ait until BiocStyle is updated?
Best,
Ioannis
Fra: Martin Morgan
Sendt: søndag 1. desember 2019 11:51
Til: Benjamin Jean-Marie Tremblay ; Ioannis Vardaxis
Kopi: bioc-devel@r-project.org
Emne: Re: [Bioc-devel] Error in Vignette of package
Thanks for that insight,
Hey,
I am trying to build my package Vegnette and I get the following error:
! LaTeX Error: Command \VerbBar already defined.
Or name \end... illegal, see p.192 of the manual.
I tried to find what this means with no luck.
Best,
Ioannis
[[alternative HTML version deleted
anch is the location where devel builds from.
Martin
On 7/17/19, 5:46 AM, "Bioc-devel on behalf of Ioannis Vardaxis"
mailto:bioc-devel-boun...@r-project.org> on
behalf of ioannis.varda...@ntnu.no<mailto:ioannis.varda...@ntnu.no>> wrote:
My seesionInfo:
sessionInfo
dist’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
Also, I cannot push to RELEASE_3_10 because I get error:
$git checkout RELEASE_3_10
error: pathspec 'RELEASE_3_10' did not match any file(s) known to git
Shouldn’t I use the R devel version?
Be
g package(s) 'stringdist'
trying URL
'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/stringdist_0.9.5.2.tgz'
Content type 'application/x-gzip' length 567740 bytes (554 KB)
==
downloaded 554 KB
On Fri, Jul 12, 2
sees the inherited S4 method before your S3 method, and the solution is to
> change your S3 method to S4. Best practice would do this for all S3 methods
> defined on S4 classes.
>
> Martin
>
> On 7/8/19, 10:46 AM, "Bioc-devel on behalf of Ioannis Vardaxis"
&
Hey,
My package (MACPET) has been crashing lately. The error I get is from the
vignette:
Error in .Vector_summary(object, ...) : unused argument (heatmap = TRUE)
Calls: ... withCallingHandlers -> withVisible -> eval -> eval ->
summary -> summary
Execution halted
When I call the summary funct
ences. Rbowtie maps 73% on the other hand.
Thanks for the help!
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
From: Wei Shi mailto:s...@wehi.edu.au>>
Date: Sunday, 26 November 2017 at 23:08
To: Ioannis Vardaxis
mailto:ioannis.varda...@ntnu.no>>, Martin Morgan
mailto:martin.mor...@roswellpark
I used Rbowtie and the mapping was done in 7 minutes, the results where fine
too. Rsubread had been running for 2 days so I had to stop it.
But anyway I can use Rbowtie which is nice :)
Ioannis Vardaxis
Stipendiat NTNU
Sendt fra min iPhone
26. nov. 2017 kl. 04:14 skrev Martin Morgan
my algorithm. But if I cannot use anything else than Rsubread
then I might write that the user at this point has to run bowtie with the
given command and then return to the package. However I try to avoid that
if possible.
Ioannis
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 24/11/2017, 19:11
using it, and this is a big problem if I cannot use bowtie inside a
bioconductor package.
Thanks
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 12/11/2017, 23:54, "A.E.S." wrote:
>On Sun, 12 Nov 2017 22:22:56 +
>Ryan Thompson wrote:
>
>> Hi,
>>
>> I d
allowed to make use of those algorithms in my
bioconductor package, with the appropriate references off course.
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
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https
r
platforms, how can I make it work in general?
I replaced pdf_document2 with pdf_document by the way.
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 27/10/2017, 20:08, "Bioc-devel on behalf of Ioannis Vardaxis"
wrote:
>Hey,
>
>Here is the
or: processing vignette 'MACPET.Rmd' failed with diagnostics:
savedir does not exist!
However I am not getting any such error on my mac so it is quite difficult to
find out how they are caused.
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
From: "Shepherd, Lori"
mailto:lo
Hey,
One quick question. When I push again now, do I need to change the version
from 0.99.0 to 0.99.1 or does it change automatically?
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 27/10/2017, 19:03, "Hervé Pagès" wrote:
>Adding 'SystemRequirements: C++11' wor
Hey,
Ok, I have made the changes to the DESCRIPTION file adding the c++11 you
suggested, and also fixed the Rd files. I will try to push the package
again soon and see what I get.
Thanks,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 27/10/2017, 19:03, "Hervé Pagès" wrote
immediate importance.
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 27/10/2017, 08:01, "Hervé Pagès" wrote:
>Hi Ioannis,
>
>The links to the build results generated during the submission
>process are permanent (or at least remain valid for several months),
>
the
script:
#include for example, although I did that and the errors are
there.
The package builds and runs, but I¹m sure I am gonna get errors again
when I submit it.
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 27/10/2017, 08:01, "Hervé Pagès" wrote:
>Hi I
7;MACPET.Rproj', 'NAMESPACE'
Calls: -> do.call -> -> find_vignette_product
Execution halted
However, when I move the Rmd file outside the package, for example on my
desktop, and knit it there, I don't get any error, it only happens when inside
the package folders
exists in CRAN...
* Checking for support site registration...
* Maintainer is registered at support site!
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 3
For detailed information about these checks, see the BiocCheck
vignette, available at
http://bioconductor.org/packages/3.5/bioc/vignettes/B
t seems like it is quite random if I get en error or not.
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
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Create a folder \inst and place the REFERENCES.bib in it. (see attached)
Then in the R function add: #’ @references \insertRef{ENCODE_1}{PkgA}.
You have to have the Rdpack installed.
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 07/11/16 13:49, "Ioannis Vardaxis"
wrote:
>
>
mary.Rd:78: unknown macro '\insertRef'
* Checking package NEWS...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 76 lines (0%) are > 80 characters
long.
* NOTE: Consider indenting lines wit
rtRef'
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 07/11/16 02:36, "Martin Morgan" wrote:
>On 11/06/2016 06:10 PM, Ioannis Vardaxis wrote:
>> Hi,
>>
>> For the references I just used @references \insertRef{key}{pkg}, and
>> although it shows up
is required
to be placed in /inst/doc”
But if I do that the bioCheck gives an error, if I don’t then Rcheck gives
an error. If I place vignettes in /inst/doc then Rcheck checks it without
any error.
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 06/11/16 23:59, "Martin Morgan" wrote:
&
are
using the double tab that you need.
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
On 06/11/16 22:04, "Ioannis Vardaxis"
wrote:
>
>
>
>On 05/11/16 16:21, "Martin Morgan" wrote:
>
>>On 11/05/2016 11:12 AM, Ioannis Vardaxis wrote:
>>> Hi,
little differently.
Moreover, when I run biocheck I get en error that I don't have any biocviews. I
read the manual for creating those, but it is very difficult to understand. Do
I do this after I upload the package to github or on my MAC?
Best
--
Ioannis Vardaxis
Stipendiat IMF
Hi,
Is it acceptable to use the compiler R-package to compile some functions which
use a lot of time? The running time reduces significantly if I do that.
Best,
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
[[alternative HTML version deleted
For me, running biocLite(c("rtracklayer", "S4Vectors", "XVector", "IRanges",
"Biostrings", "GenomicRanges", "GenomicAlignments"))
Worked and solved the error.
Ioannis
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
From: Kevi
I also get the same error when I use InteractionSet::GInteractions(Granges,
Granges).
I downloaded IRanges, GenomicRanges and InteractionSet packages from the source.
How can I solve this error?
Best,
Ioannis
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
[[alternative
Ioannis Vardaxis
Stipendiat NTNU
Sendt fra min iPhone
Videresendt melding:
Fra: "bioconductorseat...@gmail.com<mailto:bioconductorseat...@gmail.com>"
mailto:bioconductorseat...@gmail.com>>
Dato: 26. oktober 2016 kl. 00.55.14 CEST
Til: Ioannis Vardaxis
mailto:ioannis
em?
Best,
Ioannis
--
Ioannis Vardaxis
Stipendiat IMF
NTNU
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