[Bioc-devel] error in bumphunter unit test (Shepherd, Lori)
Jayaram Kancherla
jk@nche @end|ng |rom um|@c@@umd@edu
Thu Apr 4 20:59:07 CEST 2019
Hi Samuela,
We are kind of having a similar issue with the metagenomeSeq package. I was wondering if you were able to figure out the cause for the issue in the package?
For us, the package fails during the build process `devtools::build()` on a code block in the vignette that uses gss. If i run the same exact code block in the interactive R-console on R-devel, things run normally. everything else finishes without errors, `devtools::install()` and `devtools::check()` except for the build.
Thank you,
Jayaram
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Today's Topics:
1. Remaining windows build error (Erik Fasterius)
2. Re: Remaining windows build error (Shepherd, Lori)
3. Re: Error when building BgeeCall package on Mac OS (Martin Morgan)
4. error in bumphunter unit test (Samuela Pollack)
5. Re: error in bumphunter unit test (Shepherd, Lori)
6. Bioconductor 3.9 contributed annotation package deadline
(Van Twisk, Daniel)
7. Vignette Latex error (Karl Stamm)
8. Re: Call for collaborators/advice (Aaron Lun)
9. How to define S4 method for class from another package
(Stephen Martin Pederson)
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Message: 1
Date: Tue, 2 Apr 2019 10:11:50 +0000
From: Erik Fasterius <erik.fasterius using outlook.com>
To: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: [Bioc-devel] Remaining windows build error
Message-ID: <8D6A7AFB-6BDF-4157-A39E-03BB54A00F18 using outlook.com>
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I am still getting a Windows build error in my seqCAT package. I thought this was a problem with VariantAnnotation after an update, which also seemed to be the case after communication with Valerie Obenchain. My package was apparently not the only package affected by this, and I was told the problem was being worked on. What is the status on this?
I would very much like my package to successfully build on all platforms (OS X and Linux are fine) before the deadline for the next Bioconductor release. Is there anything I can do here?
Erik
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Message: 2
Date: Tue, 2 Apr 2019 12:10:49 +0000
From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
To: Erik Fasterius <erik.fasterius using outlook.com>,
"bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Remaining windows build error
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Thank you. We are still looking into the issue and hope to have it resolved soon.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Erik Fasterius <erik.fasterius using outlook.com>
Sent: Tuesday, April 2, 2019 6:11:50 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Remaining windows build error
I am still getting a Windows build error in my seqCAT package. I thought this was a problem with VariantAnnotation after an update, which also seemed to be the case after communication with Valerie Obenchain. My package was apparently not the only package affected by this, and I was told the problem was being worked on. What is the status on this?
I would very much like my package to successfully build on all platforms (OS X and Linux are fine) before the deadline for the next Bioconductor release. Is there anything I can do here?
Erik
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Message: 3
Date: Tue, 2 Apr 2019 13:21:35 +0000
From: Martin Morgan <mtmorgan.bioc using gmail.com>
To: Julien Wollbrett <julien.wollbrett using sib.swiss>,
"bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Error when building BgeeCall package on Mac
OS
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I added a response to your issue at
https://github.com/Bioconductor/Contributions/issues/1002#issuecomment-478991986
encouraging you (again) to avoid installing software on the user system; there are basic problems with this approach, and the correct solution is to list kallisto as a SystemDependency: in your DESCRIPTION file.
Maritn
On 4/2/19, 4:17 AM, "Bioc-devel on behalf of Julien Wollbrett" <bioc-devel-bounces using r-project.org on behalf of julien.wollbrett using sib.swiss> wrote:
Hello,
My package (called BgeeCall) is under review and passed R CMD Build and
R CMD Check for Linux and windows.
I still have an error on Mac. I tried to reproduce it using different
versions of R (3.5 and 3.6) and different OS
versions (Sierra and El Capitan). I tried on 5 different computers but
still not able to reproduce this error.
Does anyone have any idea on the origin of this error ? What should I
try to do to solve it?
dyld: Library not loaded: @rpath/libz.1.dylib
Referenced from: /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/kallisto/kallisto
Reason: image not found
Will run kallisto using this command line : /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/kallisto/kallisto quant -i /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/intergenic_0.1/6239/kallisto/transcriptome_WBcel235/transcriptome.idx -o /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/intergenic_0.1/6239/kallisto/transcriptome_WBcel235/annotation_WBcel235_84/SRX099901_subset -t 1 --single -l 180 -s 30 --bias /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rinst1406e55617de6/BgeeCall/extdata/SRX099901_subset/SRR350955_subset.fastq.gz
dyld: Library not loaded: @rpath/libz.1.dylib
Referenced from: /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/kallisto/kallisto
Reason: image not found
You can access to the submission issue here :
https://github.com/Bioconductor/Contributions/issues/1002
Thank you for your answers.
Julien Wollbrett
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Message: 4
Date: Tue, 2 Apr 2019 10:17:57 -0400
From: Samuela Pollack <spollack using jimmy.harvard.edu>
To: Bioc-devel <bioc-devel using r-project.org>
Subject: [Bioc-devel] error in bumphunter unit test
Message-ID: <16dff631-da1e-354b-727d-263ddb3067d2 using jimmy.harvard.edu>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Dear Bioconductor,
Our bumphunter package is failing its unit tests fairly spectacularly:
the pval algorithm seems to be returning a data frame full of zeroes.
Unfortunately, I have not been able to reproduce this behavior. I have
instantiated an EC2 instance with the devel AMI, updated all the
packages, installed bumphunter and its dependencies, and run the unit
tests without errors.
My sessionInfo indicates all R dependencies are identical to the
snapshot on the devel build report. However, two things may be causing
the disparity in results:
(i) bumphunter uses 'doParallel' and 'foreach' at the point that it is
failing; is it possible for me to confirm that I am using the same
version of these as the build system used. (Note: we are failing even
when doParallel defaults to sequential execution, so the low-level
interface does not seem to be relevant.)
(ii) The devel AMI is running R 3.6 release 75543 and the build system
is running release 76205. Could this be the discrepancy we're looking
for? We are reluctant to reinstall all of R+Bioc unless it looks relevant.
Any other suggestions would be very helpful. We haven't touched the
package in months and are totally buffaloed why it has decided to fail
just days before the new release.
thanks in advance for any advice you can offer,
- Sam
------------------------------
Message: 5
Date: Tue, 2 Apr 2019 15:06:36 +0000
From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
To: Samuela Pollack <spollack using jimmy.harvard.edu>, Bioc-devel
<bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] error in bumphunter unit test
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<BN8PR12MB31889B491B751FF6B7074C58F9560 using BN8PR12MB3188.namprd12.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
The version of R devel being used could be significant. There have been a number of changes in R devel that could be the culprit.
Could be completely unrelated but one such example is the random number generator updates:
https://stat.ethz.ch/pipermail/bioc-devel/2019-March/014776.html
Please make sure you are using the most recent R-devel.
The version of packages being utilized on the build system will be the versions listed in the build report page:
http://bioconductor.org/checkResults/3.9/bioc-LATEST/
You could always do a BiocManager::valid() to test a valid install and if any packages should be updated.
Are you using a bioconductor provided devel docker images? If you are, the devel docker image are updated weekly. You might want to pull the latest version. A locally pull docker image does not update automatically.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Samuela Pollack <spollack using jimmy.harvard.edu>
Sent: Tuesday, April 2, 2019 10:17:57 AM
To: Bioc-devel
Subject: [Bioc-devel] error in bumphunter unit test
Dear Bioconductor,
Our bumphunter package is failing its unit tests fairly spectacularly:
the pval algorithm seems to be returning a data frame full of zeroes.
Unfortunately, I have not been able to reproduce this behavior. I have
instantiated an EC2 instance with the devel AMI, updated all the
packages, installed bumphunter and its dependencies, and run the unit
tests without errors.
My sessionInfo indicates all R dependencies are identical to the
snapshot on the devel build report. However, two things may be causing
the disparity in results:
(i) bumphunter uses 'doParallel' and 'foreach' at the point that it is
failing; is it possible for me to confirm that I am using the same
version of these as the build system used. (Note: we are failing even
when doParallel defaults to sequential execution, so the low-level
interface does not seem to be relevant.)
(ii) The devel AMI is running R 3.6 release 75543 and the build system
is running release 76205. Could this be the discrepancy we're looking
for? We are reluctant to reinstall all of R+Bioc unless it looks relevant.
Any other suggestions would be very helpful. We haven't touched the
package in months and are totally buffaloed why it has decided to fail
just days before the new release.
thanks in advance for any advice you can offer,
- Sam
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Message: 6
Date: Tue, 2 Apr 2019 17:59:44 +0000
From: "Van Twisk, Daniel" <Daniel.VanTwisk using RoswellPark.org>
To: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: [Bioc-devel] Bioconductor 3.9 contributed annotation package
deadline
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Hello Biocondcutor Community!
This is just a friendly reminder that our contributed package deadline for the upcoming Bioconductor 3.9 release is April 24th.
Also, we plan to have our db0 packages completed by April 8th.
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, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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Message: 7
Date: Tue, 2 Apr 2019 17:03:09 -0500
From: Karl Stamm <karl.stamm using gmail.com>
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Vignette Latex error
Message-ID:
<CAMgEeFVGTT9DAcRbfE74VD4+EZpB4wr-9LvJ0sV-fdYNmqvmOg using mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
I'm having a build error on only the OSX servers.
* creating vignettes ... ERROR
--- re-building ‘rgsepd.Rnw’ using knitr
Error: processing vignette 'rgsepd.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rgsepd.tex' failed.
LaTeX errors:
! Use of \blx using bbl@verbadd using i doesn't match its definition.
l.142 \verb
The tex file is written by the Rnw with knitr, so maybe it's a knitr
problem, or an incompatibility to the OSX side?? I tried removing
all references to \verb and that doesnt seem to have done anything.
I want to get the package building without errors before the brach
lockdown in a few weeks.
Since it builds on my end just fine, and also on the Windows and Linux
servers, surely it's a build server platform specific problem. Maybe
Knitr is not supported anyone and I need to change everything over to
another RMD format ?
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Message: 8
Date: Tue, 2 Apr 2019 21:54:08 -0700
From: Aaron Lun <infinite.monkeys.with.keyboards using gmail.com>
To: Luke Klein <lklei001 using ucr.edu>, bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Call for collaborators/advice
Message-ID: <ad2edc06-02dc-2771-b82f-a3fdbb988f79 using gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Breaker breaker.
> 1) A package to define a base (virtual) "Interactions" class. This would
> basically have a constant "Vector" store with a "Hits" object specifying
> the pairwise interactions between elements in the constant store. One
> could also distinguish between "SelfInteractions" (constant store) and
> the more general "Interactions" (two stores, possibly of different
> types, e.g., genomic interval -> protein interactions). A variety of
> methods would be available here to do manipulations and such.
https://github.com/LTLA/IndexedRelations (WIP)
> 2) A package to define an "Interactions" subclass where the store is a
> genomic interval, with basic methods to operate on such classes. Methods
> such as findOverlaps(), linkOverlaps() and boundingBox() would probably
> go here. @Luke, a binning method could also conceivably go here.
https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/issues/37
> All of this is open for discussion, if people are interested and willing
> to volunteer. These changes will not make the next release anyway.
What he said.
-A
> On 22/03/2019 19:54, Aaron Lun wrote:
>> Hi Luke,
>>
>> Do you mean bins or bin pairs?
>>
>> If you want to just bin the coverage in terms of the linear genome,
>> there should be ways to do that outside of InteractionSet or
>> GenomicInteractions. This is just dealing with standard genomic
>> interval data; extract the anchor coordinates and plug it in elsewhere.
>>
>> If you want to collate region pairs into bin pairs; I don't know of a
>> dedicated function to do this from a GInteractions object (diffHic
>> only does this from raw read data). You'll need to figure out what to
>> do to regions that cross bin boundaries.
>>
>> The simplest way to mimic this behaviour right now is to generate
>> another GInteractions object containing ALL POSSIBLE bin pairs (use
>> combn with a constant set of bin regions) and plug that into
>> countOverlaps. This will generate loads of zeroes, though, so is not
>> the most efficient way to do this. You could get a sparser form with
>> linkOverlaps but this requires more work to get the counts.
>>
>> I have some more thoughts about the Bioconductor Hi-C infrastructure,
>> but my laptop battery's running out and I left my charger in my new
>> apartment. So that'll have to wait until tomorrow.
>>
>> -A
>>
>>
>> On 22/03/2019 09:31, Luke Klein wrote:
>>> I am writing a package that will extend the GenomicInteractions
>>> class. I am a statistician, so I may not know best practices when
>>> it comes to extending existing classes (eg. should I make a new slot
>>> or simply add a column to the `elementMetadata`? Are there existing
>>> functions that already do what I am attempting?).
>>>
>>> I am not familiar with Bioc-Devel decorum, so if asking this here is
>>> inappropriate, kindly let me know.
>>>
>>> About my project:
>>>
>>> In the first step, I am hoping to implement a HiC binning function on
>>> HiC data contained in a GenomicInteractions set. I aim to:
>>>
>>> - Reorder the anchor pairs (I will explain in more detail to anyone
>>> that wants to help)
>>> - Collapse the regions to the desires bin width
>>> - Sum the counts within each bin
>>> - Update the anchors to agree with the new/updated regions
>>>
>>> This will set the stage for the new class that I hope to create for
>>> HiC domain calling, but I need to achieve the above tasks first.
>>>
>>> All the best to everyone!
>>>
>>> —*Luke Klein*
>>> PhD Student
>>> Department of Statistics
>>> University of California, Riverside
>>> lklei001 using ucr.edu <mailto:lklei001 using ucr.edu>
>>>
>>>
>>>
>>>
>>>
>>>
------------------------------
Message: 9
Date: Wed, 3 Apr 2019 05:19:07 +0000
From: Stephen Martin Pederson <stephen.pederson using adelaide.edu.au>
To: "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: [Bioc-devel] How to define S4 method for class from another
package
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Hi,
I'm really struggling with how to use an S4 class defined in another package, where I would like to define a method for it in my package. By way of simple example, I'd like to use a DNAStringSet to define an expected GC distribution based on a given fragment size. I had defined the method
setMethod("getGcDistn", "DNAStringSet", function(myArgs){myBody})
after using setGeneric() to define the generic getGcDistn.
When submitting to BioC, I was advised that this is not permissable & I'm trying to figure out what is the best etiquette & best practice. I haven't really turned up much guidance through numerous searches. Do I just write a standard function which checks the class and executes the code as required without using S4 dispatch?
(Disclaimer: I'm very easily confused by the simplest things)
Thanks in advance,
Steve
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