter_1.72.0.tar.gz'
Content type 'application/x-gzip' length 1437803 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/DESeq2_1.34.0.tar.gz'
Content type 'application/x-gzip' length 2088431 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

* installing *source* package ‘AnnotationDbi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘rlang’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘AnnotationDbi’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/AnnotationDbi’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/annotate’
ERROR: dependencies ‘AnnotationDbi’, ‘annotate’ are not available for package ‘genefilter’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/genefilter’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/geneplotter’
ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/DESeq2’

The downloaded source packages are in
    ‘/private/var/folders/2h/43w_ny0s7zj2hjdp5tn1bjjh0000gn/T/Rtmp5e9i3r/downloaded_packages’
Warning messages:
1: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
2: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
  unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
7: In .inet_warning(msg) :
  installation of package ‘annotate’ had non-zero exit status
8: In .inet_warning(msg) :
  installation of package ‘genefilter’ had non-zero exit status
9: In .inet_warning(msg) :
  installation of package ‘geneplotter’ had non-zero exit status
10: In .inet_warning(msg) :
  installation of package ‘DESeq2’ had non-zero exit status
> library("DESeq2")
Error in library("DESeq2") : there is no package called ‘DESeq2’

For mme the problem it is can not connexion at URL. I watched the URL and is not defined...

I'm use 4.1.2 R version and i installed on my mac docker and Xquartz.

thanks for your help
Bioconductor Install DESeq2 • 8.4k views
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0
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You really have to learn reading through messages:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called ‘rlang’

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how can i change the loadNamespace?

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0
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The critical part of that error message is this:

there is no package called ‘rlang’

Which indicates that you should install that package first.

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It is problem 'rlang' is installed. And i have installed 'genefilters' (another probleme) from source file in bioconductor in me terminal. I'm check install in terminal (open /Library/Frameworks/R.framework/Resources/library) it is succes. After i have load 'genefilter' in R, i have erreur :

> library(rlang)
> library(genefilter)
Error: package or namespace load failed for ‘genefilter’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/genefilter/libs/genefilter.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/genefilter/libs/genefilter.so, 0x0006): tried: '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/genefilter/libs/genefilter.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e')), '/usr/lib/genefilter.so' (no such file)

But i have not problem for 'rlang' load...

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I have problem for compilation of DESeq2

> BiocManager::install("DESeq2")
...
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘DESeq2’
...
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [DESeq2.so] Error 1
ERROR: compilation failed for package ‘DESeq2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/DESeq2’

The downloaded source packages are in
    ‘/private/var/folders/2h/43w_ny0s7zj2hjdp5tn1bjjh0000gn/T/RtmpA7qjyO/downloaded_packages’
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0
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The arm64 here indicates you haven't followed my advice to look at the previous posts about installing Bioc on M1.

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0
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what is the current state with the new M chip ? does it work well now ?

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0
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I hade a similar issue.

You have installed the arm64 version of R, which Bioconductor 3.14 does not support. Expanding on what Mike Love mentioned, 3.16 now supports arm64 version of R. The only issue is that 3.16 is very new, so not all Bioconductor libraries support arm64 yet AFAIK.

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A note, I've just pushed a new version of DESeq2 to Bioc that doesn't depend on genefilter, which should propagate in 24 hrs. It's in devel already, and on github.

https://bioconductor.org/packages/devel/bioc/html/DESeq2.html

https://github.com/mikelove/DESeq2

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niels ▴ 10
@0e0215df
Last seen 2.0 years ago
United States

I was having issues getting DESeq2 running as well and it ended up being that I had to install gfortran in order to get packages like genefilter working which made it possible to get DESeq2 running correctly... I installed gfortran from gcc: https://gcc.gnu.org/wiki/GFortranBinaries

and then followed advice from here: https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/#gfortran

to get R to access the gfortran install by creating a Makevars (~/.R/Makevars) file with the following:

# manual gfortran install from gcc
FLIBS   =-L/usr/local/gfortran/lib
F77     = /usr/local/gfortran/bin/gfortran
FC      = /usr/local/gfortran/bin/gfortran

and from there I was able to install the bioconductor packages that were breaking on the libgfortran loading... (I had to create the .R directory in my user location and create the Makevars file but after restarting my R instance it worked)...
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2
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I just got a new M1 the other week and if (at least with the current R 4.2) you install the ARM version from https://cran.r-project.org/bin/macosx/ and then follow what they advise here https://mac.r-project.org/tools/ (gfortran, recommended system dependencies, Xcode) I could install DESeq2 (and every Bioc package so far) with no issues (everything from source).

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yeah, I had already installed gfortran from the gcc.gnu.org page and so wanted to keep using that install and so far this option has worked. I haven't had to install everything from source but I'm pretty sure that genefilter was installed from source... Good to know about the mac.r-project site. Sounds like, for DESeq at least, this should no longer be an issue...

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hopefully!

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1
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Thanks for posting this update.

After having many users struggle with genefilter installation, I've just copied over the small function that we use from that package so we can cut out genefilter as a dependency (it was an import). I'll do some testing, and maybe I can port this to release branch.

https://github.com/mikelove/DESeq2/commit/8dd1af35a8223645bb4937d72c5ceea1da93a8ea

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FWIW I just ported this change to release (3.16).

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@mikelove
Last seen 7 days ago
United States

Can you search the support site for the posts on how to install Bioconductor on M1.

You can search by adding "site:support.bioconductor.org" when using Google.
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Hello Michael, I didn't find your advice to solve this problem by googling. Could you please send me a link to find your posts? Thanks!!!

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Note that ARM64 binaries are now available.

https://stat.ethz.ch/pipermail/bioc-devel/2022-September/019178.html

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