Re: [Bioc-devel] Website Not Updating

[Chengyang . Ji12]

Hi,



I added �Phylogenetics� and �SNP� to BiocViews of my package sitePath in both 
release and develop version. Wonder if that�s causing the problem. Because 
�Phylogenetics� is a legit BiocViews so far as I know but was never used 
before. And changing BiocViews is not �bug fix� update which might break the 
webpage rendering?



Just want to help you pinpoint the cause and if it is really me, what do I do 
to help fix it.



Best,

Chengyang



Sent from Mail for Windows 10



From: Shepherd, Lori
Sent: 18 June 2020 22:02
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Website Not Updating



Hello All,

It was brought to our attention that our website was not updating over the last 
few days.  You may see outdated or missing package landing pages.  We are 
working on a fix that should be implemented by the end of the day today.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] updating package on the development version

[Dwivedi, Bhakti]

Hi,

I am trying to update previous release of my package (GISPA) on the development 
version.

I pushed the changes and new release GISPA 1.13.1 following 
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

But, I do not see the change on the bioconductor development version 
http://bioconductor.org/packages/devel/bioc/html/GISPA.html. Where can I view 
the changes and make sure it passed all the checks?

Regards,
Bhakti





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Re: [Rd] valgrind false positive on R startup?

[Toby Hocking]

Great, that works for me, thanks!
If this is an issue with glibc, has it been reported to the glibc devs, and
are they working on a fix?

On Tue, Jun 9, 2020 at 9:12 PM Prof Brian Ripley 
wrote:

> It is known, with a known workaround, see e.g.
> https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt .  Set
> suppressions in ~/.valgrindrc, e.g. the CRAN check machine has
>
> --suppressions=/data/blackswan/ripley/wcsrtombs.supp
>
> It is an issue in your OS (glibc), not TRE nor R.
>
> On 10/06/2020 00:21, Toby Hocking wrote:
> > Hi all,
> >
> > I'm on Ubuntu 18.04, running R-4.0.0 which I compiled from source, and
> > using valgrind I am always seeing the following message. Does anybody
> > else see that? Is that a known false positive? Any ideas how to
> > fix/suppress? Seems related to TRE, do I need to upgrade that?
> >
> > (base) tdhock@maude-MacBookPro:~/R/binsegRcpp$ R --vanilla -d valgrind
> > -e 'extSoftVersion()'
> > ==9565== Memcheck, a memory error detector
> > ==9565== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
> > ==9565== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright
> info
> > ==9565== Command: /home/tdhock/lib/R/bin/exec/R --vanilla -e
> extSoftVersion()
> > ==9565==
> > ==9565== Conditional jump or move depends on uninitialised value(s)
> > ==9565==at 0x55AB9E0: __wcsnlen_sse4_1 (strlen.S:147)
> > ==9565==by 0x5598EC1: wcsrtombs (wcsrtombs.c:104)
> > ==9565==by 0x551EB20: wcstombs (wcstombs.c:34)
> > ==9565==by 0x50BAA07: wcstombs (stdlib.h:154)
> > ==9565==by 0x50BAA07: tre_parse_bracket_items (tre-parse.c:336)
> > ==9565==by 0x50BAA07: tre_parse_bracket (tre-parse.c:453)
> > ==9565==by 0x50BAA07: tre_parse (tre-parse.c:1380)
> > ==9565==by 0x50B2498: tre_compile (tre-compile.c:1920)
> > ==9565==by 0x50AFBE0: tre_regcompb (regcomp.c:150)
> > ==9565==by 0x4FA9F42: do_gsub (grep.c:2023)
> > ==9565==by 0x4F79045: bcEval (eval.c:7090)
> > ==9565==by 0x4F8572F: Rf_eval (eval.c:723)
> > ==9565==by 0x4F8754E: R_execClosure (eval.c:1888)
> > ==9565==by 0x4F88316: Rf_applyClosure (eval.c:1814)
> > ==9565==by 0x4F85902: Rf_eval (eval.c:846)
> > ==9565==
> >
> > R version 4.0.0 (2020-04-24) -- "Arbor Day"
> > Copyright (C) 2020 The R Foundation for Statistical Computing
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under certain conditions.
> > Type 'license()' or 'licence()' for distribution details.
> >
> >Natural language support but running in an English locale
> >
> > R is a collaborative project with many contributors.
> > Type 'contributors()' for more information and
> > 'citation()' on how to cite R or R packages in publications.
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> >> extSoftVersion()
> >  zlib
> bzlib
> >  "1.2.11" "1.0.6,
> 6-Sept-2010"
> >xz
>  PCRE
> >   "5.2.2"   "10.31
> 2018-02-12"
> >   ICU
> TRE
> >"60.2""TRE 0.8.0 R_fixes
> (BSD)"
> > iconv
>  readline
> >  "glibc 2.27"
> "7.0"
> >  BLAS
> > "/home/tdhock/lib/R/lib/libRblas.so"
> >>
> >>
> > ==9565==
> > ==9565== HEAP SUMMARY:
> > ==9565== in use at exit: 40,492,919 bytes in 9,170 blocks
> > ==9565==   total heap usage: 19,784 allocs, 10,614 frees, 62,951,535
> > bytes allocated
> > ==9565==
> > ==9565== LEAK SUMMARY:
> > ==9565==definitely lost: 0 bytes in 0 blocks
> > ==9565==indirectly lost: 0 bytes in 0 blocks
> > ==9565==  possibly lost: 0 bytes in 0 blocks
> > ==9565==still reachable: 40,492,919 bytes in 9,170 blocks
> > ==9565==   of which reachable via heuristic:
> > ==9565== newarray   : 4,264 bytes in 1
> blocks
> > ==9565== suppressed: 0 bytes in 0 blocks
> > ==9565== Rerun with --leak-check=full to see details of leaked memory
> > ==9565==
> > ==9565== For counts of detected and suppressed errors, rerun with: -v
> > ==9565== Use --track-origins=yes to see where uninitialised values come
> from
> > ==9565== ERROR SUMMARY: 46 errors from 1 contexts (suppressed: 0 from 0)
> > (base) tdhock@maude-MacBookPro:~/R/binsegRcpp$
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
>
> --
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>

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[Rd] stats::screeplot suggestion

[Michael Friendly]

 Hi

Here is a suggestion/request for stats::screeplot

* Please allow to change xlab and ylab.  The attached file does that, and maintains current 
behavior. Reason: strictly speaking, ylab should be "Variance" (singular). It would also 
be better to have an explicit label for the X axis: "Component"

In the would-be-nice-if category, I suggest addition of a type="cumulative" chart, a line 
graph of cumulative % of variance, labeled "% Variance" by default.

-Michael

- screeplot.default.R -

screeplot.default <- function (x, npcs = min(10, length(x$sdev)),
   type = c("barplot", "lines"),
   xlab = "",
   ylab = "Variances",
   main = deparse(substitute(x)), ...)
{
    main
    type <- match.arg(type)
    pcs <- x$sdev^2
    xp <- seq_len(npcs)
    dev.hold()
    on.exit(dev.flush())
    if (type == "barplot")
    barplot(pcs[xp], names.arg = names(pcs[xp]), main = main,
    ylab = ylab, ...)
    else {
    plot(xp, pcs[xp], type = "b", axes = FALSE, main = main,
    xlab = xlab, ylab = ylab, ...)
    axis(2)
    axis(1, at = xp, labels = names(pcs[xp]))
    }
    invisible()
}



--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, ASA Statistical Graphics Section
York University  Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:   http://www.datavis.ca  |  @datavisFriendly
Toronto, ONT  M3J 1P3 CANADA

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[Bioc-devel] Website Not Updating

[Shepherd, Lori]

Hello All,

It was brought to our attention that our website was not updating over the last 
few days.  You may see outdated or missing package landing pages.  We are 
working on a fix that should be implemented by the end of the day today.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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[Bioc-devel] Bioconductor package devel site not updating

[Hoffman, Gabriel]

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Re: [Bioc-devel] Bioconductor credentials issue

[Nitesh Turaga]

Hi Chris,

This is a very strange problem which I haven’t come across before. But let me 
say this though, the fact that this email "benjamin.haibe.ka...@utoronto.ca 
” is connected to your username, 
Github ID and has your SSH keys is not correct. 

I fixed this last time by making you an account and giving you access through 
an account registered to christopher.ee...@outlook.com. I’m not sure what 
happened there? Any insight? 

Nitesh


> On Jun 17, 2020, at 10:51 AM, Chris Eeles  
> wrote:
> 
> Hello Bioconductor team,
> 
> I am having issues accessing our labs Bioconductor repositories and also 
> cannot login to the Bioconductor credentials website.
> 
> I had a similar issue less than a month ago, which Nitesh from the core team 
> helped me resolve. At that time I was able to login to Bioconductor 
> credentials for both 
> benjamin.haibe.ka...@utoronto.ca (my 
> PI's maintainer email) as well as 
> christopher.ee...@outlook.com (my 
> GitHub account) and could push to upstream for all my packages. I can no 
> longer do any of those things and do not get an email when I attempt to reset 
> the password on the credentials account for 
> christopher.ee...@outlook.com.
> 
> Recently, two of my package submissions (RadioGx, ToxicoGx) were accepted. 
> This is the only change I can think of which may be the source of the issue.
> 
> If someone could advise on how to resolve this issue, it would be appreciated.
> 
> I have updates I am waiting to push to RadioGx.
> 
> Thanks for your assistance.
> 
> Best,
> ---
> Christopher Eeles
> Software Developer
> BHK Laboratory
> Princess Margaret Cancer Centre
> University Health Network
> 
> 
> 
> 
> 
> 
> 
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> 
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Re: [R-pkg-devel] R_MAKEVARS_USER fail to pass down to sub-makes?

[Jan Gorecki]

Thank you Jim,
That was the problem indeed. Too bad it is not mentioned in the manual.

On Wed, Jun 17, 2020 at 8:33 PM Jim Hester  wrote:
>
> I think the issue is likely that you seem to be using a relative path to the 
> R_MAKEVARS_USER file, it needs to be an absolute path as the installation is 
> run in a temporary directory not from the directory you call `R CMD INSTALL` 
> from.
> I observed similar behavior to what you describe when I had the MAKEVARS_USER 
> file as a relative path, but using an absolute path produced the expected 
> result.
>
> On Mon, Jun 1, 2020 at 8:04 AM Jan Gorecki  wrote:
>>
>> Hi package devel support,
>>
>> I am trying to use R_MAKEVARS_USER to customize build, rather than
>> .R/Makevars. It is properly displayed from config CFLAGS but during
>> package install it doesn't seem to work.
>>
>> In R-admin in "6.3.3 Customizing package compilation" there is:
>>
>> > Note that these mechanisms do not work with packages which fail to pass 
>> > settings down to sub-makes, perhaps reading etc/Makeconf in makefiles in 
>> > subdirectories.
>>
>> It seems that it applies to me. How should I debug that? to make this
>> env var respected? Note that my pkg has src/Makevars to handle openmp
>> switch nicely
>> Thank you
>>
>> system("R_MAKEVARS_USER=library/gcc/O3/Makevars R CMD config CFLAGS")
>> -O3
>>
>> system("R_MAKEVARS_USER=library/gcc/O3/Makevars R CMD INSTALL
>> --library=library/gcc/O3 mypkg_1.0.0.tar.gz")
>> * installing *source* package 'mypkg' ...
>> ** using staged installation
>> ** libs
>> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG-fopenmp -fpic  -g
>> -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=.
>> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
>> -D_FORTIFY_SOURCE=2 -g  -c assign.c -o assign.o
>>
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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[Rd] fixed url for R-release windows binaries

[Jan Gorecki]

Dear R-developers,

Could we have a fixed url to fetch current R-release windows binaries?
Like we do for R-devel
https://cloud.r-project.org/bin/windows/base/R-devel-win.exe

Something like the following would do
https://cloud.r-project.org/bin/windows/base/R-release-win.exe

Thank you,
Jan Gorecki

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[Bioc-devel] How to set dimnames inside constructor function?

[Muad Abd El Hay]

Hello everyone,

This is my first attempt at writing a package (wrote it in S3 and now 
porting it to S4). So it might be a trivial question.

I am trying to extend the SummarizedExperiment object for calcium 
imaging data (no gene names as features). Features/rownames are the 
number of the frames and colnames are the cells/ROIs.

Inside the constructor function, I wanted to set the rownames and 
colnames as below:

```R
   se <- SummarizedExperiment(list(raw=raw),
  rowData = DataFrame(time = time),
  ...)
   dimnames(se) <- list(paste("f", 1:nrow(se), sep=""),
paste("name", 1:ncol(se), sep="_"))
   .CalciumExperiment(se)
```

But I keep getting the following error:

```R
Error in `assays<-`(`*tmp*`, withDimnames = withDimnames, ..., value = 
`*vtmp*`) :
   please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
   withDimnames=FALSE)) <- value' when the dimnames on the supplied
   assay(s) are not identical to the dimnames on CalciumExperiment 
object
   'x'
```

I also tried using `rownames(se)`and `colnames(se)`with the same error. 
Setting the `dimnames`, `colnames`, or `rownames` on the `raw` matrix 
beforehand also did not work.

Am I missing something fundamental here?

Thank you in advance!
Best wishes,
Muad Abd El Hay
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[Bioc-devel] Maintainer transfer

[Jakob Wirbel]

Hi all,

Recently, the maintainership for the SIAMCAT package on Bioconductor was 
transferred from Konrad Zych (konrad.z...@embl.de) to me and the 
DESCRIPTION file in the Bioconductor repository was updated already. 
Therefore, I tried to activate my account in the BiocCredentials app, 
but it seems that my email address is not associated with a maintainer 
of a Bioconductor package yet. What do I need to do in order to activate 
my account?

Thank you for your help!

Jakob


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