dyld: Library not loaded: @rpath/libc++abi.1.dylib
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Entering edit mode
@jordanberg-15710
Last seen 3.4 years ago

I continually get the error:

dyld: Library not loaded: @rpath/libc++abi.1.dylib

  Referenced from: /Users/jordanberg/anaconda3/lib/libc++.1.0.dylib

  Reason: image not found

make: *** [aes.o] Abort trap: 6

 

I get this when running R in the interactive mode via command line when I try to install biocLite, and presumably when try to install DESeq2 in the same manner. I need to be able to run these installs in an R script in the command line. It seems like others have had similar issues (see https://support.bioconductor.org/p/95587/) which was fixed by updating the binaries. Does this mean that all ~30 binaries are bad? Any help would be appreciated. Command line output and sessionInfo() is included below.

The same thing happens when I try:

biocLite("DESeq2")

But when I then type "library("DESeq2") it responds with Error in library(DESeq2) : there is no package called ‘DESeq2’

 

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help

> biocLite()

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.1 (2017-06-30).

Installing package(s) ‘Biobase’, ‘IRanges’, ‘AnnotationDbi’

also installing the dependencies ‘bit’, ‘digest’, ‘bit64’, ‘memoise’, ‘Rcpp’, ‘S4Vectors’, ‘RSQLite’

 

trying URL 'https://cran.rstudio.com/src/contrib/bit_1.1-12.tar.gz'

Content type 'application/x-gzip' length 53737 bytes (52 KB)

==================================================

downloaded 52 KB

 

trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.15.tar.gz'

Content type 'application/x-gzip' length 122095 bytes (119 KB)

==================================================

downloaded 119 KB

 

trying URL 'https://cran.rstudio.com/src/contrib/bit64_0.9-7.tar.gz'

Content type 'application/x-gzip' length 125539 bytes (122 KB)

==================================================

downloaded 122 KB

 

trying URL 'https://cran.rstudio.com/src/contrib/memoise_1.1.0.tar.gz'

Content type 'application/x-gzip' length 11025 bytes (10 KB)

==================================================

downloaded 10 KB

 

trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.16.tar.gz'

Content type 'application/x-gzip' length 3763400 bytes (3.6 MB)

==================================================

downloaded 3.6 MB

 

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/S4Vectors_0.16.0.tar.gz'

Content type 'application/x-gzip' length 432152 bytes (422 KB)

==================================================

downloaded 422 KB

 

trying URL 'https://cran.rstudio.com/src/contrib/RSQLite_2.1.0.tar.gz'

Content type 'application/x-gzip' length 2191526 bytes (2.1 MB)

==================================================

downloaded 2.1 MB

 

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Biobase_2.38.0.tar.gz'

Content type 'application/x-gzip' length 1656734 bytes (1.6 MB)

==================================================

downloaded 1.6 MB

 

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/IRanges_2.12.0.tar.gz'

Content type 'application/x-gzip' length 485066 bytes (473 KB)

==================================================

downloaded 473 KB

 

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/AnnotationDbi_1.40.0.tar.gz'

Content type 'application/x-gzip' length 4336842 bytes (4.1 MB)

==================================================

downloaded 4.1 MB

 

* installing *source* package ‘bit’ ...

** package ‘bit’ successfully unpacked and MD5 sums checked

** libs

clang -I/Users/user/anaconda3/lib/R/include -DNDEBUG   -I/Users/user/anaconda3/include   -fPIC  -I/Users/user/anaconda3/include  -c attrutil.c -o attrutil.o

dyld: Library not loaded: @rpath/libc++abi.1.dylib

  Referenced from: /Users/user/anaconda3/lib/libc++.1.0.dylib

  Reason: image not found

make: *** [attrutil.o] Abort trap: 6

ERROR: compilation failed for package ‘bit’

* removing ‘/Users/user/anaconda3/lib/R/library/bit’

* installing *source* package ‘digest’ ...

** package ‘digest’ successfully unpacked and MD5 sums checked

** libs

clang -I/Users/user/anaconda3/lib/R/include -DNDEBUG   -I/Users/user/anaconda3/include   -fPIC  -I/Users/user/anaconda3/include  -c aes.c -o aes.o

dyld: Library not loaded: @rpath/libc++abi.1.dylib

  Referenced from: /Users/user/anaconda3/lib/libc++.1.0.dylib

  Reason: image not found

make: *** [aes.o] Abort trap: 6

ERROR: compilation failed for package ‘digest’

* removing ‘/Users/user/anaconda3/lib/R/library/digest’

* installing *source* package ‘Rcpp’ ...

** package ‘Rcpp’ successfully unpacked and MD5 sums checked

** libs

clang++  -I/Users/user/anaconda3/lib/R/include -DNDEBUG -I../inst/include/  -I/Users/user/anaconda3/include   -fPIC  -I/Users/user/anaconda3/include  -c Date.cpp -o Date.o

dyld: Library not loaded: @rpath/libc++abi.1.dylib

  Referenced from: /Users/user/anaconda3/lib/libc++.1.0.dylib

  Reason: image not found

make: *** [Date.o] Abort trap: 6

ERROR: compilation failed for package ‘Rcpp’

* removing ‘/Users/user/anaconda3/lib/R/library/Rcpp’

* installing *source* package ‘S4Vectors’ ...

** libs

clang -I/Users/user/anaconda3/lib/R/include -DNDEBUG   -I/Users/user/anaconda3/include   -fPIC  -I/Users/user/anaconda3/include  -c AEbufs.c -o AEbufs.o

dyld: Library not loaded: @rpath/libc++abi.1.dylib

  Referenced from: /Users/user/anaconda3/lib/libc++.1.0.dylib

  Reason: image not found

make: *** [AEbufs.o] Abort trap: 6

ERROR: compilation failed for package ‘S4Vectors’

* removing ‘/Users/user/anaconda3/lib/R/library/S4Vectors’

* installing *source* package ‘Biobase’ ...

** libs

clang -I/Users/user/anaconda3/lib/R/include -DNDEBUG   -I/Users/user/anaconda3/include   -fPIC  -I/Users/user/anaconda3/include  -c Rinit.c -o Rinit.o

dyld: Library not loaded: @rpath/libc++abi.1.dylib

  Referenced from: /Users/user/anaconda3/lib/libc++.1.0.dylib

  Reason: image not found

make: *** [Rinit.o] Abort trap: 6

ERROR: compilation failed for package ‘Biobase’

* removing ‘/Users/user/anaconda3/lib/R/library/Biobase’

ERROR: dependency ‘bit’ is not available for package ‘bit64’

* removing ‘/Users/user/anaconda3/lib/R/library/bit64’

ERROR: dependency ‘digest’ is not available for package ‘memoise’

* removing ‘/Users/user/anaconda3/lib/R/library/memoise’

ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’

* removing ‘/Users/user/anaconda3/lib/R/library/IRanges’

ERROR: dependencies ‘bit64’, ‘memoise’, ‘Rcpp’ are not available for package ‘RSQLite’

* removing ‘/Users/user/anaconda3/lib/R/library/RSQLite’

ERROR: dependencies ‘Biobase’, ‘IRanges’, ‘RSQLite’, ‘S4Vectors’ are not available for package ‘AnnotationDbi’

* removing ‘/Users/user/anaconda3/lib/R/library/AnnotationDbi’

 

 

> sessionInfo()

R version 3.4.1 (2017-06-30)

Platform: x86_64-apple-darwin14.5.0 (64-bit)

Running under: macOS High Sierra 10.13.4

 

Matrix products: default

BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

 

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

 

other attached packages:

[1] BiocInstaller_1.28.0

 

loaded via a namespace (and not attached):

[1] compiler_3.4.1 tools_3.4.1   

DESeq2 biocLite • 2.2k views
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Entering edit mode
Mike Smith ★ 5.1k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg / de.NBI

It looks like this is an issue in combining clang, gfortran and R from Anaconda - there's more detailed info at https://github.com/ContinuumIO/anaconda-issues/issues/8900

There's some advice given on that site, but I don't know enough about Anaconda to suggest whether it's appropriate. You may have a good reason for using Anaconda, but if I were you I wouldn't use it to manage my R installation and instead use the 'standard' route by downloading the PKG binary from https://cran.r-project.org/bin/macosx/

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Perfect, that was very helpful! I ran "conda uninstall r" and "conda uninstall r-base" to ensure all conda-based R downloads were completely removed (checked via "which r" and ensuring that it did not show R in an anaconda folder). DESeq2 is downloading and loading fine in R interactive mode in command line.

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