[Rd] PKG_LIBS in make child processes

2016-10-10 Thread Ulrich Bodenhofer
[cross-posted from bioc-devel list] Hi all, I have a subtle question related to how R CMD SHLIB handles variables in make child processes. In more detail: I am the maintainer of the 'msa' package which has been in Bioconductor since April 2015. This package integrates three open-source librar

Re: [Rd] optim(…?=, =?utf-8?Q?method=‘L-BFGS-B’) stops with an error message while violating the lower bound

2016-10-10 Thread Avraham Adler
I believe the code can be found here: http://users.iems.northwestern.edu/~nocedal/lbfgsb.html. Specifically, lbfgsb.f in version 3.0 starts: This is a modified version of L-BFGS-B. Minor changes in the updated c code appear preceded by a line comment as follows c c c-jlm-jn c c Major c

[Rd] Bug/Inconsistency in merge() with all.x when first nonmatching column in y is matrix

2016-10-10 Thread Russ Hamilton via R-devel
I've noticed inconsistent behavior with merge() when using all.x=TRUE. After some digging I found the following test cases: 1) The snippet below doesn't work as expected, as the non-matching columns of rows in a but not b take the value from the first matching row instead of being NA: --- Snip >>>

Re: [Rd] optim(…?=, =?utf-8?Q?method=‘L-BFGS-B’) stops with an error message while violating the lower bound

2016-10-10 Thread Martin Maechler
> Spencer Graves > on Sat, 8 Oct 2016 18:03:43 -0500 writes: [.] > 2. It would be interesting to know if the > current algorithm behind optim and optimx with > method='L-BFGS-B' incorporates Morales and Nocedal (2011) > 'Remark on “Algorithm