DESeq2 Installation Errors
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price793 • 0
@price793-24165
Last seen 4.3 years ago

Hi,

I have had problems installing the "DESeq2" package. I am new to working in R and have had a lot of problems installing DESeq2 package in R. I have tried several installation methods and have not been able to successfully install this package. I keep getting non-zero exit statuses for another package. Here is the error message: Warning message: In install.packages(...) : installation of package ‘GenomeInfoDbData’ had non-zero exit status

Do you think you could help me install this? I've tried a lot of things and I'm stuck. The version of R that I am using right now is 4.0.
deseq2 software error • 3.1k views
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Providing the error message is helpful, but what's also helpful is to provide the installation command line you used.

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Okay, thank you for letting me know.

I tried installing the "GenomeInfoDbData" before posting this information but it keeps reporting a non-zero exit status. I'll post that information. I tried this code to install Bioconductor and I received this output: 

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install()
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Old packages: 'backports'
Update all/some/none? [a/s/n]: 
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
          binary source needs_compilation
backports  1.1.9 1.1.10              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y
installing the source package ‘backports’

trying URL 'https://cran.rstudio.com/src/contrib/backports_1.1.10.tar.gz'
Content type 'application/x-gzip' length 19465 bytes (19 KB)
==================================================
downloaded 19 KB

dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
  Expected in: /usr/lib/libSystem.B.dylib

/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34:   993 Done                    echo 'tools:::.install_packages()'
       994 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
    ‘/private/var/folders/yq/0npyx_c53h11vckppmcv5vmc0000gn/T/Rtmpuvn0DW/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘backports’ had non-zero exit status
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1
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Try answering 'no' when asked to install from source.

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0
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When I was prompted with the "Do you want to install from sources the package which needs compilation? (Yes,/no/cancel)" I entered "no" and the attached text is the message that was generated (also, I'm still trying to install the package "DESeq2"). 

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/backports_1.1.9.tgz'
Content type 'application/x-gzip' length 75401 bytes (73 KB)
==================================================
downloaded 73 KB


The downloaded binary packages are in
    /var/folders/yq/0npyx_c53h11vckppmcv5vmc0000gn/T//Rtmpuvn0DW/downloaded_packages
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0
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Does that mean that library(backports) now works?

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When I load that package I get the following text:

library(backports)

Attaching package: ‘backports’

The following object is masked from ‘package:phyloseq’:

import

Also, is there an issue because I'm using Mac OS 10.12.6? I understand that some of the package may be written for a more up to date computer plat form but from my understanding when I replied "no" to the updates I should still be able to use an older version. Is that the correct interpretation?

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0
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When I load that package I get the following text: 

library(backports)

Attaching package: ‘backports’

The following object is masked from ‘package:phyloseq’:

    import

Also, is there an issue because I'm using Mac OS 10.12.6? I understand that some of the package may be written for a more up to date computer plat form but from my understanding when I replied "no" to the updates I should still be able to use an older version. Is that the correct interpretation?

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0
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The above output from library(backports) is fine -- nothing to worry about, the most current version of 'backports' easily available for your computer is ready to go...

To format text as 'code', select the entire text to be formatted and click on the '101010' button in the formatting bar.

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0
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It seemed like you were trying to install DESeq2, but that there were problems with GenomeInfoDbData. I think people were expecting you to enter

BiocManager::install("GenomeInfoDbData")

as a step in trouble-shooting. What happens now with this command, remembering that you do not wish to install backports from source?

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@mikelove
Last seen 1 day ago
United States

Use BiocManager::install(...) as in the Install directions on the Bioconductor main page for recent versions of R.

If a package doesn’t install post the code and the error. Also you can try installing the one package that is failing.
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0
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Okay, thank you for letting me know.

I tried installing the "GenomeInfoDbData" before posting this information but it keeps reporting a non-zero exit status. I'll post that information. I tried this code to install Bioconductor and I received this output: 

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install()
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Old packages: 'backports'
Update all/some/none? [a/s/n]: 
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
          binary source needs_compilation
backports  1.1.9 1.1.10              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y
installing the source package ‘backports’

trying URL 'https://cran.rstudio.com/src/contrib/backports_1.1.10.tar.gz'
Content type 'application/x-gzip' length 19465 bytes (19 KB)
==================================================
downloaded 19 KB

dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13)
  Expected in: /usr/lib/libSystem.B.dylib

/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34:   993 Done                    echo 'tools:::.install_packages()'
       994 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
    ‘/private/var/folders/yq/0npyx_c53h11vckppmcv5vmc0000gn/T/Rtmpuvn0DW/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘backports’ had non-zero exit status
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0
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Hey, I have the same probelm using mac. Did you manage to install it in an other way?

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