[Rd] sparse.model.matrix Generates Non-Existent Factor Levels if Ord.factor Columns Present

Good day, Sometimes, sparse.model.matrix outputs a dgCMatrix which has column names consisting of factor levels that were not in the original dataset. The first factor appears to be correctly transformed, but the following factors don't. For example: diamonds <- as.data.frame(ggplot2::diamonds

[Rd] Trailing underscores on C function names

In the fastmatch package, version 1.1-0, there is a C function called "ctapply_", with a trailing underscore. However, the NAMESPACE's call to useDynLib refers to "ctapply", without the trailing underscore. % grep ctapply NAMESPACE {R,src}/* NAMESPACE:useDynLib(fastmatch, C_fmatch = fmatch, C_cta

Re: [Rd] release build of ChemmineR failing

This is not the right place to report Bioconductor issues. Even if it were you have not provided adequate reproduction steps. source("https://bioconductor.org/biocLite.R";) biocLite("ChemmineR") library(ChemmineR) works fine for me. When you find the correct venue for reporting this issue I hope

Re: [Rd] rsvg on mac

Hi Kevin, I can't imagine what gave you the idea that r-devel is an appropriate place to make requests regarding bioconductor build infrastructure. It is not. Best, Ista On Wed, Feb 7, 2018 at 10:59 AM, Kevin Horan wrote: > > The ChemmineR build is failing on the mac due to a new dependency not

[Rd] release build of ChemmineR failing

The release version of ChemmineR is failing on windows. It seems to be a build script issue though, possibly something on your side. The package was building fine a few weeks ago and I have not modified it. Can you please have a look? Thanks. "C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e "l

[Rd] rsvg on mac

The ChemmineR build is failing on the mac due to a new dependency not being available, the package "rsvg". Would it be possible to install that on the mac build machine? Thanks. http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-install.html Kevin

[Rd] saveRDS() overwrites file when object is not found

I ran into this behaviour when accidentally running a line of code that I shouldn't have. When saving over an rds with an object that's not found, I would have expected saveRDS to not touch the file. saveRDS(iris, "test.rds") file.size("test.rds") #> [1] 1080 saveRDS(no_object_here, "test.rds") #

[Rd] Possible typo in the C source code of R

Good morning, I am Martin Bodin, a postdoc at the CMM in Santiago de Chile, and I am currently in the process of formalising (a part of) the R language into the Coq proof assistant. This work makes me look frequently at the source code of R. I have noticed a strange line in the file src/main/util

Re: [Rd] Possible bug in package installation when R_ICU_LOCALE is set

I can reproduce this on Linux, so it is not Windows-specific. > sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Arch Linux Matrix products: default BLAS/LAPACK: /usr/lib/libopenblas_haswellp-r0.2.20.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NU

[Rd] Possible bug in package installation when R_ICU_LOCALE is set

On a Windows computer (other platforms not tested), installing a package from source may fail if the environment variable R_ICU_LOCALE is set, depending on the package and the locale. For example, after setting R_ICU_LOCALE to "fi_FI", install.packages("seriation", type = "source") (package ve

[Rd] Warning from Sys.junction when using network drive.

I am running 3.4.3 on a windows server and I ran the code in a new session. I get a warning when running packrat::init() on a project that is located on a windows network drive. The warning I get is Warning message: cannot set reparse point 'U:/packrat5/packrat/lib-R/base', reason 'Access is