Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
Thanks Dan, much appreciated. On 25/05/16 19:13, Dan Tenenbaum wrote: - Original Message - From: "Aaron Lun" <a...@wehi.edu.au> To: "Dan Tenenbaum" <dtene...@fredhutch.org> Cc: "bioc-devel" <bioc-devel@r-project.org> Sent: Tuesday, May 24, 2016 11:04:59 AM Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX Yep, works on my machine as well. Seems like it would be a pain to have to do it manually every time csaw (or deepSNV, or diffHic) gets re-installed, though. I should stress that I didn't do anything special to my R installation to get it to install packages in a different place. As far as I know, that's just what R decided to do by itself. (I never run R with sudo permissions, so it wouldn't be able to put packages in the central R installation folder anyway.) So I think it's worth seriously thinking about whether this scenario should be supported; a user (i.e., me) would reasonably expect that BioC packages would work off the bat on this "standard" setting. Perhaps the csaw.so library can be built with static linkage to the libhts.a? Or maybe I'm just spouting rubbish here. I don't know, I never do any serious work on a Mac. Martin just provided a fix that worked in my testing--Rhtslib now links statically against htslib. I have committed the fix and bumped the version of all packages that depend directly on Rhtslib, in release and devel. Thanks, Dan Cheers, Aaron On 24/05/16 18:42, Dan Tenenbaum wrote: - Original Message - From: "Dan Tenenbaum" <dtene...@fredhutch.org> To: "Aaron Lun" <a...@wehi.edu.au> Cc: "bioc-devel" <bioc-devel@r-project.org> Sent: Tuesday, May 24, 2016 9:38:01 AM Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX - Original Message - From: "Dan Tenenbaum" <dtene...@fredhutch.org> To: "Aaron Lun" <a...@wehi.edu.au> Cc: "bioc-devel" <bioc-devel@r-project.org> Sent: Tuesday, May 24, 2016 8:51:30 AM Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX - Original Message - From: "Aaron Lun" <a...@wehi.edu.au> To: "bioc-devel" <bioc-devel@r-project.org> Sent: Tuesday, May 24, 2016 8:06:13 AM Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX 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. I can't reproduce this issue after installing the binaries of csaw and Rhtslib. I believe that htslib is statically linked inside of Rhtslib so you don't need your own installation of htslib on your machine in order to use it.If you look at the Mac tarball (https://bioconductor.org/packages/release/bioc/bin/macosx/mavericks/contrib/3.3/Rhtslib_1.4.2.tgz) untar it and go to the Rhtslib/lib directory you see the following files: libhts.0.dylib libhts.a libhts.dylib ...in addition to Rhtslib.so which is in Rhtslib/libs. Actually I can induce issues if I install Rhtslib in a different library directory, which is what you were saying. Will look into this a little. The following seems to fix it: cd ~/Library/R/3.3/csaw/libs # change dtenenba to your username in the below sudo install_name_tool -change "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib" "/Users/dtenenba/Library/R/3.3/Rhtslib/lib/libhts.0.dylib" csaw.so (the sudo may not be necessary) Then I can require(csaw) and it works. I'm not sure if there is something that the bioc group should be doing about thiswe'll discuss it when we meet soon. Dan Dan Dan 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 o
Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
- Original Message - > From: "Aaron Lun" <a...@wehi.edu.au> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, May 24, 2016 11:04:59 AM > Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX > Yep, works on my machine as well. Seems like it would be a pain to have > to do it manually every time csaw (or deepSNV, or diffHic) gets > re-installed, though. > > I should stress that I didn't do anything special to my R installation > to get it to install packages in a different place. As far as I know, > that's just what R decided to do by itself. (I never run R with sudo > permissions, so it wouldn't be able to put packages in the central R > installation folder anyway.) > > So I think it's worth seriously thinking about whether this scenario > should be supported; a user (i.e., me) would reasonably expect that BioC > packages would work off the bat on this "standard" setting. Perhaps the > csaw.so library can be built with static linkage to the libhts.a? > > Or maybe I'm just spouting rubbish here. I don't know, I never do any > serious work on a Mac. > Martin just provided a fix that worked in my testing--Rhtslib now links statically against htslib. I have committed the fix and bumped the version of all packages that depend directly on Rhtslib, in release and devel. Thanks, Dan > Cheers, > > Aaron > > > On 24/05/16 18:42, Dan Tenenbaum wrote: >> >> >> - Original Message - >>> From: "Dan Tenenbaum" <dtene...@fredhutch.org> >>> To: "Aaron Lun" <a...@wehi.edu.au> >>> Cc: "bioc-devel" <bioc-devel@r-project.org> >>> Sent: Tuesday, May 24, 2016 9:38:01 AM >>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX >> >>> - Original Message - >>>> From: "Dan Tenenbaum" <dtene...@fredhutch.org> >>>> To: "Aaron Lun" <a...@wehi.edu.au> >>>> Cc: "bioc-devel" <bioc-devel@r-project.org> >>>> Sent: Tuesday, May 24, 2016 8:51:30 AM >>>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX >>> >>>> - Original Message - >>>>> From: "Aaron Lun" <a...@wehi.edu.au> >>>>> To: "bioc-devel" <bioc-devel@r-project.org> >>>>> Sent: Tuesday, May 24, 2016 8:06:13 AM >>>>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX >>>> >>>>> 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. >>>> >>>> >>>> I can't reproduce this issue after installing the binaries of csaw and >>>> Rhtslib. >>>> I believe that htslib is statically linked inside of Rhtslib so you don't >>>> need >>>> your own installation of htslib on your machine in order to us
Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
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
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
<dtene...@fredhutch.org<mailto:dtene...@fredhutch.org>> wrote:
- Original Message -
From: "Jason Serviss" <jason.serv...@ki.se<mailto:jason.serv...@ki.se>>
To: "Aaron Lun" <a...@wehi.edu.au<mailto:a...@wehi.edu.au>>
Cc: "bioc-devel" <bioc-devel@r-project.org<mailto:bioc-devel@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 <a...@wehi.edu.au<mailto:a...@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.
Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
- Original Message - > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Aaron Lun" <a...@wehi.edu.au> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, May 24, 2016 9:38:01 AM > Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX > - Original Message - >> From: "Dan Tenenbaum" <dtene...@fredhutch.org> >> To: "Aaron Lun" <a...@wehi.edu.au> >> Cc: "bioc-devel" <bioc-devel@r-project.org> >> Sent: Tuesday, May 24, 2016 8:51:30 AM >> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX > >> - Original Message ----- >>> From: "Aaron Lun" <a...@wehi.edu.au> >>> To: "bioc-devel" <bioc-devel@r-project.org> >>> Sent: Tuesday, May 24, 2016 8:06:13 AM >>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX >> >>> 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. >> >> >> I can't reproduce this issue after installing the binaries of csaw and >> Rhtslib. >> I believe that htslib is statically linked inside of Rhtslib so you don't >> need >> your own installation of htslib on your machine in order to use it.If you >> look >> at the Mac tarball >> (https://bioconductor.org/packages/release/bioc/bin/macosx/mavericks/contrib/3.3/Rhtslib_1.4.2.tgz) >> untar it and go to the Rhtslib/lib directory you see the following files: >> >> libhts.0.dylib >> libhts.a >> libhts.dylib >> >> ...in addition to Rhtslib.so which is in Rhtslib/libs. >> > > Actually I can induce issues if I install Rhtslib in a different library > directory, which is what you were saying. Will look into this a little. The following seems to fix it: cd ~/Library/R/3.3/csaw/libs # change dtenenba to your username in the below sudo install_name_tool -change "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib" "/Users/dtenenba/Library/R/3.3/Rhtslib/lib/libhts.0.dylib" csaw.so (the sudo may not be necessary) Then I can require(csaw) and it works. I'm not sure if there is something that the bioc group should be doing about thiswe'll discuss it when we meet soon. Dan > Dan > > >> Dan >> >> >> >>> >>> 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] stats4parallel 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 S4Vector
Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
- Original Message -
> From: "Aaron Lun" <a...@wehi.edu.au>
> To: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Tuesday, May 24, 2016 8:06:13 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> 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.
I can't reproduce this issue after installing the binaries of csaw and Rhtslib.
I believe that htslib is statically linked inside of Rhtslib so you don't need
your own installation of htslib on your machine in order to use it.If you look
at the Mac tarball
(https://bioconductor.org/packages/release/bioc/bin/macosx/mavericks/contrib/3.3/Rhtslib_1.4.2.tgz)
untar it and go to the Rhtslib/lib directory you see the following files:
libhts.0.dylib
libhts.a
libhts.dylib
...in addition to Rhtslib.so which is in Rhtslib/libs.
Dan
>
> 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] stats4parallel 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_0.18.0BiocInstaller_1.22.2
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.34.3XVector_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_1.0-6RCurl_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 inte...{{dropped:6}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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
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 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] stats4parallel 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_0.18.0BiocInstaller_1.22.2
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.34.3XVector_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_1.0-6RCurl_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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
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] stats4parallel 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_0.18.0BiocInstaller_1.22.2
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.34.3XVector_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_1.0-6RCurl_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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
