Install DESeq2 problem for macbook pro M1 Max
1
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Entering edit mode
Victor • 0
@d87ca81c
Last seen 3 months 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 • 1.0k 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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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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@mikelove
Last seen 1 day 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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