Good day,
I have an S4 class with some slots in my Bioconductor package. One of the slots
stores the range of top variables to try during feature selection (the
variables might be ranked by some score, like a t-test). The empty constructor
looks like
setMethod("ResubstituteParams", "missing",
Hi Hervé,
On 10/13/21 12:43 PM, Hervé Pagès wrote:
On 12/10/2021 15:43, Pariksheet Nanda wrote:
The function in question is:
replace_unstranded <- function (gr) {
idx <- strand(gr) == "*"
if (length(idx) == 0L)
^
Not related to the "internal logical
Cheers, Luke!
Indeed, the bug could not be caught both using the address sanitizer
approach pointed out by Henrik nor valgrind in this particular case.
But adding the watchpoint to R_LogicalNAValue worked!
I now have the call stack of the offending functions sample() and
simulate(). For
Hi Alan,
On 13/10/2021 11:22, alan murphy wrote:
Hi all,
I'm the developer of the MungeSumstats package which is currently timing out on
the nightly builds for windows (riesling1) but doesn't have any errors:
Thank you for letting us know. We will begin the deprecation process.
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel
Hello BioC core team,
The predictionet Bioconductor package is out of date and we no longer wish to
maintain it. Would it be possible to begin the deprecation process?
Thanks for your assistance.
Best,
---
Christopher Eeles
Software Developer
BHK
Hello,
The release 3.13 branch of Bioconductor is now frozen. You will not be able to
push to this RELEASE_3_13 branch of your package again.
Please review the release schedule
http://bioconductor.org/developers/release-schedule/ for more information.
Best regards,
Nitesh Turaga
Scientist
Hi all,
I'm the developer of the MungeSumstats package which is currently timing out on
the nightly builds for windows (riesling1) but doesn't have any errors:
https://bioconductor.org/checkResults/3.14/bioc-LATEST/MungeSumstats/riesling1-checksrc.html.
My question is whether there is a reason
Hi
The release 3.13 branch will be frozen after the next 2 hours. After today, you
will not be able push to this branch.
Please refer to http://bioconductor.org/developers/release-schedule/.
Best regards,
Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Update: I defined the JAGS_HOME environment variable on riesling1 as
suggested off-list by Martin (thanks Martin), so now rjags can be loaded
again. This should solve the problem for CNVrd2, HiLDA, infercnv, and
MADSEQ.
I did the same on tokay2 (Windows server for the 3.13 builds) where the
Hi Pariksheet,
On 12/10/2021 15:43, Pariksheet Nanda wrote:
The function in question is:
replace_unstranded <- function (gr) {
idx <- strand(gr) == "*"
if (length(idx) == 0L)
^
Not related to the "internal logical NA value has been modified" error
but
Since the package is building cleanly in devel, we will undeprecate the
package. Thank you for your contiued contributions to Bioconductor.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton
___
Bioc-devel@r-project.org mailing list
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The Bioconductor Team is continuing to identify packages that will be
deprecated in the next release to allow for the Bioconductor community to
respond accordingly. The list will be updated monthly. This is the current list
of deprecated packages for Bioc 3.14 :
Maintainer requested
The most likely culprit is C code that is modifying a logical vector
without checking whether this is legitimate for R semantics
(i.e. making sure MAYBE_REFERENCED or at least MAYBE_SHARED is FALSE).
If that is the case, then this is legitimate for C code to do in
principle, so UBSAN and valgrind
The problem with using gdb is you'd find yourself in the garbage collector, but
perhaps quite removed from where the corruption occurred, e.g., gc() might /
will likely be triggered after you've returned to the top-level evaluation
loop, and the part of your code that did the corruption might
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