i advocated pkgnet and included a png but email seems to have been rejected
On Wed, Mar 3, 2021 at 7:29 AM Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > I am happy to engage in a discussion about this, although I'm not sure that > I am ultimately interested in having two packages. > > But first I would like to look at some dependency graphs. I am wondering > what makes the dependency tree this big (and my tree is smaller than yours, > but still big: library(minfi) gives me 16 attached packages and 89 loaded > packages for the current release). This includes some part of the tidyverse > which we don't really use much though (and which could probably get removed > from the package with almost no work). > > What's the current best tool for dependency graphs in Bioconductor? > pkgDepTools? > > Best, > Kasper > > On Mon, Mar 1, 2021 at 6:24 PM Carlos Ruiz <carlos.r...@isglobal.org> > wrote: > > > Dear Bioc developers, > > > > I have been developing different packages to analyze DNA methylation. In > > all of them, I have used minfi's class GenomicRatioSet to manage DNA > > methylation data, in order to take profit of the features of > > RangedSummarizedExperiment. > > > > Although I am very happy with the potential of the class, importing its > > definition from minfi, makes me add the package to imports. As minfi has > a > > high number of dependencies (129 in the current release), my packages end > > up having hundreds of dependencies too. This is particularly problematic > as > > I do not use any of the other functions of minfi. > > > > I am wondering whether it could be possible to move minfi's class (or at > > least GenomicRatioSet) to a lighter package, so people developing > packages > > on DNA methylation could rely on this class without having to import the > > whole minfi package and its dependencies. > > > > Thank you very much, > > -- > > > > Carlos Ruiz > > > > -- > > > > > > This message is intended exclusively for its addressee and may contain > > information that is CONFIDENTIAL and protected by professional privilege. > > If > > you are not the intended recipient you are hereby notified that any > > dissemination, copy or disclosure of this communication is strictly > > prohibited > > by law. If this message has been received in error, please > > immediately notify > > us via e-mail and delete it. > > > > > > > > DATA PROTECTION. We > > inform you that your personal data, including your > > e-mail address and data > > included in your email correspondence, are included in > > the ISGlobal > > Foundation files. Your personal data will be used for the purpose > > of > > contacting you and sending information on the activities of the above > > foundations. You can exercise your rights of access, rectification, > > cancellation and opposition by contacting the following address: > > l...@isglobal.org <mailto:l...@isglobal.org>. ISGlobal > > Privacy Policy at > > www.isglobal.org <http://www.isglobal.org/>. > > > > > > > > > > > ----------------------------------------------------------------------------------------------------------------------------- > > > > CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a > > su > > destinatario y puede contener información confidencial, por lo que la > > utilización, > > divulgación y/o copia sin autorización está prohibida por la > > legislación > > vigente. Si ha recibido este mensaje por error, le rogamos lo > > comunique > > inmediatamente por esta misma vía y proceda a su destrucción. > > > > > > > > > > > > > > > > > > > > PROTECCIÓN DE DATOS. Sus datos de carácter personal utilizados en este > > envío, incluida su dirección de e-mail, forman parte de ficheros de > > titularidad > > de la Fundación ISGlobal para cualquier > > finalidades de > > contacto, relación institucional y/o envío de información sobre > > sus > > actividades. Los datos que usted nos pueda facilitar contestando este > > correo quedarán incorporados en los correspondientes ficheros, > autorizando > > el > > uso de su dirección de e-mail para las finalidades citadas. Puede > > ejercer los > > derechos de acceso, rectificación, cancelación y oposición > > dirigiéndose a l...@isglobal.org <mailto:l...@isglobal.org>* *. Política > > de > > privacidad > > en www.isglobal.org <http://www.isglobal.org/>. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > -- > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel