[Bioc-devel] problems linking to Rhtslib on Mac OSX
Jason Serviss
jason.serviss at ki.se
Tue May 24 20:32:17 CEST 2016
Dan,
Thanks for the input. Yes, maybe it is a different problem altogether. If it is more convenient I can start another “thread” to keep the issues separated…
Due to the fact that I am running R-devel, as far as I am aware, all (?) packages need to be installed from source. I have carefully followed the instructions for installing openssl on my system and testing the installation with:
openssl version -a
gives:
OpenSSL 1.1.0-pre6-dev xx XXX xxxx
built on: reproducible build, date unspecified
platform: darwin64-x86_64-cc
compiler: cc -DDSO_DLFCN -DHAVE_DLFCN_H -DNDEBUG -DOPENSSL_THREADS -DOPENSSL_NO_STATIC_ENGINE -DOPENSSL_PIC -DOPENSSL_IA32_SSE2 -DOPENSSL_BN_ASM_MONT -DOPENSSL_BN_ASM_MONT5 -DOPENSSL_BN_ASM_GF2m -DSHA1_ASM -DSHA256_ASM -DSHA512_ASM -DMD5_ASM -DAES_ASM -DVPAES_ASM -DBSAES_ASM -DGHASH_ASM -DECP_NISTZ256_ASM -DPOLY1305_ASM -DOPENSSLDIR="\"/usr/local/ssl\"" -DENGINESDIR="\"/usr/local/lib/engines\""
OPENSSLDIR: "/usr/local/ssl"
ENGINESDIR: "/usr/local/lib/engines”
Since I am also experiencing the same problem with git2r, I don’t think that in my case the problem is isolated to openssl but I am struggling to identify what it is specifically. I can download the .zip file for either of the packages and install with R CMD INSTALL -no-test-load and see that the files (openssl.so and git2r.so) are present in the libs directory but then library(git2r) or library(openssl) generates the same warning. I also tried reinstalling the previous version of Xcode and command line tools, thinking as mentioned previously that the problem could lie there, but to no avail.
Jason
On 24 May 2016, at 19:48, Dan Tenenbaum <dtenenba at fredhutch.org<mailto:dtenenba at fredhutch.org>> wrote:
----- Original Message -----
From: "Jason Serviss" <jason.serviss at ki.se<mailto:jason.serviss at ki.se>>
To: "Aaron Lun" <alun at wehi.edu.au<mailto:alun at wehi.edu.au>>
Cc: "bioc-devel" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Sent: Tuesday, May 24, 2016 8:20:18 AM
Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
I can confirm that I am experiencing similar problems on OSX with several other
packages at the moment (openssl and git2r), I know that Xcode just updated and
am not sure if this is causing some of the problems (potentially some update
with their command line tools?)...
install.packages('openssl', type=‘source’)
...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so,
6): Symbol not found: _ERR_free_strings
Referenced from:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so
Expected in: flat namespace
in
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so
Error: loading failed
Execution halted
install.packages(‘git2r', type=‘source’)
…
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/git2r/libs/git2r.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/git2r/libs/git2r.so,
6): Symbol not found: _SSL_library_init
Referenced from:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/git2r/libs/git2r.so
Expected in: flat namespace
in
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/git2r/libs/git2r.so
Error: loading failed
Execution halted
I think this is a different problem. You are building these packages from source and they require that you have the openssl libraries and headers.
Either read the Mac section of https://github.com/jeroenooms/openssl#installation or just install the binary versions (omit type="source").
Dan
sessionInfo()
R Under development (unstable) (2016-05-23 r70660)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)
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] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.4.0
Kind Regards,
Jason Serviss
On 24 May 2016, at 17:06, Aaron Lun <alun at wehi.edu.au<mailto:alun at wehi.edu.au>> wrote:
Dear Martin and List,
I have a problem with linking to Rhtslib on Mac OSX when my R installation
directory differs from the package installation directory. Trying to load csaw
(Bioc release version) gives me:
require(csaw)
# ... whole lot of dependencies...
Loading required package: csaw
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so':
dlopen(/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so, 6): Library not
loaded:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib
Referenced from: /Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so
Reason: image not found
... which is because my Rhtslib shared library is sitting instead at
/Users/lun01/Library/R/3.3/library/Rhtslib/lib/libhts.0.dylib (along with all
my other non-recommended, non-base packages). I presume this linking failure
occurs because the Makevars file (which would normally indicate where the
shared library is living) doesn't get run when installing a prebuilt binary?
The same issue occurs with deepSNV, which is the other package that links to
Rhtslib.
Any thoughts? I don't usually use Macs, so I don't know exactly what goes on
during package installation, or whether my setup (i.e., with different
package/R locations) is atypical or not.
Aaron
sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
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 datasets
[8] methods base
other attached packages:
[1] SummarizedExperiment_1.2.2 Biobase_2.32.0
[3] GenomicRanges_1.24.0 GenomeInfoDb_1.8.1
[5] IRanges_2.6.0 S4Vectors_0.10.1
[7] BiocGenerics_0.18.0 BiocInstaller_1.22.2
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.34.3 XVector_0.12.0 edgeR_3.14.0
[4] GenomicAlignments_1.8.0 zlibbioc_1.18.0 BiocParallel_1.6.2
[7] tools_3.3.0 DBI_0.4-1 Rhtslib_1.4.2
[10] rtracklayer_1.32.0 bitops_1.0-6 RCurl_1.95-4.8
[13] biomaRt_2.28.0 RSQLite_1.0.0 limma_3.28.5
[16] GenomicFeatures_1.24.2 Biostrings_2.40.1 Rsamtools_1.24.0
[19] XML_3.98-1.4
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}
_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list