Re: [Bioc-devel] BiocManager now on CRAN

[Jason Serviss]

Hello Marcel,

I notice that the package I maintain, ClusterSignificance, is included in this 
list although I am unsure why. In your previous mail you say:

After the next couple of weeks or so, we will be identifying packages in
bioc-devel (3.8) that still
mention BiocInstaller / biocLite.

I don’t find any mention of BiocInstaller or biocLite in the 
ClusterSignificance vignette and it is a bit unclear to me what “make changes 
to their ... package code to support the use of `BiocManager`” specifically 
entails. Would you mind expanding on what criteria, other than usage of 
BiocInstaller or biocLite in the vignette, that might cause packages to appear 
in your gist?

Kind Regards,
Jason Serviss


On 13 Jul 2018, at 23:11, Marcel Ramos 
mailto:marcel.ramospe...@roswellpark.org>> 
wrote:

biocLite


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Re: [Bioc-devel] Fixing bugs in release version

[Jason Serviss]

Eugenia,

The easiest way to see the logs for git.bioc master branch is to look here: 
http://bioconductor.org/developers/gitlog/. They have an RSS feed for both the 
master and release branch as well. Since I don’t use RSS I instead did the 
following:

1) cloned your repo from git.bioc: git clone 
https://git.bioconductor.org/packages/Onassis
2) Use git fetch to allow me to checkout the RELEASE_3_7 branch: git fetch
3) Checked out the RELEASE_3_7 branch: git checkout RELEASE_3_7
4) Then looked at the commit history: git log

The latest commit (at the top) is ce0fb68.
5) If I look at the DESCRIPTION file: less DESCRIPTION
it shows Version: 1.2.1.

I believe this is correct, although, I am not an expert either. Maybe someone 
will chime in and confirm that I am giving you the correct procedure.

On the RELEASE_3_7 branch in your Github repo (not git.bioc) I can see that the 
version was changed from 1.2.1 to 1.3.1 in the most recent commit (def6111) 
here: 
https://github.com/eugeniaeueu/Onassis/commit/def6111f80db3ed03a991416ce724425d2027d01…
 but, as far as I can tell, you have not pushed that commit to git.bioc and, 
therefore, the version on git.bioc is correct (1.2.1).

Hope this was somewhat helpful.

Kind Regards,
Jason




On 12 Jul 2018, at 16:51, Eugenia Galeota 
mailto:eugenia.gale...@gmail.com>> wrote:

Before the bug fixes I was just working on a master and devel branch on my 
Github connected with bioconductor repository (through upstream). When I 
decided to fix some of the bugs in the release version I just followed the 
instructions in the page that I linked in the first message. It's when I also 
created the RELEASE_3_7 branch in my git repository. After that, in one of the 
commits I noticed that the version in the DESCRIPTION file changed to 3 (but I 
can't remember how it happened, that's why I wrote that maybe I messed up with 
the DESCRIPTION file) and when I tried to change it back to 2 git returned an 
error message saying that it's impossible to bump older versions:

host016:Onassis egaleota$ git status
On branch RELEASE_3_7
Your branch is ahead of 'upstream/RELEASE_3_7' by 1 commit.
  host016:Onassis egaleota$ git checkout master
Switched to branch 'master'
Your branch is ahead of 'origin/master' by 1 commit.
  (use "git push" to publish your local commits)
host016:Onassis egaleota$  git push upstream master
Counting objects: 5, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (5/5), done.
Writing objects: 100% (5/5), 2.33 KiB | 2.33 MiB/s, done.
Total 5 (delta 3), reused 0 (delta 0)
remote: Error: Illegal version bump from '1.3.0' to '1.2.1'. Check
remote: http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To git.bioconductor.org<http://git.bioconductor.org>:packages/Onassis.git

Anyway, since I'm not an expert, I have another simple question. Where can I 
find the commit logs in git.bioc? I usually looked at git logs on my local 
machine with the command "git logs" but the commit ids (
commit 629cb9c4c34b82866c11b14dc2972fedc163c411) are different from those used 
by Jason ((ce0fb68)).
Thank you for this discussion.
Eugenia



2018-07-12 16:20 GMT+02:00 Jason Serviss 
mailto:jason.serv...@ki.se>>:
Mike,

Thanks for your reply. I understand that there is no “automatic syncing” 
between Github and git.bioc and that changes made on Github need to be 
explicitly pushed to git.bioc to be reflected in the packages available via 
biocLite. Although, it would seem as though, from Eugenia’s original question, 
her intentions were to make a change in Github on the release branch and then 
transfer those changes to git.bioc. After looking a bit more carefully, it 
would seem that Eugenia’s last commit on git.bioc (ce0fb68) indeed has version 
1.2.1 although in her Github repo she has made on subsequent commit where she 
changed the version back to 1.3.1 (def6111). Makes perfect sense then… I should 
have looked a bit more closely initially.

Regards,
Jason



On 12 Jul 2018, at 14:58, Mike Smith 
mailto:grimbo...@gmail.com>> wrote:

Hi Jason,

There is no explicit connection between Github and 
git.bioconductor.org<http://git.bioconductor.org/> (I'm going to call this 
git.bioc from now on)  Only changes that are pushed to git.bioc will be 
reflected in the packages available via 
www.bioconductor.org<http://www.bioconductor.org/> and biocLite().  You can 
make any changes you like to a repo on Github and similarly create branches 
with any name you want, but this is completely separate from Bioconductor.  
Having a  RELEASE_X_Y branch on Github and making a change there does not 
automatically mean it gets sent to git.bioc.

Many people like to maintain a Github repository in addition to git.bioc as it 
provides many useful features for social coding (comments, issues, text search 
etc) but it's entirely possible to ignore Github completely after your package 
has been a

Re: [Bioc-devel] Fixing bugs in release version

[Jason Serviss]

Mike,

Thanks for your reply. I understand that there is no “automatic syncing” 
between Github and git.bioc and that changes made on Github need to be 
explicitly pushed to git.bioc to be reflected in the packages available via 
biocLite. Although, it would seem as though, from Eugenia’s original question, 
her intentions were to make a change in Github on the release branch and then 
transfer those changes to git.bioc. After looking a bit more carefully, it 
would seem that Eugenia’s last commit on git.bioc (ce0fb68) indeed has version 
1.2.1 although in her Github repo she has made on subsequent commit where she 
changed the version back to 1.3.1 (def6111). Makes perfect sense then… I should 
have looked a bit more closely initially.

Regards,
Jason



On 12 Jul 2018, at 14:58, Mike Smith 
mailto:grimbo...@gmail.com>> wrote:

Hi Jason,

There is no explicit connection between Github and 
git.bioconductor.org<http://git.bioconductor.org/> (I'm going to call this 
git.bioc from now on)  Only changes that are pushed to git.bioc will be 
reflected in the packages available via 
www.bioconductor.org<http://www.bioconductor.org/> and biocLite().  You can 
make any changes you like to a repo on Github and similarly create branches 
with any name you want, but this is completely separate from Bioconductor.  
Having a  RELEASE_X_Y branch on Github and making a change there does not 
automatically mean it gets sent to git.bioc.

Many people like to maintain a Github repository in addition to git.bioc as it 
provides many useful features for social coding (comments, issues, text search 
etc) but it's entirely possible to ignore Github completely after your package 
has been accepted.

It sounds like you're interested in using both git.bioc and Github, in which 
case the instructions at 
https://bioconductor.org/developers/how-to/git/push-to-github-bioc/ might help 
with keeping them in sync.

Mike

On Thu, 12 Jul 2018 at 11:53, Jason Serviss 
mailto:jason.serv...@ki.se>> wrote:
Mike,

It would appear that the version on Eugenia’s RELEASE_3_7 branch on her git 
repo is 1.3.1 
(https://github.com/eugeniaeueu/Onassis/commit/def6111f80db3ed03a991416ce724425d2027d01)
 so why is it 1.2.1 on the Bioconductor repo?

p.s. have recently been struggling with a similar issue so, just asking to try 
to get a better understanding

Kind Regards,
Jason

> On 12 Jul 2018, at 11:12, Mike Smith 
> mailto:grimbo...@gmail.com>> wrote:
>
> It looks to me like you have made the changes correctly.  When I checkout
> your packages you have versions 1.3.1 and 1.2.1 for the master and
> RELEASE_3_7 branches respectively.
>
> -> % git checkout --quiet master && cat DESCRIPTION | grep Version
> Version: 1.3.1
>
> -> % git checkout --quiet RELEASE_3_7 && cat DESCRIPTION | grep Version
> Version: 1.2.1
>
> The reason it still says 1.2.0 on the landing page is that there can be
> delay before changes in the git repository propagate to the home pge.  You
> can check the last time a snapshot of your packages was taken on
> http://bioconductor.org/checkResults/release/bioc-LATEST/Onassis/ For you
> this was Snapshot Date: 2018-07-10 16:46:08 -0400 (Tue, 10 Jul 2018) which
> is before your commit with the version bump.  It would expect the change to
> propagate through sometime today.
>
> Mike
>
> On Thu, 12 Jul 2018 at 10:52, Eugenia Galeota 
> mailto:eugenia.gale...@gmail.com>>
> wrote:
>
>> Good morning,
>> I'm writing because I tried to fix some bugs in the current release version
>> of my package Onassis.
>> I followed these instructions (
>>
>> https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>> )
>> but maybe I messed up with the version in the DESCRIPTION file. In the
>> Bioconductor page RELEASE_3_7
>> https://www.bioconductor.org/packages/3.7/bioc/html/Onassis.html Onassis
>> has 1.2.0 version, while actually in the repository I don't know how I am
>> at version 1.3.1 (shouldn't it be a development version?).
>> Will my bug fixes be available in the RELEASE_3_7 to users installing the
>> package?
>>
>> I thought that Onassis version after the bug fixes, should have been 1.2.1.
>> Is that correct? How can I update just the current Onassis package in
>> RELEASE_3_7 (the current one) ?
>> Thanks Eugenia
>>
>> --
>> Eugenia Galeota, PhD
>> Center for Genomic Science of IIT@SEMM
>> Computational Epigenomics
>> Email: eugenia.gale...@iit.it<mailto:eugenia.gale...@iit.it>
>> Tel: +39 02 9437 5046
>> Via Adamello 16, 20139 Milan, Italy
>>
>>[[alternative HTML version deleted]]
>>
>> ___
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Re: [Bioc-devel] Fixing bugs in release version

[Jason Serviss]

Mike,

It would appear that the version on Eugenia’s RELEASE_3_7 branch on her git 
repo is 1.3.1 
(https://github.com/eugeniaeueu/Onassis/commit/def6111f80db3ed03a991416ce724425d2027d01)
 so why is it 1.2.1 on the Bioconductor repo? 

p.s. have recently been struggling with a similar issue so, just asking to try 
to get a better understanding

Kind Regards,
Jason 

> On 12 Jul 2018, at 11:12, Mike Smith  wrote:
> 
> It looks to me like you have made the changes correctly.  When I checkout
> your packages you have versions 1.3.1 and 1.2.1 for the master and
> RELEASE_3_7 branches respectively.
> 
> -> % git checkout --quiet master && cat DESCRIPTION | grep Version
> Version: 1.3.1
> 
> -> % git checkout --quiet RELEASE_3_7 && cat DESCRIPTION | grep Version
> Version: 1.2.1
> 
> The reason it still says 1.2.0 on the landing page is that there can be
> delay before changes in the git repository propagate to the home pge.  You
> can check the last time a snapshot of your packages was taken on
> http://bioconductor.org/checkResults/release/bioc-LATEST/Onassis/ For you
> this was Snapshot Date: 2018-07-10 16:46:08 -0400 (Tue, 10 Jul 2018) which
> is before your commit with the version bump.  It would expect the change to
> propagate through sometime today.
> 
> Mike
> 
> On Thu, 12 Jul 2018 at 10:52, Eugenia Galeota 
> wrote:
> 
>> Good morning,
>> I'm writing because I tried to fix some bugs in the current release version
>> of my package Onassis.
>> I followed these instructions (
>> 
>> https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>> )
>> but maybe I messed up with the version in the DESCRIPTION file. In the
>> Bioconductor page RELEASE_3_7
>> https://www.bioconductor.org/packages/3.7/bioc/html/Onassis.html Onassis
>> has 1.2.0 version, while actually in the repository I don't know how I am
>> at version 1.3.1 (shouldn't it be a development version?).
>> Will my bug fixes be available in the RELEASE_3_7 to users installing the
>> package?
>> 
>> I thought that Onassis version after the bug fixes, should have been 1.2.1.
>> Is that correct? How can I update just the current Onassis package in
>> RELEASE_3_7 (the current one) ?
>> Thanks Eugenia
>> 
>> --
>> Eugenia Galeota, PhD
>> Center for Genomic Science of IIT@SEMM
>> Computational Epigenomics
>> Email: eugenia.gale...@iit.it
>> Tel: +39 02 9437 5046
>> Via Adamello 16, 20139 Milan, Italy
>> 
>>[[alternative HTML version deleted]]
>> 
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Re: [Bioc-devel] ClusterSignificance version number

[Jason Serviss]

Lori,

Thanks for your quick response! Ok, it was the fact that 
https://git.bioconductor.org/packages/ClusterSignificance is devel by default 
that was not clear to me (potentially obvious in hindsight). Thanks for 
clearing this up!

Kind Regards,
Jason

On 10 Jul 2018, at 11:41, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

There is no problem with the versions.

The master branch is the devel branch -  and the DESCRIPTION on our git server 
is 1.9.0
The RELEASE_3_7 branch is the release 3.7 branch - and the DESCRIPTION on our 
git serve is 1.8.0

When you clone the repository git clone 
https://git.bioconductor.org/packages/ClusterSignificance  By default you are 
in the master (devel) branch.  So it would show the description as 1.9.0  
unless you checkout the release branch. See:
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/


Your downloaded tar was from release (hence the 3.7/bioc  and the 1.8.0 version)
https://master.bioconductor.org/packages/3.7/bioc/src/contrib/ClusterSignificance_1.8.0.tar.gz


The devel tar that shows 1.9.0 would  be from 3.8
https://master.bioconductor.org/packages/3.8/bioc/src/contrib/ClusterSignificance_1.9.0.tar.gz




Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Jason Serviss mailto:jason.serv...@ki.se>>
Sent: Tuesday, July 10, 2018 5:06:59 AM
To: bioc-devel
Subject: [Bioc-devel] ClusterSignificance version number

Hello,

I maintain the ClusterSignificance package which recently encountered a build 
fail. While investigating the problem I noticed that it would seem that there 
is an issue with the version numbering (quite possibly my fault). Both the 
master and RELEASE_3_7 branches were bumped to version 1.9.0 on April 30th 
although it would seem, per Bioconductor convention, that the RELEASE_3_7 
branch should have version 1.8.0. Cloning from the git repo (git clone 
https://git.bioconductor.org/packages/ClusterSignificance), the DESCRIPTION 
file shows version 1.9.0 but if I download the Source Package 
(ClusterSignificance_1.8.0.tar.gz<https://master.bioconductor.org/packages/3.7/bioc/src/contrib/ClusterSignificance_1.8.0.tar.gz>)
 version 1.8.0 is listed in the DESCRIPTION file. Could someone from 
Bioconductor please have a look at this and let me know if/what steps I need to 
take to fix this or if there is just some sort of misunderstanding on my part?

Kind Regards,
Jason Serviss


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[Bioc-devel] ClusterSignificance version number

[Jason Serviss]

Hello,

I maintain the ClusterSignificance package which recently encountered a build 
fail. While investigating the problem I noticed that it would seem that there 
is an issue with the version numbering (quite possibly my fault). Both the 
master and RELEASE_3_7 branches were bumped to version 1.9.0 on April 30th 
although it would seem, per Bioconductor convention, that the RELEASE_3_7 
branch should have version 1.8.0. Cloning from the git repo (git clone 
https://git.bioconductor.org/packages/ClusterSignificance), the DESCRIPTION 
file shows version 1.9.0 but if I download the Source Package 
(ClusterSignificance_1.8.0.tar.gz<https://master.bioconductor.org/packages/3.7/bioc/src/contrib/ClusterSignificance_1.8.0.tar.gz>)
 version 1.8.0 is listed in the DESCRIPTION file. Could someone from 
Bioconductor please have a look at this and let me know if/what steps I need to 
take to fix this or if there is just some sort of misunderstanding on my part?

Kind Regards,
Jason Serviss


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Re: [Bioc-devel] Maintainers submit your SSH public keys

[Jason Serviss]

Hello,

What exactly is ment with “Github id”? My Github username?

Kind Regards,
Jason


On 12 Jul 2017, at 18:16, Turaga, Nitesh 
> wrote:

Hi Samuel,


This is a great question.


You are not required to create a Github repository for your package. But, if 
you are actively maintaining your package, and would like to take advantage of 
the social coding features and the extended Bioconductor community it is a 
really good idea.


If you want to just maintain it on our Git server, once you have SSH access, 
you are welcome to do that as well. This is highlighted in our documentation 
https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-11-maintain-without-github.md.


We welcome feedback on the documentation, and FAQ section 
(https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/faq.md)



Best Regards,


Nitesh




From: Samuel E Zimmerman 
>
Sent: Wednesday, July 12, 2017 11:49 AM
To: Turaga, Nitesh; Ramon Diaz-Uriarte; 
bioc-devel@r-project.org
Subject: RE: [Bioc-devel] Maintainers submit your SSH public keys

Dear Nitesh,

This may seem like an obvious question, but if we have not created a repository 
for our packages yet, should we create a GitHub repository using the directions 
here:

https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-1-svn-to-github.md


Thank you.

Best,
Sam

From: Bioc-devel 
[bioc-devel-boun...@r-project.org] on 
behalf of Turaga, Nitesh 
[nitesh.tur...@roswellpark.org]
Sent: Wednesday, July 12, 2017 11:29 AM
To: Ramon Diaz-Uriarte; 
bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Maintainers submit your SSH public keys

Hi Ramon,

This is a good question. Your key will be processed every 24 hours. If you
have already submitted, then, you should be able to work through the
documentation provided
(https://github.com/Bioconductor/bioc_git_transition/tree/master/doc).
Working through the documentation to check everything is in order helps
everyone in the Bioconductor community too.

Or a simple way to check is, make a change in your cloned package, ideally
it is a �version bump� in the DESCRIPTION file. Then, try to git add �>
commit �> push the change up to the new git server. These steps are given
in our documentation,

https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenari
o-11-maintain-without-github.md#clone-and-setup-the-package-on-your-local-m
achine


https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenari
o-11-maintain-without-github.md#make-and-commit-changes-to-your-local-repos
itory


We appreciate feedback on this.

Best,

Nitesh

P.S We have already processed your previous submission. Don�t worry, we
don�t process duplicate submissions.


Dear Nitesh,

I just filled it up again, though I think I did fill up and hit
send/submit
a few days ago. Is there a way for me to confirm it has worked?


Best,


R.



On Wed, 12-07-2017, at 14:50:14, Turaga, Nitesh
> wrote:
Hi Maintainers,

Please submit your (SSH public key or GitHub id) and SVN id in this
google
form https://goo.gl/forms/eg36vcBkIUjfZfLe2. It will only take a minute
[https://lh6.googleusercontent.com/aTIh4yWF4TsFYR95qIA_lBuCgvLJ88Q4WzDmdBuie6ndQirxWI0jhfRBF7eO-n3W6SE=w1200-h630-p]

git / svn transition: ssh keys
goo.gl
Use this form to link your existing svn credentials with access permissions to 
the new Bioconductor git repository. To do this, we need an ssh public key. You 
might have added these to github, see https://github.com/your-github-id.keys. 
Alternatively, you may provide the ssh public key directly, e.g., copy-pasting 
~/.ssh/id_rsa.pub. To generate ssh key pairs, see 
https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/



or
less.

This is a crucial step to the transition, which is going to happen soon.
You will be able to test/complain/learn about the new git server during
Bioc2017 (Boston - July 26th onwards), and will be good to go from the
day
of transition. It is critical for maintainers who are actively
maintaining
their package on Bioconductor.

We have received very few SSH public keys so far from the 1300+
maintainers in Bioconductor.


Best Regards,

Nitesh




This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee
or agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,

Re: [Bioc-devel] building packages that depend on openssl (was Re: problems linking to Rhtslib on Mac OSX)

[Jason Serviss]

Dan,

Alright, I guess for the time being the most practical solution is to work in 
the R-release version and, potentially, deal with this problem at a later date. 
Thanks again!

Jason


> On 24 May 2016, at 20:46, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
> 
> [renamed the thread]
> 
> - Original Message -
>> From: "Jason Serviss" <jason.serv...@ki.se>
>> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>> Cc: "Aaron Lun" <a...@wehi.edu.au>, "bioc-devel" <bioc-devel@r-project.org>
>> Sent: Tuesday, May 24, 2016 11:32:17 AM
>> Subject: 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:
>> 
> 
> Why are you using R-devel? Bioconductor (even its devel version) does not use 
> R-devel.
> So your question may not really be a Bioconductor question.
> 
> If you are intending to work with the devel version of Bioconductor (3.4) it 
> runs on R.3.3.0.
> CRAN binaries are available for that version of R. Bioconductor is not yet 
> providing Mac binaries for Bioconductor 3.4 due to an ill-timed hardware 
> crash, but we are working on getting them building agains oon.
> 
> So...first, decide whether you really need R-devel. If so, you could try 
> installing the R-3.3.0 binaries of git2r and openssl. They may work.
> If they don't (and I see now that you tried this already without luck) you 
> might want to talk to the maintainer of openssl about this, which is 
> incidentally not a Bioconductor package.
> 
> But if you don't need R-devel, then you don't have to do anything special, 
> just:
> biocLite(c("git2r","openssl"))
> 
> Dan
> 
> 
>> 
>> 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 =

Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

[Jason Serviss]

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

[Jason Serviss]

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 <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/3.3/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}}
> 
> ___