Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "
Lori,
Thank you for the clarification. I will try it.
Yasir
From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, April 26, 2018 6:14 AM
To: Rahmatallah, Yasir; joris.m...@ugent.be
Cc: bioc-devel
Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in
package yy does not exist "
The packages will not be rejected for this WARNING, but please see the
suggestion in the previous response that also might help clear them up.
https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences<https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_R-2Dexts.html-23Cross-5F002dreferences=DwQFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU=6dH_sMZpCoB-KuxO9R71HqnXe_adTLdH4CpO5hxfSj4=>
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel
<bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on
behalf of Joris Meys <joris.m...@ugent.be<mailto:joris.m...@ugent.be>>
Sent: Thursday, April 26, 2018 4:30:08 AM
To: Rahmatallah, Yasir
Cc: bioc-devel
Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in
package yy does not exist "
On Wed, Apr 25, 2018 at 11:52 PM, Rahmatallah, Yasir
<yrahmatal...@uams.edu<mailto:yrahmatal...@uams.edu>>
wrote:
> Dear all,
>
> Build report show that many packages still have check warnings due to
> missing file links (cross referencing pages from other packages) under
> windows. The issue happens because there are different man pages for
> different operating systems. My package (GSAR) shows the same warning under
> Windows in the build report, although it locally passes R CMD build and R
> CMD check without warnings. Although not a perfect solution, substituting
> the linking in the .Rd file \code{\link[pkg:bar]{foo}} with
> \code{\link{foo}} or \code{\link[pkg]{foo}} was suggested in a recent
> discussion
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013315.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2018-2DApril_013315.html=DwMFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU=Mv-R1qX6544OBh7KthjZO_bsy4Vi1k7I8cQ4lcxDVN4=>
Actually, that is the correct solution. As per "Writing R Extensions",
\link[pkg]{name} searches for a html file with the name name.html in
package pkg. In a number of cases the name of the html help file is not the
same as the function you want to point to. For example, ppois and qpois etc
are discussed in a page called Poisson. Also in "Writing R Extensions" they
mention that if you want to use another name as a link, you should do
\link[pkg:name]{foo}. In our example: \link[stats:Poisson]{ppois}
https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences<https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_R-2Dexts.html-23Cross-5F002dreferences=DwMFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU=6dH_sMZpCoB-KuxO9R71HqnXe_adTLdH4CpO5hxfSj4=>
>
> I understood that although a check warning is produced (under Windows
> only), it will be accepted (considered as advice) and packages that
> currently show it will proceed to Bioc release. Is that correct? There are
> still many packages showing this warning in yesterday's report
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/#show=warnings<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.7_bioc-2DLATEST_-23show-3Dwarnings=DwMFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU=loZl-moADbYBJHjxIwCU5MzqJc2uYVLPa0i7psS3eg0=>
>
As this is the case for even recommended packages like the survival
package, I don't see how this would be a reason to reject a package. But it
still makes sense to adapt your links in the way it is specified in the
official R manual.
Cheers
Joris
--
Joris Meys
Statistical consultant
Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3DCoupure-2Blinks-2B653-2C-25C2-25A0B-2D9000-2BGent-2C-25C2-25A0Belgium-26entry-3Dgmail-26source-3Dg=DwMFAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=RbKe4MFAcV0_xq_8rPWd
Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "
Dear all,
Build report show that many packages still have check warnings due to missing
file links (cross referencing pages from other packages) under windows. The
issue happens because there are different man pages for different operating
systems. My package (GSAR) shows the same warning under Windows in the build
report, although it locally passes R CMD build and R CMD check without
warnings. Although not a perfect solution, substituting the linking in the .Rd
file \code{\link[pkg:bar]{foo}} with \code{\link{foo}} or
\code{\link[pkg]{foo}} was suggested in a recent discussion
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013315.html
I understood that although a check warning is produced (under Windows only), it
will be accepted (considered as advice) and packages that currently show it
will proceed to Bioc release. Is that correct? There are still many packages
showing this warning in yesterday's report
http://bioconductor.org/checkResults/3.7/bioc-LATEST/#show=warnings
Thank you,
Yasir
Yasir Rahmatallah, PhD
Assistant Professor
Department of Biomedical Informatics
University of Arkansas for Medical Sciences (UAMS)
4301 W. Markham St., slot 782, office 476, Little Rock, AR 72205
-Original Message-
From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Vincent
Carey
Sent: Wednesday, April 18, 2018 2:14 PM
To: Martin Morgan
Cc: bioc-devel; ramon.d...@iib.uam.es
Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in
package yy does not exist "
yes, the [] is a habit i need to break. ok, we'll get by.
On Wed, Apr 18, 2018 at 3:09 PM, Martin Morgan < martin.mor...@roswellpark.org>
wrote:
>
>
> On 04/18/2018 02:45 PM, Vincent Carey wrote:
>
>>
>>
>> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan <
>> martin.mor...@roswellpark.org >
>> wrote:
>>
>>
>>
>> On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
>>
>>
>> Dear Martin,
>>
>> On Fri, 06-April-2018, at 18:59:00, Martin Morgan
>> > > wrote:
>>
>> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
>>
>> I have recently faced a similar warning.
>> This is when a link to a help page of another package is
>> broken (there is
>> not such help page). Although those could be false
>> positives:
>> mclapply help page does exists in parallel package.
>> as.MAList does exists in devel limma
>>
>>
>> when \link-ing to another package, from RShowDoc("R-exts")
>> section 2.5
>> the [] has to name the html help page, not the name of the
>> function. For
>> instance, `mclapply` is documented on a man page called
>> mcdummies.Rd
>> (!), so '\link[parallel:mcdummies]{nearest} would
>> presumably not
>>
>>
>> I am confused here: as far as I can tell, there is an
>> mclapply.html file:
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__stat.ethz.ch_R-2D
>> manual_R-2Ddevel_library_parallel_html_m=DwIFaQ=27AKQ-AFTMvLXtgZ7
>> shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuF
>> MuI=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI=pdAHJUFvmcwWmj0ex
>> F6lMOOuP8Dv-l3xeaCJK8C7VCI=
>> clapply.html
>>
>> > Dmanual_R-2Ddevel_library_parallel_html_=DwIFaQ=27AKQ-AFTMvLXtgZ7
>> shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuF
>> MuI=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI=ZmZcWjEF0mMhZfp_F
>> fBLbP0o7TSjRcTe-C5vLFDMxt8=
>> mclapply.html>
>>
>> In addition, when I use the \link[parallel:mcdummies] I get a
>> warning when
>> testing under Linux.
>>
>>
>> yeah, this is a pretty good one. If you look at
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wch_r-2Dsource_tree_trunk_src_library_parallel_man=DwIFaQ=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI=9d8xOxiij058sxHT_J9Nqk3e-z0Hwh4CoSXVNelJqu4=
>>
>> > r-2Dsource_tree_trunk_src_library_parallel_man=DwIFaQ=27AKQ-AFTMv
>> LXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR
>> 5qqwuFMuI=Mf6oKgfVoxBJjWof6fMJ-1myGyFr7UZ2iMg6_7bpavI=9d8xOxiij05
>> 8sxHT_J9Nqk3e-z0Hwh4CoSXVNelJqu4=>
>>
>> you'll see that there are different man pages for different
>> operating systems. On windows there is mcdummies, on unix mclapply &
>> friends. This seems like a bad idea (users comparing notes to work
>> through a problem get different help pages!). I don't really know
>> how to link explicitly to these in a conditional manner.
>>
>>
>> Does this
Re: [Bioc-devel] problem in building package GSAR
Thank you Vincent and Wolfgang. With my limited knowledge of ‘subversion’, I
overlooked this step. I think this will fix the problem.
Thank you very much.
Yasir
From: Vincent Carey [mailto:st...@channing.harvard.edu]
Sent: Monday, August 08, 2016 8:38 AM
To: Rahmatallah, Yasir
Cc: Wolfgang Huber; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] problem in building package GSAR
you have to do "svn add" for any new source files to be archived
On Mon, Aug 8, 2016 at 9:35 AM, Rahmatallah, Yasir
<yrahmatal...@uams.edu<mailto:yrahmatal...@uams.edu>> wrote:
Dear Wolfgang,
I believe I did upload the source code (.R) of the new functions as well as
their manual pages (.Rd).
First I checked out a copy of the development version using
svn co --username=y.rahmatallah --password=mypassword
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSAR<https://urldefense.proofpoint.com/v2/url?u=https-3A__hedgehog.fhcrc.org_bioconductor_trunk_madman_Rpacks_GSAR=AwMFaQ=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=lx5W6NJufGtK2Piccfk2o1lwPSqbwlJ_llxcnqLlPxY=tm_13HP_LE6GOytjpeaJYCkYBOfNZcj9_gZLegjOp_Y=>
I got the folder "GSAR" in the current directory. Then I added the source (.R)
and manual page (.Rd) for each new function under the R and man folders
respectively, modified the 'namespace' file by adding the new function names,
and bumped the 3rd digit in the version field of the 'description' file and
changed the 'Date' field too. When all this was done, I used
cd GSAR
svn update
svn commit --username=y.rahmatallah --password=mypassword -m "commit 1"
I always followed these steps in the past, but this is the first time I added
new functions. Is there anything wrong in these steps?
Regards,
Yasir
-Original Message-
From: Wolfgang Huber [mailto:whu...@embl.de<mailto:whu...@embl.de>]
Sent: Saturday, August 06, 2016 4:39 AM
To: Rahmatallah, Yasir
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] problem in building package GSAR
Dear Yasir
Did you actually upload the source code of these new function to the subversion
server?
I get, right now
huber@boltzmann:~/madman/Rpacks/GSAR/R$ svn info .
…
URL:
https://urldefense.proofpoint.com/v2/url?u=https-3A__hedgehog.fhcrc.org_bioconductor_trunk_madman_Rpacks_GSAR_R=AwIFaQ=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI=jPnOxdZIGTe1L7i8CInlw-CbMQm_bUkUVqc5J0M5Bbw=YAk1b3miMlDYhwEUngUguZsC6-Q_iOJupf6-Wl9e-aI=
Revision: 119920
…
"grep AggrF *” in that directory does not yield any results.
"grep radial *” finds radial_ranking but not radial.ranking etc.
Wolfgang
> On Aug 6, 2016, at 0:34 GMT+2, Rahmatallah, Yasir
> <yrahmatal...@uams.edu<mailto:yrahmatal...@uams.edu>> wrote:
>
> Hi,
>
> I recently added 6 more functions to package GSAR. I added the R files
> and manual pages for the new functions. I updated the namespace file
> accordingly. I can build the package successfully on my windows PC and
> 'R CMD check' returns no errors or warnings. I can install the package
> and it works fine on my PC. I use svn to update the development
> version (current development version is 1.7.2). The last update
> returned the following error
>
> ** testing if installed package can be loaded Error in
> namespaceExport(ns, exports) :
> undefined exports: AggrFtest, radial.ranking, MDtest, RMDtest,
> findMST2.PPI, TestGeneSets
> Error: loading failed
>
> The undefined exports are the 6 new functions I added to the package. It's
> like they are declared in the namespace file but they don't exist elsewhere.
> Any idea what causes this error? Help is appreciated. The contents of the
> namespace file are shown below:
>
> export(
> AggrFtest,
> HDP.ranking,
> radial.ranking,
> WWtest,
> KStest,
> MDtest,
> RKStest,
> RMDtest,
> GSNCAtest,
> findMST2,
> findMST2.PPI,
> plotMST2.pathway,
> TestGeneSets
> )
>
> import(igraph)
> importFrom("stats", "cor", "dist", "sd", "var.test", "p.adjust")
> importFrom("graphics", "legend", "mtext", "par", "plot", "title")
>
> Thank you,
> Yasir
>
> --
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[Bioc-devel] problem in building package GSAR
Hi,
I recently added 6 more functions to package GSAR. I added the R files and
manual pages for the new functions. I updated the namespace file accordingly. I
can build the package successfully on my windows PC and 'R CMD check' returns
no errors or warnings. I can install the package and it works fine on my PC. I
use svn to update the development version (current development version is
1.7.2). The last update returned the following error
** testing if installed package can be loaded
Error in namespaceExport(ns, exports) :
undefined exports: AggrFtest, radial.ranking, MDtest, RMDtest, findMST2.PPI,
TestGeneSets
Error: loading failed
The undefined exports are the 6 new functions I added to the package. It's like
they are declared in the namespace file but they don't exist elsewhere. Any
idea what causes this error? Help is appreciated. The contents of the namespace
file are shown below:
export(
AggrFtest,
HDP.ranking,
radial.ranking,
WWtest,
KStest,
MDtest,
RKStest,
RMDtest,
GSNCAtest,
findMST2,
findMST2.PPI,
plotMST2.pathway,
TestGeneSets
)
import(igraph)
importFrom("stats", "cor", "dist", "sd", "var.test", "p.adjust")
importFrom("graphics", "legend", "mtext", "par", "plot", "title")
Thank you,
Yasir
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Re: [Bioc-devel] error message - package GSAR
Thank you Dan for clarification. I guess I had bad luck in the last build.
Yasir
-Original Message-
From: Dan Tenenbaum [mailto:dtene...@fredhutch.org]
Sent: Thursday, May 05, 2016 3:26 PM
To: Rahmatallah, Yasir
Cc: bioc-devel
Subject: Re: [Bioc-devel] error message - package GSAR
This is an issue that was reported 3 years ago
(http://thr3ads.net/r-devel/2013/04/2193760-Failed-to-locate-the-texi2pdf-output-file)
and has not been fixed, probably because it is extremely hard to reproduce. It
tends to happen on random packages from one day to the next. In fact, in
today's build report which is coming out in a few minutes, the problem does not
occur.
So you don't need to do anything.
Dan
- Original Message -
> From: "Rahmatallah, Yasir" <yrahmatal...@uams.edu>
> To: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Thursday, May 5, 2016 12:28:35 PM
> Subject: [Bioc-devel] error message - package GSAR
> Hi,
>
> I'm the maintainer of package GSAR. Last Tuesday's build produced the
> following error message for the Windows platform only
>
> Warning: running command
> '"C:\Users\BIOCBU?1\AppData\Local\Programs\MIKTEX?1.9\miktex\bin\texify.exe"
> --quiet --pdf "GSAR.tex" --max-iterations=20 -I
> "E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I
> "E:/biocbld/bbs-3.3-bioc/R/share/texmf/bibtex/bst"' had status 1 Error
> in find_vignette_product(name, by = "texi2pdf", engine = engine) :
> Failed to locate the 'texi2pdf' output file (by engine
> 'utils::Sweave') for vignette with name 'GSAR'. The following files exist in
> directory '.':
> 'Bioconductor.sty', 'GSAR-KCMLplot.pdf', 'GSAR-mst.pdf',
> 'GSAR-mst2plot.pdf', 'GSAR.Rnw', 'GSAR.bib', 'GSAR.tex', 'unsrturl.bst'
> Calls: -> find_vignette_product Execution halted
>
> It seems that the PDF file of the vignette cannot be found. Since the
> package passes on Linux and Mac platforms, I assume the source of
> error is not in the vignette's .tex file itself. There is no line in
> the vignette's code that changes the working directory and all other
> files in the directory are being listed in the error message. Any idea what
> caused this error and how to fix it?
>
> Regards,
> Yasir
>
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[Bioc-devel] error message - package GSAR
Hi,
I'm the maintainer of package GSAR. Last Tuesday's build produced the following
error message for the Windows platform only
Warning: running command
'"C:\Users\BIOCBU?1\AppData\Local\Programs\MIKTEX?1.9\miktex\bin\texify.exe"
--quiet --pdf "GSAR.tex" --max-iterations=20 -I
"E:/biocbld/bbs-3.3-bioc/R/share/texmf/tex/latex" -I
"E:/biocbld/bbs-3.3-bioc/R/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for
vignette with name 'GSAR'. The following files exist in directory '.':
'Bioconductor.sty', 'GSAR-KCMLplot.pdf', 'GSAR-mst.pdf', 'GSAR-mst2plot.pdf',
'GSAR.Rnw', 'GSAR.bib', 'GSAR.tex', 'unsrturl.bst'
Calls: -> find_vignette_product
Execution halted
It seems that the PDF file of the vignette cannot be found. Since the package
passes on Linux and Mac platforms, I assume the source of error is not in the
vignette's .tex file itself. There is no line in the vignette's code that
changes the working directory and all other files in the directory are being
listed in the error message. Any idea what caused this error and how to fix it?
Regards,
Yasir
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Re: [Bioc-devel] build problem in package GSAR
Thank you Dan. Apologies for not being up to date regarding the issue.
Yasir
From: Dan Tenenbaum <dtene...@fredhutch.org>
Sent: Friday, April 1, 2016 7:32:06 PM
To: Rahmatallah, Yasir
Cc: bioc-devel
Subject: Re: [Bioc-devel] build problem in package GSAR
The issue has already been fixed and that should be reflected in Sunday's build
report. Recent emails to R-devel have discussed the problem, which is related
to a new toolchain for building windows packages, intended to be used with the
soon-to-be-released R-3.3.0.
Dan
- Original Message -
> From: "Rahmatallah, Yasir" <yrahmatal...@uams.edu>
> To: "Marc Carlson" <mcarl...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Friday, April 1, 2016 4:42:09 PM
> Subject: [Bioc-devel] build problem in package GSAR
> Hi,
>
> I am the author of package GSAR. Just today I noticed that the development
> version 1.5.0 shows a build error under the Windows platform only. This error
> was not there a couple of days ago when I last checked. The error message is
> related to the 'igraph' package:
>
> Error in base::.Call("R_igraph_make_weak_ref", key, value, finalizer, :
> "R_igraph_make_weak_ref" not available for .Call() for package "igraph"
>
> I'm not sure why this happened now since package 'igraph' (version 1.0.1) was
> not updated since the last release of Bioconductor. If the error is related to
> an update in 'igraph', the build error would have happened under all platforms
> and not only under Windows!
> To make things worse, today is the deadline for packages to pass ''R CMD
> build''
> and ''R CMD check'' without error.
> Help is appreciated.
>
> Best Regards,
>
> Yasir Rahmatallah, PhD
> Postdoctoral Fellow
> Department of Biomedical Informatics
> University of Arkansas for Medical Sciences (UAMS)
> 4301 West Markham, Slot #782
> Little Rock, AR 72205
> Office: +1-501-603-1674
>
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[Bioc-devel] build problem in package GSAR
Hi,
I am the author of package GSAR. Just today I noticed that the development
version 1.5.0 shows a build error under the Windows platform only. This error
was not there a couple of days ago when I last checked. The error message is
related to the 'igraph' package:
Error in base::.Call("R_igraph_make_weak_ref", key, value, finalizer, :
"R_igraph_make_weak_ref" not available for .Call() for package "igraph"
I'm not sure why this happened now since package 'igraph' (version 1.0.1) was
not updated since the last release of Bioconductor. If the error is related to
an update in 'igraph', the build error would have happened under all platforms
and not only under Windows!
To make things worse, today is the deadline for packages to pass ''R CMD
build'' and ''R CMD check'' without error.
Help is appreciated.
Best Regards,
Yasir Rahmatallah, PhD
Postdoctoral Fellow
Department of Biomedical Informatics
University of Arkansas for Medical Sciences (UAMS)
4301 West Markham, Slot #782
Little Rock, AR 72205
Office: +1-501-603-1674
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[Bioc-devel] Announcing the new R pakage GSAR
Hello,
I would like to announce the availability of the new R package 'GSAR' released
recently with Bioconductor 3.0. The package offers a suite of tests to perform
self-contained gene set analysis (GSA). We would highly appreciate your
feedback and suggestions to help us improve the package.
Short Description:
Package GSAR provides a set of statistical methods for self-contained gene set
analysis. The methods work for gene expressions obtained from microarrays or
RNA-Seq count data (given proper normalization is used). The package consists
of two-sample multivariate nonparametric statistical methods to test a null
hypothesis against specific alternative hypotheses, such as differences in
shift, scale or correlation structure between two conditions. Multivariate
generalizations of the Kolmogorov-Smirnov and Wald-Wolfowitz runs tests using
the minimum spanning tree are available. It also offers a graphical
visualization scheme for correlation networks to examine the change in the net
correlation structure of a gene set between two conditions.
Best Regards,
Yasir Rahmatallah, Ph.D.
Postdoctoral Fellow
Division of Biomedical Informatics
University of Arkansas for Medical Sciences (UAMS)
4301 West Markham, Slot #782
Little Rock, AR 72205
Office: 501-603-1674
Fax: 501-526-5964
Email: yrahmatal...@uams.edu
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