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cristian
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@cristian-13977
Last seen 6.3 years ago
Hi,
I have posted this question on Biostars but it was suggested that this website is more appropriate: https://www.biostars.org/p/273228/#273242
I am having problems installing the Bioconductor package AnnotationDbi on my Mac OSX:
biocLite('AnnotationDbi', ask = FALSE, lib = 'output/software/r/package/installation/')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).
Installing package(s) ‘AnnotationDbi’
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/AnnotationDbi_1.38.2.tar.gz'
Content type 'application/x-gzip' length 4278787 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/cr517/Documents/phd/project/output/software/r/package/installation/Rcpp/libs/Rcpp.so':
dlopen(/Users/cr517/Documents/phd/project/output/software/r/package/installation/Rcpp/libs/Rcpp.so, 6): Library not loaded: @rpath/./libgfortran.3.dylib
Referenced from: /Users/cr517/Documents/phd/project/output/software/r/package/installation/Rcpp/libs/Rcpp.so
Reason: image not found
ERROR: lazy loading failed for package ‘AnnotationDbi’
* removing ‘/Users/cr517/Documents/phd/project/output/software/r/package/installation/AnnotationDbi’
The downloaded source packages are in
‘/private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpLXmGgy/downloaded_packages’
Updating packages 'effects', 'multcomp'
trying URL 'https://cran.rstudio.com/src/contrib/effects_4.0-0.tar.gz'
Content type 'application/x-gzip' length 1282402 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/src/contrib/multcomp_1.4-7.tar.gz'
Content type 'application/x-gzip' length 607663 bytes (593 KB)
==================================================
downloaded 593 KB
* installing *source* package ‘effects’ ...
** package ‘effects’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/cr517/Documents/phd/project/output/software/r/package/installation/survival/libs/survival.so':
dlopen(/Users/cr517/Documents/phd/project/output/software/r/package/installation/survival/libs/survival.so, 6): Library not loaded: @rpath/./libgfortran.3.dylib
Referenced from: /Users/cr517/Documents/phd/project/output/software/r/package/installation/survival/libs/survival.so
Reason: image not found
ERROR: lazy loading failed for package ‘effects’
* removing ‘/usr/local/lib/R/3.4/site-library/effects’
* restoring previous ‘/usr/local/lib/R/3.4/site-library/effects’
* installing *source* package ‘multcomp’ ...
** package ‘multcomp’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Error: package or namespace load failed for ‘survival’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/cr517/Documents/phd/project/output/software/r/package/installation/survival/libs/survival.so':
dlopen(/Users/cr517/Documents/phd/project/output/software/r/package/installation/survival/libs/survival.so, 6): Library not loaded: @rpath/./libgfortran.3.dylib
Referenced from: /Users/cr517/Documents/phd/project/output/software/r/package/installation/survival/libs/survival.so
Reason: image not found
Error : package ‘survival’ could not be loaded
ERROR: lazy loading failed for package ‘multcomp’
* removing ‘/usr/local/lib/R/3.4/site-library/multcomp’
* restoring previous ‘/usr/local/lib/R/3.4/site-library/multcomp’
The downloaded source packages are in
‘/private/var/folders/z2/rt6qxntd3tg5bjmqlqnm0mdm0000gn/T/RtmpLXmGgy/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘AnnotationDbi’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘effects’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :
installation of package ‘multcomp’ had non-zero exit status
It seems to start failing here:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
I have copied my session info below:
> sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin16.5.0 (64-bit) Running under: macOS Sierra 10.12.6 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_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices utils [7] datasets methods base other attached packages: [1] BiocInstaller_1.26.1 IRanges_2.10.3 S4Vectors_0.14.4 [4] Biobase_2.36.2 graph_1.54.0 BiocGenerics_0.22.0 [7] rmarkdown_1.6 dplyr_0.7.3 loaded via a namespace (and not attached): [1] doBy_4.5-15 knitr_1.17 assertthat_0.2.0 [4] evaluate_0.10.1 DBI_0.7 backports_1.1.0 [7] withr_2.0.0 pkgconfig_2.0.1 devtools_1.13.3 [10] bindr_0.1 rlang_0.1.2 rprojroot_1.2 [13] Matrix_1.2-11 base64enc_0.1-3 stringr_1.2.0 [16] memoise_1.1.0 magrittr_1.5 compiler_3.4.0 [19] RColorBrewer_1.1-2 MASS_7.3-47 stringi_1.1.5 [22] yaml_2.1.14 grid_3.4.0 tools_3.4.0 [25] digest_0.6.12 bindrcpp_0.2 Rcpp_0.12.12 [28] jsonlite_1.5 R6_2.2.2 htmltools_0.3.6 [31] glue_1.1.1 BiocParallel_1.10.1 lattice_0.20-35 [34] tibble_1.3.4 gtable_0.2.0
Could someone help me, please?
Thanks.
Best, C.
This behaviour is interesting:
library(AnnotationDbi) Error: package or namespace load failed for ‘AnnotationDbi’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Users/cr517/Documents/phd/project/output/software/r/package/installation/bit/libs/bit.so': dlopen(/Users/cr517/Documents/phd/project/output/software/r/package/installation/bit/libs/bit.so, 6): Library not loaded: @rpath/./libgfortran.3.dylib Referenced from: /Users/cr517/Documents/phd/project/output/software/r/package/installation/bit/libs/bit.so Reason: image not found > .libPaths() [1] "/Users/cr517/Documents/phd/project/output/software/r/package/installation" [2] "/usr/local/lib/R/3.4/site-library" [3] "/usr/local/Cellar/r/3.4.0_1/R.framework/Versions/3.4/Resources/library" > library(AnnotationDbi, lib.loc = '/usr/local/lib/R/3.4/site-library/') Attaching package: ‘AnnotationDbi’ The following object is masked from ‘package:dplyr’: selectIt seems that AnnotationDbi is correctly installed in /usr/local/lib/R/3.4/site-library/ but R does not try to load it from there because it fails from loading it from /Users/cr517/Documents/phd/project/output/software/r/package/installation?
C.