[Bioc-devel] Strange warning message on build server moscato2

2015-03-11 Thread Rainer Johannes
dear all! I have submitted a new package that builds nicely on all machines except the windows server moscato2. I get a strange warning message, that I do not quire understand: Warning: multiple methods tables found for 'score'. I have no function or method score defined in my package. Any

Re: [Bioc-devel] AnnotationHubData Error: Access denied: 530

2015-04-11 Thread Rainer Johannes
point. cheers, jo On 11 Apr 2015, at 00:54, Marc Carlson mcarl...@fredhutch.orgmailto:mcarl...@fredhutch.org wrote: On 04/10/2015 12:18 PM, Rainer Johannes wrote: dear Sonali, Herve, On 10 Apr 2015, at 19:59, Herv� Pag�s hpa...@fredhutch.orgmailto:hpa...@fredhutch.orgmailto:hpa...@fredhutch.org

[Bioc-devel] Suggestion: export function fetchChromLengthsFromEnsembl in GenomicFeatures

2015-04-11 Thread Rainer Johannes
I wanted to ask whether it would be possible to export the functions fetchChromLengthsFromEnsembl and fetchChromLengthsFromEnsemblPlants in GenomicFeatures, as I find these methods quite useful to retrieve chromosome lengths. best, jo ___

Re: [Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency

2015-06-09 Thread Rainer Johannes
dear Ludwig, On 09 Jun 2015, at 10:46, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.demailto:ludwig.geistlin...@bio.ifi.lmu.de wrote: Dear Johannes, Thx for providing the great EnsDb packages! One question: As of now, I am able to choose between TxDb and EnsDb for genomic coordinates

Re: [Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency

2015-06-09 Thread Rainer Johannes
dear Robert and Ludwig, the EnsDb packages provide all the gene/transcript etc annotations for all genes defined in the Ensembl database (for a given species and Ensembl release). Except the column/attribute entrezid that is stored in the internal database there is however no link to NCBI or

Re: [Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency

2015-06-10 Thread Rainer Johannes
update: seems something is strange with the index... when I load the ensembl-77 DNA for mouse I get two files, the fasta file and the index and I can extract the sequences, while in the example below I just got the fasta file On 10 Jun 2015, at 10:11, Rainer Johannes johannes.rai

Re: [Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency

2015-06-11 Thread Rainer Johannes
:38, Rainer Johannes johannes.rai...@eurac.edumailto:johannes.rai...@eurac.edu wrote: dear Ludwig, On 09 Jun 2015, at 10:46, Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.demailto:ludwig.geistlin...@bio.ifi.lmu.de wrote: Dear Johannes, Thx for providing the great EnsDb packages! One

[Bioc-devel] Gviz: implementing support for FaFiles from AnnotationHub

2015-11-09 Thread Rainer Johannes
Dear All, dear Florian, I’m currently working on a Gviz-hack that would enable to use the FaFiles provided from AnnotationHub directly as SequenceTracks in Gviz. I think that might be a nice addition, since that way both Ensembl based annotations (e.g. as EnsDbs) and Ensembl genome fasta files

Re: [Bioc-devel] Gviz: implementing support for FaFiles from AnnotationHub

2015-11-09 Thread Rainer Johannes
# my amazing changes >svn diff > Gviz.diff # ... as a diff for Florian > > ____ > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer > Johannes [johannes.rai...@eurac.edu] > Sent: Monday, November 09, 2015 10:08 AM > T

Re: [Bioc-devel] Gviz: implementing support for FaFiles from AnnotationHub

2015-11-09 Thread Rainer Johannes
w, you are busy :-) > I will just wait until I receive all of you patches before adding them to > the official package release. > Florian > > On 09/11/15 16:08, "Bioc-devel on behalf of Rainer Johannes" > <bioc-devel-boun...@r-project.org on behalf of johannes.rai...@eu

[Bioc-devel] Gviz: GeneRegionTrack from EnsDb objects

2015-11-04 Thread Rainer Johannes
Dear Florian, I’ve forked the (Bioconductor-mirror) Gviz repository on github and added support to create GeneRegionTracks from EnsDb objects. It works analogously to GeneRegionTracks from TxDb, but provides in addition gene or tx biotypes, gene names and gene models of all (not only protein

[Bioc-devel] Missing "release-3.2" branch of my package

2015-10-19 Thread Rainer Johannes
Dear all, somehow my ensembldb package is missing the release-3.2 branch in the Bioconductor-mirror repository on github. Is there something I should have done myself? I thought that the branches are created automatically with each new Bioconductor release. Thanks for all suggestions and help

Re: [Bioc-devel] Missing "release-3.2" branch of my package

2015-10-19 Thread Rainer Johannes
git mirrors that halted the update. I am working on it now and release 3.2 branches for all packages should be available soon. Sorry for the confusion Jim On Oct 19, 2015 5:47 AM, "Rainer Johannes" <johannes.rai...@eurac.edu<mailto:johannes.rai...@eurac.edu>> wrote: Dear

[Bioc-devel] Test coverage for packages not calculated/updated?

2015-12-04 Thread Rainer Johannes
Dear all, I know that’s not a really urgent and important thing, but to me it seems that the code coverage/test coverage badges are not calculated or updated anymore. For example, on http://bioconductor.org/packages/devel/bioc/html/FamAgg.html it says test coverage unknown suggesting that there

[Bioc-devel] Extending biovizBase and ggbio packages

2015-12-14 Thread Rainer Johannes
Dear all, I’ve modified the biovizBase and ggbio packages so that they do directly support EnsDb annotations (just like annotations provided by TxDb objects/packages). Is there a way I could provide these changes? I’ve directly contacted Tengfei last week, but did not get any reply yet…

Re: [Bioc-devel] Extending biovizBase and ggbio packages

2015-12-14 Thread Rainer Johannes
> convenience wrappers like subset() and sort(). Like > transcripts(sort(subset(db, seqname == "chr1"), by = geneSymbol)). > > Thanks, > Michael > > On Mon, Dec 14, 2015 at 4:12 AM, Rainer Johannes > <johannes.rai...@eurac.edu> wrote: >> Dear all

Re: [Bioc-devel] Extending biovizBase and ggbio packages

2015-12-15 Thread Rainer Johannes
s. We should try hard to > reduce this. > > Michael > > On Tue, Dec 15, 2015 at 1:37 AM, Rainer Johannes > <johannes.rai...@eurac.edu> wrote: >> OK, the modifications are in the repositories: >> https://github.com/jotsetung/biovizBase >> https://github

[Bioc-devel] Use of EnsDb in the AnnotationDbi framework

2016-01-07 Thread Rainer Johannes
Dear all, thanks to Vince’s suggestion I have now implemented the central AnnotationDbi methods “columns”, “keys”, “keytypes” and “select” for EnsDb objects in my ensembldb package version 1.3.11 (EnsDb are TxDb like annotation packages/objects tailored to Ensembl based annotations). Thus,

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

2016-01-08 Thread Rainer Johannes
haps something that could be handled when population the >> hub, but I'm not sure how rtracklayer could automatically derive the >> chromosome names. >> >> On Fri, Jan 8, 2016 at 2:37 AM, Rainer Johannes >> <johannes.rai...@eurac.edu> wrote: >>> dear

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

2016-01-09 Thread Rainer Johannes
te that in general the seqlevels() setter allows more than >>> renaming the seqlevels. It also allows dropping, adding, and shuffling >>> them. But you don't need to support all that. Supporting renaming would >>> already go a long way. See selectMethod("seqlevels<-&quo

[Bioc-devel] New package: FamAgg - familial aggregation analysis in large pedigrees

2015-12-01 Thread Rainer Johannes
dear All, we’re pleased to announce that our package, FamAgg, has been added to Bioconductor. FamAgg provides methods to investigate familial aggregation in large pedigrees and other pedigree analysis and plotting utilities. cheers, jo ___

Re: [Bioc-devel] Troubles using R/Bioc-devel with Mac OS X El Capitan 10.11.1

2015-11-18 Thread Rainer Johannes
Could be that gcc via homebrew takes a while… especially if it is compiling that stuff from source… > On 18 Nov 2015, at 14:46, Ludwig Geistlinger > wrote: > > While I am following Jo's suggestions on installing gcc via homebrew on my > mac laptop (is it

Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

2016-01-11 Thread Rainer Johannes
Just as an info… EnsDb objects/packages (from ensembldb package) provide similar functionality than the TxDb, are tailored to Ensembl annotations and can be build from the GTF files from Ensembl (which can be fetched via AnnotationHub; it’s all described in the ensembldb vignette). cheers, jo

Re: [Bioc-devel] Problem with seqnames of TwoBitFile from AnnotationHub

2016-01-10 Thread Rainer Johannes
ay in to annotation hub; this is against Sean's >>> advice and I'm not really a big fan of this. >>> >>> I like the idea of being able to dynamically remap the seqlevels when the >>> 2bit file is loaded by AnnotationHub, which would require Herve's >>>

[Bioc-devel] seqlevelsStyle: EnsDb integration with UCSC based annotations

2016-02-01 Thread Rainer Johannes
Dear All! Just wanted to let you know that I just pushed the last changes to the ensembldb package (version 1.3.14) that allow an easier integration with non-Ensembl based annotation. In detail, I’ve implemented the seqlevelsStyle and seqlevelsStyle<- method from the GenomeInfoDb and now it’s

Re: [Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

2016-01-19 Thread Rainer Johannes
al argument that is > accepted by the "exonsBy" method for EnsDb objects. > > Let me know if you run into problems with this. > > Cheers, > H. > > On 01/18/2016 06:46 AM, Rainer Johannes wrote: >> Dear all, >> >> I’m having hard times to e

[Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

2016-04-30 Thread Rainer Johannes
Dear all, I was wondering, you think it would be possible to make the transcriptLength function in GenomicFeatures a method and export that? Reason is that I have also implemented a transcriptLength function (actually presently a method in order to allow that to be used for EnsDb and TxDb

Re: [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

2016-05-04 Thread Rainer Johannes
in.mor...@roswellpark.org> wrote: > > On 05/02/2016 03:46 AM, Rainer Johannes wrote: >> Hi Herve, >> >> passing down additional arguments to the internal exonsBy, cdsBy, >> fiveUTRsByTranscript and threeUTRsByTranscript would do it! That >> would be great

Re: [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

2016-05-02 Thread Rainer Johannes
ld work out-of-the-box on EnsDb objects. > Would that work? > > H. > > On 04/30/2016 04:05 AM, Rainer Johannes wrote: >> Dear all, >> >> I was wondering, you think it would be possible to make the transcriptLength >> function in GenomicFeatures a method

[Bioc-devel] Recent changes in xcms

2017-01-26 Thread Rainer Johannes
Dear all, we are currently in the middle of refactoring and updating the xcms package, which could cause (on the short term) some problems in packages depending on functionality from xcms. In the long run everything should work and integration of functionality from xcms in other packages

[Bioc-devel] How to update annotation packages

2016-09-16 Thread Rainer Johannes
Dear all, I wanted to update the EnsDb.* annotation packages I originally provided, but I didn't find any guide how to do that in the "Developer resources" on the Bioconductor website (although it could well be that I overlooked it). How can I update my annotation packages? thanks, jo

Re: [Bioc-devel] RMassBank build error

2016-10-07 Thread Rainer Johannes
run again into the random memory problems that we had in MSnbase (issue https://github.com/lgatto/MSnbase/issues/138) jo > On 7 Oct 2016, at 20:14, Rainer Johannes <johannes.rai...@eurac.edu> wrote: > > we could try to switch back from the C-constructors to the "old" ones, I'll

Re: [Bioc-devel] github mirror and svn out of sync

2016-09-21 Thread Rainer Johannes
(which is in sync with BioC svn) as I did have nasty merge conflicts doing a `git merge master`. jo > On 21 Sep 2016, at 13:38, Martin Morgan <martin.mor...@roswellpark.org> wrote: > > On 09/21/2016 12:01 AM, Rainer Johannes wrote: >> Dear all, >> >>

[Bioc-devel] github mirror and svn out of sync

2016-09-20 Thread Rainer Johannes
Dear all, I recently observed that the svn and the github mirror of `ensembldb` is out of sync. Is this something specific to `ensembldb` or is this a general problem? Is there anything I could do to fix this? thanks, jo ___ Bioc-devel@r-project.org

[Bioc-devel] github-mirror of ensembldb out of sync with BioC svn

2016-10-19 Thread Rainer Johannes
I just wanted to report that the github-mirror for ensembldb is out of sync with the BioC svn. You're most likely already working on that. In any rate, thanks for your great work! ___ Bioc-devel@r-project.org mailing list

Re: [Bioc-devel] programming note: return() is a function call

2016-11-14 Thread Rainer Johannes
Fixed in ensembldb thanks Martin! > On 14 Nov 2016, at 11:37, Martin Morgan wrote: > > An interested R-help thread (starting at > https://stat.ethz.ch/pipermail/r-help/2016-November/443123.html) points out > that return() is treated as a function by the R

Re: [Bioc-devel] RMassBank build error

2016-10-10 Thread Rainer Johannes
hing else. >> >> Anyway, if we don't manage to find an acceptable solution for MSnbase, I >> will submit an RMassBank patch that will sort the error (and other >> things resulting from MSnbase improvements) out. What would be the best >> way to submit a patch - email, a pu

Re: [Bioc-devel] Problem pushing new versions of xcms via git svn dcommit

2017-01-03 Thread Rainer Johannes
Hi Steffen and Laurent, one problem with xcms is that the 'devel' branch on sneumann/xcms is the real 'master' branch. I would suggest to create a new branch on github, e.g. 'biocdevel' and to link that one to the BioC svn (means also that update_remotes.sh can not be user right away - the svn

Re: [Bioc-devel] Something about time out errors

2017-03-27 Thread Rainer Johannes
Do you have code fetching data from web resources? I also sometimes get timeout errors on ensembldb and I guess it's because in some unit tests I'm fetching data from the ensembl ftp server. jo > On 27 Mar 2017, at 18:37, Martin Morgan wrote: > > On 03/27/2017

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-04 Thread Rainer Johannes
that > maybe a smoother path would have been to notify the maintainers > of these packages first and wait that they make the required > changes (i.e. to import the filters from AnnotationFilter) > before modifying ensembldb. Maybe for next time ;-) > > Cheers, > H. >

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-04 Thread Rainer Johannes
loping without having to wait for Gviz? These come from biovizBase which Gviz imports. I've sent Micheal the fixes for biovizBase and ggbio that should fix this. We need to wait for the changes to be propagated, since also for ensembldb I get today still version 1.99.12 but not the new 1.99.

[Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-03 Thread Rainer Johannes
Dear all, I've just committed a change in ensembldb (version 1.99.13) that removes all filter classes from it and imports them from the AnnotationFilter package. This change will break biovizBase and ggbio (and all packages downstream of them, e.g. Gviz). I've already sent Michael Lawrence

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-06 Thread Rainer Johannes
on). Thanks. On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence <lawrence.mich...@gene.com<mailto:lawrence.mich...@gene.com> wrote: Sorry I have been traveling. Will get to it soon. On Apr 4, 2017 12:58 PM, "Rainer Johannes" <johannes.rai...@eurac.edu<mailto:johannes.rai...

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-07 Thread Rainer Johannes
ges have not been committed to Bioc yet (asked Laurent for that). I did also fix wiggleplotr and made a pull request, but the developer did not yet react to that. cheers, jo > https://bioconductor.org/checkResults/3.5/bioc-LATEST/Pbase/malbec2-buildsrc.html > > H. > > >

Re: [Bioc-devel] Recent error in FamAgg with R-3.4rc

2017-04-19 Thread Rainer Johannes
An update: the fixed gap package is now in CRAN (https://cran.r-project.org/web/packages/gap/index.html). Once the Windows build machine uses/installs this updated CRAN package, the error in FamAgg will be fixed. cheers, jo On 19 Apr 2017, at 13:04, Rainer Johannes <johannes.rai...@eurac.

Re: [Bioc-devel] Recent error in FamAgg with R-3.4rc

2017-04-19 Thread Rainer Johannes
Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Rainer Joha

[Bioc-devel] Recent error in FamAgg with R-3.4rc

2017-04-19 Thread Rainer Johannes
Dear all, Somehow the FamAgg fails building with the recent R-3.4rc in Windows. I tracked down the error and it comes from a fortran code in a function from the "gap" CRAN package I'm using in one of the functions. I contacted the developer and in the meantime implemented a workaround in

[Bioc-devel] Vignette for xcms fails to build on tokay1

2017-07-27 Thread Rainer Johannes
Dear all, one of the xcms vignettes fails to build on tokay1 recently with the error message: Warning: running command '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf "xcmsDirect.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.6-bioc/R/share/texmf/tex/latex" -I

Re: [Bioc-devel] xcms adjustRtime-obiwarp Error

2017-07-27 Thread Rainer Johannes
Dear Riccardo, I will look closer into this. In the meantime it might help if you try a different binSize in the ObiwarpParam. Also, could you please add an issue with this error on https://github.com/sneumann/xcms ? I can then track and relate all changes to the issue. thanks, jo On 27 Jul

[Bioc-devel] github mirror out of sync for ensembldb

2017-04-27 Thread Rainer Johannes
Hi, the github mirror for ensembldb seems to be out of sync with the BioC svn, i.e. the DESCRIPTION in https://github.com/Bioconductor-mirror/ensembldb/blob/master/DESCRIPTION is still at version 1.99.14 while in the svn it's already 2.1.0. First I thought the sync is not yet finished, but

Re: [Bioc-devel] github mirror out of sync for ensembldb

2017-05-03 Thread Rainer Johannes
date to the package and after committing the change to the Bioc svn ensembldb was synced successfully. > aCGH actually had a RELEASE_3_5 branch; I'll investigate why aCGH and at > least some other packages have not been fully updated after the branch. > > Martin > > >>

Re: [Bioc-devel] mzR: pwiz is now the default backend

2017-05-23 Thread Rainer Johannes
actually, I got quite some segfaults lately with the Ramp backend (was default up to now). With the pwiz backend I don't get them anymore. Also, in xcms we were manually setting the backend to pwiz and did not experience any problems. cheers, jo On 23 May 2017, at 18:35, Laurent Gatto

[Bioc-devel] Generic for write to BiocGenerics

2017-09-18 Thread Rainer Johannes
Dear all! We are currently implementing mzML write support in `MSnbase` and did implement a `write` method for the S4 objects in `MSnbase`. Now, the question is whether it might not be better to define a `write` S4 generic in `BiocGenerics`? cheers, jo

Re: [Bioc-devel] Generic for write to BiocGenerics

2017-09-19 Thread Rainer Johannes
the args and >> their defaults, tab-completion also works on the arguments, and the user >> does not struggle in finding the man page (like s/he does sometimes >> with generic and methods, especially when those are defined in >> different packages). >> >> H. >> &g

[Bioc-devel] Increase timeout for mzR on Windows?

2017-10-11 Thread Rainer Johannes
Hi, would it be possible to increase the allowed build and check times for mzR on Windows? Building mzR takes very long due to the compilation of the included proteowizard (and boost?) code so there is not much we can do to speed that up. On linux and macOS all is fine, but we get TIMEOUT

Re: [Bioc-devel] EXTERNAL: Increase timeout for mzR on Windows?

2017-10-11 Thread Rainer Johannes
Dear Martin, > On 11 Oct 2017, at 13:05, Martin Morgan <martin.mor...@roswellpark.org> wrote: > > On 10/11/2017 03:48 AM, Rainer Johannes wrote: >> Hi, >> would it be possible to increase the allowed build and check times for mzR >> on Windows?

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

2017-09-12 Thread Rainer Johannes
Hi Aditya, you could check the more recent ensembldb EnsDb databases to see if there is something in them you might need/want. I've added protein annotations to them (as provided by Ensembl). They contain the Ensembl protein domains, the AA sequence, all protein domain families (as defined/linked

Re: [Bioc-devel] fixing 'path' not being exported by 'Rsamtools'

2017-12-19 Thread Rainer Johannes
Thanks Herve I did also fix it in ensembldb but didn't push to Bioc yet - well, have to pull your changes now instead :) cheers, jo > On 20 Dec 2017, at 04:08, Hervé Pagès wrote: > > Hi Robert, > > Gviz depends on ensembldb which needed to have its NAMESPACE adjusted >

Re: [Bioc-devel] packages modifying 'library' during R CMD check

2017-12-02 Thread Rainer Johannes
Thanks Val I'll fix that for `xcms`. Is it enough to fix the devel version, or should we also fix the Bioc 3.6 release version? cheers, jo > On 29 Nov 2017, at 15:43, Obenchain, Valerie > wrote: > > Hi developers, > > Several Bioconductor packages have

[Bioc-devel] mapping between genomic, transcript and protein positions in ensembldb

2017-12-06 Thread Rainer Johannes
Dear all, just wanted to inform you that I've implemented functions to map between genomic coordinates and coordinates in transcripts and proteins (and vice versa) in ensembldb (since all of the required data is available in EnsDb packages). I'm open to suggestions, improvements etc cheers,

Re: [Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

2018-01-07 Thread Rainer Johannes
I'll test on mac and windows cheers, jo > On 7 Jan 2018, at 22:57, Neumann, Steffen wrote: > > Hi, > > Following the bug report in > https://github.com/sneumann/mzR/issues/143 > > there is a branch with a fix in > https://github.com/sneumann/mzR/pull/144 > > that

[Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

2018-02-08 Thread Rainer Johannes
Dear all, one of the unit tests in ensembldb is failing because of a problem in GenomicFeatures::extractTranscriptSeqs (I guess): library(BSgenome.Hsapiens.NCBI.GRCh38) bsg <- BSgenome.Hsapiens.NCBI.GRCh38 library(EnsDb.Hsapiens.v86) all <- extractTranscriptSeqs(bsg, EnsDb.Hsapiens.v86) Error

[Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

2018-02-12 Thread Rainer Johannes
Dear all, I'm unable to push my recent changes to FamAgg to the Bioconductor git repo (see below for the error message). I did try the suggested fix but without any success - seems the duplicated commits are in Bioconductor and not github. thankful for any help or advise The error message is:

Re: [Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

2018-02-13 Thread Rainer Johannes
k they still derive from the git git-svn setup). I could live with the git history not being clean. So, from my side, you could go ahead and remove the pre-receive hook. funnily, I have also duplicated commits in ensembldb, but there I'm still able to push to Bioconductor git without probl

Re: [Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

2018-02-09 Thread Rainer Johannes
; > Cheers, > H. > > On 02/08/2018 10:48 PM, Rainer Johannes wrote: >> OK, seems we're getting closer - just updated all packages. Now the error is: >> Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function 'windows' for

Re: [Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

2018-02-08 Thread Rainer Johannes
that is a cool feature -- I didn't even know it existed. it will be even > cooler when it resumes working ;-) > > > > --t > > On Thu, Feb 8, 2018 at 2:34 PM, Rainer Johannes <johannes.rai...@eurac.edu> > wrote: > Dear all, > > one of the unit tests

Re: [Bioc-devel] Duplicate commits in mimager package

2018-03-06 Thread Rainer Johannes
I recently had a similar problem with my FamAgg and ensembldb packages. I had to remove the duplicated commits with `git rebase -i ` (i.e. interactive rebasing). During/after that I had to fix some merge conflicts and ended overwriting my github master with the cleaned history (`git push -f

Re: [Bioc-devel] Windows

2018-04-17 Thread Rainer Johannes
t; on Tokay2> >> >> Martin mentioned that he changed the wording in >> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e >> , so more recently than your version of R-devel. >> >> Mike >> >> On 16 April 2018 at 11:57, Ra

[Bioc-devel] Windows

2018-04-16 Thread Rainer Johannes
Dear all, we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in Rd files to functions and methods in other packages. Example: we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that works nicely on Linux and

Re: [Bioc-devel] Windows

2018-04-16 Thread Rainer Johannes
ipermail/bioc-devel/2018-April/013156.html > > I think you should be able to get round it by including the name of Rd file > you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I > haven't actually tested this though). > > Mike > > On 16 April 2018 at 0

Re: [Bioc-devel] ProteomicsAnnotationHubData duplicated commits

2018-09-03 Thread Rainer Johannes
Hi Laurent, I had the same problem with my ensembldb and FamAgg packages (guess the duplicated commits were introduced by my old git-svn setup). The solution for me was to iteratively do a git rebase (`git rebase -i ` with of the last commit before any duplicates) removing all duplicated

[Bioc-devel] BiocManager and local Bioconductor mirror

2018-11-08 Thread Rainer Johannes
Dear all, I like the new BiocManager package with its new possibilities to install specific versions of Bioconductor - but what I miss is the possibility to specify a local Bioconductor mirror from which to install packages. Our calculation clusters don't have direct internet access, so I am