[Bioc-devel] Error for voom() in limma package

2019-06-18 Thread Lan Huong Nguyen
vir = envir) : object 'ties' of mode 'function' was not found Please let me know how the issue can be addressed. Best, Lan -- Lan Huong Nguyen PhD Candidate ICME Stanford University Huang Building 475 Via Ortega, Stanford, CA 94305 (650) 723-2560 <https://w

Re: [Bioc-devel] failing package TimeSeriesExperiment

2019-06-17 Thread Lan Huong Nguyen
Dear Lori, I sorry for a late response. I have finally found time to look into the package error. I fixed the current error while check is performed for TimeSeriesExperiment, however, there is another that I cannot address due to dependencies. My package uses a voom() function from limma package.

Re: [Bioc-devel] SummarizedExperiment warning upon loading

2018-12-03 Thread Lan Huong Nguyen
0] compiler_3.6.0 GenomeInfoDbData_1.2.0 Let me know if you see a potential fix. Best, Lan On Sun, Dec 2, 2018 at 9:38 AM Martin Morgan wrote: > A good place to start is to verify that your packages are all from the > same release > > BiocManager::valid() > > and the

[Bioc-devel] SummarizedExperiment warning upon loading

2018-12-01 Thread Lan Huong Nguyen
Hi everyone, I am working with R 3.6 on macOS mojave, and I installed the SummarizedExperiment from BiocManager 3.9. Whenever the package is loaded I get the following warning: Warning: multiple methods tables found for ‘lengths' Did anyone encounter this problem? Any suggestions for fixes? Bes

Re: [Bioc-devel] Activating account

2018-10-31 Thread Lan Huong Nguyen
made at git.bioconductor.org to your local repository. The push to origin > sends the version bump commit from your local repository to github. > > > > Martin > > > > *From: *Lan Huong Nguyen > *Date: *Wednesday, October 31, 2018 at 5:29 PM > *To: *"mtmorgan.b...@

Re: [Bioc-devel] Activating account

2018-10-31 Thread Lan Huong Nguyen
er and build > successfully. The package will then propagate and be available in release > as version 1.0.0. Since you are using BiocFileCache, it is likely that any > future problems with the server will not be catastrophic like this – the > file will already be available locally. > > >

[Bioc-devel] Fwd: Activating account

2018-10-31 Thread Lan Huong Nguyen
-- Forwarded message - From: Lan Huong Nguyen Date: Wed, Oct 31, 2018 at 1:16 PM Subject: Re: [Bioc-devel] Activating account To: Dear Martin, Thank you for checking that and for reviewing my package. I thought that TimeSeriesExperiment would be incorporated in 3.8 release

[Bioc-devel] Activating account

2018-10-31 Thread Lan Huong Nguyen
Hi! My package TimeSeriesExperiment has been accepted, but I can't activate my account on the following website. https://git.bioconductor.org/BiocCredentials/account_activation/ I receive the following message: "m...@email.com is not associated with a maintainer of a Bioconductor package. Pleas

Re: [Bioc-devel] Changing a name of a package already under review

2018-10-25 Thread Lan Huong Nguyen
Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Turaga, Nitesh > *Sent:* Monday, Octobe

[Bioc-devel] Changing a name of a package already under review

2018-10-22 Thread Lan Huong Nguyen
Hi, I was wondering if it is possible to change the name of the package which is already under review. This is because, after obtaining some commentary on the implementation and restructuring my package I thought that another name might be appropriate. Best, Lan [[alternative HTML versio