Re: [Bioc-devel] about deprecate package DNABarcode

2024-03-27 Thread Sun Wenjie
Hi Pedro, Tilo has responded and is currently updating the DNABarcode package. Best, Wenjie From: Pedro Sánchez Sánchez Sent: Wednesday, March 20, 2024 1:58 PM To: Kern, Lori Cc: Sun Wenjie; bioc-devel@r-project.org Subject: Re: [Bioc-devel] about

Re: [Bioc-devel] FATAL: W any packages/*** *** DENIED by fallthru

2023-12-07 Thread Jianqiang Sun
Hi, Thank you for updating my data, now I can push files to the Bioconductor git. Please delete my old account wuk...@bi.a.u-tokyo.ac.jp, thanks. Many thanks, JS -- Jianqiang Sun / https://aabbdd.jp Research Center for Agricultural Information Technology (RCAIT), National Agriculture and Food

Re: [Bioc-devel] FATAL: W any packages/*** *** DENIED by fallthru

2023-12-05 Thread Jianqiang Sun
change them by myself (I tried changing them in BiocCredentials, but I got an error). Many thanks, JS -- Jianqiang Sun / https://aabbdd.jp Research Center for Agricultural Information Technology (RCAIT), National Agriculture and Food Research Organization (NARO) 2023年12月5日(火) 21:30 Kern, Lori

[Bioc-devel] FATAL: W any packages/*** *** DENIED by fallthru

2023-12-04 Thread Jianqiang Sun
``` Thanks, JS -- Jianqiang Sun / https://aabbdd.jp Research Center for Agricultural Information Technology (RCAIT), National Agriculture and Food Research Organization (NARO) [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org

[Bioc-devel] Updating to Python 3: Problem with Importlib library

2020-10-01 Thread Yuxi Sun
Hi, I am writing on behalf of the development team for the package seq2pathway. After updating to python 3 and replacing the deprecated imp library with importlib library, we encountered the following problem. Our python code is included in the file

[Bioc-devel] seq2pathway install and build error

2020-09-16 Thread Yuxi Sun
Hello, We are writing on behalf of the development team for the Bioconductor package seq2pathway. There are two problems we are encountering that we wish to seek some insights from the team. 1) Our Windows installation throws this error message: Warning: *** someone has corrupted the Built

[R-pkg-devel] Difference between local R CMD check and winbuilder

2020-05-21 Thread Hongying Sun
Hello, My package passed the R CMD check locally on my desktop with Windows system, but not the winbuilder. These are both done on R-4.0.0. Does this happen to anyone else? Here is the error: * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically

Re: [Rd] Infrequent but steady NULL-pointer caused segfault in as.POSIXlt.POSIXct (R 3.4.4)

2019-08-04 Thread Sun Yijiang
ormation/updates. If this ends up being a bug in R, please report > (and with a reproducible example, if it is not obvious from the source > code). > > Best > Tomas > > > On 8/2/19 10:23 AM, Sun Yijiang wrote: > > The R script I run daily for hours looks like

[Rd] Infrequent but steady NULL-pointer caused segfault in as.POSIXlt.POSIXct (R 3.4.4)

2019-08-02 Thread Sun Yijiang
The R script I run daily for hours looks like this: while (!finish) { Sys.sleep(0.1) time = as.integer(format(Sys.time(), "%H%M")) # always crash here if (new.data.timestamp() <= time) next # ... do some jobs for about 2 minutes ... gc() } Basically it waits for new

Re: [Rd] Race condition on parallel package's mcexit and rmChild

2019-05-20 Thread Sun Yijiang
ported > to R-patched. In fact rmChild() is used in mccollect(wait=FALSE). > > Best > Tomas > > On 5/19/19 11:39 AM, Sun Yijiang wrote: > > I've been hacking with parallel package for some time and built a > > parallel processing framework with it. However, although ver

[Rd] Race condition on parallel package's mcexit and rmChild

2019-05-20 Thread Sun Yijiang
I've been hacking with parallel package for some time and built a parallel processing framework with it. However, although very rarely, I did notice "ignoring SIGPIPE signal" error every now and then. After a deep dig into the source code, I think I found something worth noticing. In short,

[Rd] Race condition on parallel package's mcexit and rmChild

2019-05-20 Thread Sun Yijiang
I've been hacking with parallel package for some time and built a parallel processing framework with it. However, although very rarely, I did notice "ignoring SIGPIPE signal" error every now and then. After a deep dig into the source code, I think I found something worth noticing. In short,

Re: [Rd] Rscript fails with some packages (for example, h5)

2017-12-27 Thread Sun Yijiang
to know why. Steve Dirk Eddelbuettel <e...@debian.org>于2017年12月27日 周三21:15写道: > > Duncan, > > Very nice tutorial. However it does NOT take away from the fact that _very_ > simple_ scripts (like the one posted by Sun at the beginning of this > thread) > simply _f

Re: [Rd] Rscript fails with some packages (for example, h5)

2017-12-26 Thread Sun Yijiang
confusion. Steve 2017-12-26 20:46 GMT+08:00 Dirk Eddelbuettel <e...@debian.org>: > > On 26 December 2017 at 15:24, Sun Yijiang wrote: > | After looking into C source code, I found that Rscript by default fills > | environment variable R_DEFAULT_PACKAGES with > | "dataset

[Rd] Rscript fails with some packages (for example, h5)

2017-12-26 Thread Sun Yijiang
Consider this script (with h5 installed): $ cat test.R library(h5) name <- tempfile() f <- h5file(name) file.remove(name) $ Rscript test.R Error in initialize(value, ...) : cannot use object of class "character" in new(): class "H5File" does not extend that class Calls: h5file -> new ->

[Bioc-devel] specify the color in plotMutationSpectrum() of SomaticSignatures library

2016-02-17 Thread sun
Hi All, How can I specify the color that I would like to use in plotMutationSpectrum()? eg. plotMutationSpectrum(sca_motifs, "study", normalize = TRUE), I would like to only use "red" color here, how should I do? Thanks, Rebecca [[alternative HTML version deleted]]

Re: [Bioc-devel] fail to build a package after updating Bioconductor packages

2016-01-28 Thread Yu Sun
NSF GRFP > Kharchenko Lab > Harvard University > 10 Shattuck St #3, Countway 336B > Boston, MA 02115 > > On Jan 27, 2016, at 9:26 AM, Ge Tan <ge_...@live.com> wrote: > > The error message explains the reason. Just install pandoc and > pandoc-citeproc. > > Ge

[Bioc-devel] fail to build a package after updating Bioconductor packages

2016-01-27 Thread Yu Sun
lted > Is there someone can explain what is the problem here? Thanks! Best Yu -- Yu Sun Department of Cell and Molecular Biology BMC, Uppsala University Sweden [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Rd] [Rcpp-devel] Calling C++ from R

2011-01-22 Thread Xiaochun Sun
Many thanks for your reply. Rf_rnorm works very good with me. Xiaochun On Fri, Jan 21, 2011 at 7:38 AM, Dirk Eddelbuettel e...@debian.org wrote: On 21 January 2011 at 06:44, Douglas Bates wrote: | It is more effective to send such inquiries to the Rcpp-devel mailing | list which I am