Hello Hervé Thanks for a quick reply. I have some more questions:
1. This the report of the build of package from Bioconductor: http://bioconductor.org/spb_reports/DASC_buildreport_20170306051600.html. Here, you will see *dependencies error* in the tokay2 BUILD SRC output. Should I include these packages under Depends or Imports is fine ? Just to make sure, my package uses NMF function from NMF package and another function from cvxclustr package. 2. I have made some changes in my code (https://github.com/aayushraman/DASC) and have changed the version to 0.1.1. I would like to know if I have to do anything else to inform the Single Package Builder to rebuild and check my package again. Thanks, -Ar On Thu, Mar 16, 2017 at 11:57 AM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Ar, > > On 03/15/2017 12:57 AM, Aayush Raman wrote: > >> Hello Everyone, >> >> I have developed a Bioconductor package and submit the issue to build and >> check. I have some questions regarding on the build and BioCheck of the >> package. Here are the questions: >> >> 1. It has passed the build and check on Mac OS and Windows. However, when >> I >> am checking it on linux, I am getting the following error: >> >> "ERROR: dependencies ‘NMF’, ‘cvxclustr’ are not available for package >> ‘DASC’" >> >> Although, I know the NMF and cvxclustr are not present in the linux >> machine, I would like to know if it possible to build the package by >> installing other packages that my package depends on ? I am already >> mentioned it on DESCRIPTION file. Do I need to do anything else before >> submitting my package ? >> > > You have these packages listed in your Imports field so they will be > automatically installed by the Single Package Builder on the 3 build > machines if they are not already present. > > >> 2. After successfully building (using R CMD build) and checking (R CMD >> check), I did a BiocCheck on my package. I got 2 warnings: >> >> a. WARNING: Use FALSE instead of F (found in 1 files) >> >> I am using a function called norm (from base package) where I need to >> specify the type. The type I would like to use is Frobenius norm which is >> specified by "F/f". How can I remove this warning ? or infom bioconductor >> about this warning prior to their checks ? >> > > I don't see this when I run Rbiocdev CMD BiocCheck DASC_0.1.1.tar.gz. > Have you addressed this already? Please note that the way to specify > the type in base::norm() is with a 1-letter *string* ("O", "I", "F", > "M", or "2"). This has nothing to do with the use of F (unquoted) for > specifying the single logical value FALSE. > > >> b. WARNING: Add non-empty \value sections to the following man pages: >> data.Rd: >> >> data.Rd is a dataset that I will be uploading with our package. I would >> like to know how can I remove this error ? >> > > Man pages for data sets need a \format section instead of a \value > section. If you have one, and R CMD BiocCheck still complains about > the lack of a \value section, please ignore the warning. > > Hope this helps, > > H. > > >> Any help or advice would be much appreciated. >> >> Thanks, >> -Ar >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt >> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Yi >> ZGNUYd-khI-yvgitdzYaCkX0YYV4RafW040QHUJRo&s=-ddB-ch5A6i-pe7Q >> zHb6mH7ARR6Rap0LnufSyE_Qjvg&e= >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel