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

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

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

Hey guys, I love the org.Hs.eg.db package (and similar others for other organisms). I work a lot with LCMSMS proteomics data, and I have always missed a similar org.Hs.uniprot.db package, so I am thinking of creating that (and then sharing it on BioC, to benefit fellow proteomics R users).

[Bioc-devel] MultiAssayExperiment Subsetting Fails if Column Data Has One Column

Good day, Subsetting a MultiAssayExperiment object fails if the column data has one column but not 2 or more columns. Perhaps drop = FALSE is missing for the DataFrame subsetting. A minimal example is: rowColNames <- list(paste0("Gene", 1:10), paste0("Person", 1:10)) aTable <-

Re: [Bioc-devel] ExperimentList Contructor Failing

Good day, Whatever the problem is, it's gone with R Under Development and all packages installed from the development branch of Bioconductor. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___

Re: [Bioc-devel] Identical methods in two packages

On 09/12/2017 01:58 PM, Vincent Carey wrote: For this particular problem, it may be worth noting that

Re: [Bioc-devel] BiocStyle2: issue with wide figure command

Hi Ludwig, thank you! This sounds like an issue with your LaTeX distribution, in particular the package 'marginfix'. Please make sure that all the packages listed in the BiocStyle vignette under Appendix B "Attached LATEX packages" are installed, and possibly the up-to-date. Best, Andrzej On

[Bioc-devel] BiocStyle2: issue with wide figure command

Dear Andrzej, BiocStyle2 is a great piece of work and the new vignettes look really nice! Thank you! However, I am having a problem with the widefigure (figure*) environment, which apparently only holds for my local installation, as the same vignette builds fine here:

Re: [Bioc-devel] Identical methods in two packages

For this particular problem, it may be worth noting that http://geneontology.org/page/ontology-structure describes CC, MF, BP as "sub-ontologies" of GO. AnnotationDbi might replace its Ontology() with subontology() to acquire those tokens. On Tue, Sep 12, 2017 at 4:28 PM, Michael Lawrence

Re: [Bioc-devel] Identical methods in two packages

I think I'm going to vote for the policy that methods with identical signatures are currently unsupported by the methods package. It's tough to imagine how they might work in any reliable and natural way, and they totally break the methods package currently. In the grand scheme of things,

Re: [Bioc-devel] Identical methods in two packages

Hi Herve, I understand that there is a clash between the two identical methods. Both packages seem to have good reasons to implement their own `Ontology,character`. Such clashes are relatively frequent. My issue really is that when unloading AnnotationDbi's namespace, `Ontology,character` is

[Rd] R-devel object header changes that require reinstalling packages

For anyone using the development version of R: svn revision 73243 introduces some changes to the memory layout of R objects that require reinstalling packages using compiled code. Attempting to load incompatible packages should signal an error. These changes are to support a new extension

Re: [Bioc-devel] problem with git / svn transition: ssh keys

Please regenerate a new key and submit. > On Sep 12, 2017, at 1:26 PM, Luo Weijun wrote: > > Well, I modified the file acces by: > chmod 400 ~/.ssh/id_rsa > > it goes further, but the passphrase I stored seems not work (as below). I > couldn’t change passphrase either

Re: [Bioc-devel] problem with git / svn transition: ssh keys

Well, I modified the file acces by: chmod 400 ~/.ssh/id_rsa it goes further, but the passphrase I stored seems not work (as below). I couldn’t change passphrase either due to the same problem. Can I remove the old ssh key, regenerated/resubmit a new key? What’s the best way to proceed? luo$

Re: [Bioc-devel] problem with git / svn transition: ssh keys

http://bioconductor.org/developers/how-to/git/faq/ You need point#16 on the FAQ section. Change your permissions. > On Sep 12, 2017, at 12:35 PM, Luo Weijun wrote: > > The original file name was id_rsa.pub.pub. > I changed it to id_rsa.pub or id_rsa now. It stops

Re: [Bioc-devel] problem with git / svn transition: ssh keys

The original file name was id_rsa.pub.pub. I changed it to id_rsa.pub or id_rsa now. It stops complaining about the invalid format, but still have permission problem. ##id_rsa.pub luo$ git clone g...@git.bioconductor.org:packages/pathview Cloning into 'pathview'... Permission denied (publickey).

Re: [Bioc-devel] Identical methods in two packages

Hi Laurent, The 2 Ontology,character methods defined in AnnotationDbi and rols do very different things. The 1st one expects a vector of GO IDs and returns the GO sub-ontologies that they belong to: > Ontology(c("GO:009", "GO:012", "GO:006")) GO:009 GO:012 GO:006

Re: [Bioc-devel] problem with git / svn transition: ssh keys

What name did you store your key under? “id_rsa” or something else? Nitesh > On Sep 12, 2017, at 12:11 PM, Luo Weijun wrote: > > the following the are commands I used and output: > > luo$ git clone g...@git.bioconductor.org:packages/pathview > Cloning into 'pathview'...

Re: [Bioc-devel] ExperimentList Contructor Failing

Hi Dario, I wasn't able to reproduce this error on my version of Ubuntu. (see below) Please kindly post any future package inquiries at support.bioconductor.org. Best, Marcel --- > ExperimentList() ExperimentList class object of length 0: > BiocInstaller::biocValid() * sessionInfo() R

Re: [Bioc-devel] problem with git / svn transition: ssh keys

the following the are commands I used and output: luo$ git clone g...@git.bioconductor.org:packages/pathview Cloning into 'pathview'... key_load_public: invalid format Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights

Re: [Bioc-devel] failing Bioconductor package DeepBlueR

Hi Markus, The class cache issue is just a warning here and is distracting. What seems to break deepblue_liftover() is a recent change to rtracklayer::import.chain. Looks like commit a3c4308d928290700c6326eabda8dea4a96146e3 from Sep 4 might be the culprit. Cheers, H. On 09/12/2017 06:29 AM,

Re: [Bioc-devel] problem with git / svn transition: ssh keys

Your key is in our system. It starts with, ssh-rsa B3NzaC1yc2EDAQABAAACAQD4+kbkP7J0rkIGy81r9fO+4tCgHzQXfkthRu/MFPE7AMvZy7SeNf9WuxPQtMeOjAl It is associated with the correct package “pathview” and also “gageData”. Please give me more information to help you. Show me the exact commands

Re: [Bioc-devel] clarifying initialization for BiocCheck

Hi, I would just ignore that note. H. On 09/12/2017 07:19 AM, Ludwig Geistlinger wrote: Let's consider loading the `bods` object via `data` from the pathview package. I guess you can either use bods <- get(data("bods", package="pathview")) or bods <- NULL data("bods",

Re: [Bioc-devel] clarifying initialization for BiocCheck

Let's consider loading the `bods` object via `data` from the pathview package. I guess you can either use > bods <- get(data("bods", package="pathview")) or > bods <- NULL > data("bods", package="pathview") to make this note go away. > "Consider clarifying how 6 object(s) are initialized" >

Re: [Bioc-devel] updating Bioconductor package that is already on Github

Hi Simina, Please try again now. The issue was you didn’t submit your SVN ID “s.boca”. This is needed for people who have been maintainers before the Git transition, to associate your key to the package. For new packages this issue doesn’t apply, because we just collect their Github IDs.

[Bioc-devel] Fwd: Hook declined on a branch

Begin forwarded message: From: ni41435_ca > Subject: Re: [Bioc-devel] Hook declined on a branch Date: September 12, 2017 at 7:33:00 AM EDT To: Samuel Wieczorek > You

Re: [Bioc-devel] GenomicRanges::cbind() problem

yep, i've cloned, built and installed the latest S4Vectors and then qpgraph builds and checks cleanly. thanks robert. On 09/12/2017 03:06 PM, Michael Lawrence wrote: I think this was fixed in S4Vectors a couple of days ago but I forgot to bump the version (just did). Sorry. On Tue, Sep

[Rd] File listing on windows shows hidden files

Hello, I encounter a problem with file listing. On Linux, a hidden file is just a file starting with a "dot" but on Windows, it's a file with a special attribute. Currently, R checks if the file starts with a "dot", so it's not working on Windows. I have opened an issue in the bug tracker and

Re: [Bioc-devel] failing Bioconductor package DeepBlueR

Dear all, Our DeepBlueR package is currently not passing R CMD check in devel because of a class cache issue: http://bioconductor.org/checkResults/devel/bioc-LATEST/DeepBlueR/tokay1-checksrc.html Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics' Also

Re: [Bioc-devel] Package DMCHMM is not installed

Thanks. Everything is clear to me now. > On Sep 12, 2017, at 9:08 AM, Shepherd, Lori > wrote: > > Bioconductor has a release version and a devel version. Releases happen > twice a year (The next occurring at the end of October). All new packages > accepted

Re: [Bioc-devel] Package DMCHMM is not installed

From http://bioconductor.org/developers/package-submission/ Following acceptance of a package: Packages accepted on the tracker repository are added to the ‘devel’ branch of the Bioconductor SVN repository, with the current version number of the accepted package. Packages are then built by the

Re: [Bioc-devel] Package DMCHMM is not installed

Bioconductor has a release version and a devel version. Releases happen twice a year (The next occurring at the end of October). All new packages accepted will remain in the devel version of Bioconductor until the next schedule release. The package for that time, will only be available on

Re: [Bioc-devel] GenomicRanges::cbind() problem

I think this was fixed in S4Vectors a couple of days ago but I forgot to bump the version (just did). Sorry. On Tue, Sep 12, 2017 at 12:06 AM, Robert Castelo wrote: > dear GenomicRanges developers, > > my package qpgraph is breaking in devel due to the following behavior

Re: [Bioc-devel] Package DMCHMM is not installed

Thanks but that didn’t clarify why users should install the dev version. Why the package is not on the page http://bioconductor.org/packages/release/BiocViews.html#___Software Sorry this is first time I submitted a package to bioconductor and I am not so familiar with instructions. > On Sep

[Bioc-devel] GenomicRanges::cbind() problem

dear GenomicRanges developers, my package qpgraph is breaking in devel due to the following behavior of GenomicRanges: library(GenomicRanges) gr <- GRanges(seqnames=rep("1", 10), IRanges(1:10, width=1)) mcols(gr) DataFrame with 10 rows and 0 columns mcols(gr) <- cbind(mcols(gr),

Re: [Bioc-devel] Bioconductor package landing pages

Hi Hervé --- Thanks for pointing out all of the information available on the builds to me. Based on the information you point out, I think I've been able to add the required data set to the biotmleData package by bumping the versions on the RELEASE_3_5 and master branches appropriately (and made

[Bioc-devel] ExperimentList Contructor Failing

Good day, Although the package seems to build without errors, I can't run the basic examples of MultiAssayExperiment successfully. library(MultiAssayExperiment) > example("ExperimentList") ExprmL> ## Create an empty ExperimentList instance ExprmL> ExperimentList() Error in