date:20211022

Re: [Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

2021-10-22 Thread Vincent Carey

I found
```

Error in `toSBGN(system.file("extdata",
"biopax3-short-metabolic-pathway.owl",
package = "paxtoolsr"), outFile)`: java.lang.UnsatisfiedLinkError:
C:\Program Files\Java\jre1.8.0_311\bin\awt.dll: Can't find dependent
libraries

[ FAIL 1 | WARN 1 | SKIP 3 | PASS 58 ]
```
on a pretty stock windows install on azure.

Now it is a little bleeding edge, but maybe you could  comment on this
error?


R Under development (unstable) (2021-10-19 r81074 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United
States.utf8LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C   LC_TIME=English_United
States.utf8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] rcmdcheck_1.4.0

loaded via a namespace (and not attached):
 [1] ps_1.6.0 prettyunits_1.1.1digest_0.6.28
 crayon_1.4.1 withr_2.4.2
 [6] rprojroot_2.0.2  R6_2.5.1 cli_3.0.1
 curl_4.3.2   callr_3.7.0
[11] desc_1.4.0   tools_4.2.0  compiler_4.2.0
processx_3.5.2   pkgbuild_1.2.0
[16] xopen_1.0.0  BiocManager_1.30.16.1001


On Fri, Oct 22, 2021 at 12:25 PM Augustin Luna  wrote:

> Thanks for the responses. But they are not addressing my problem. I
> have GitHub Actions checking the package on Windows/macOS/Linux using
> Java OpenJDK 14 with tests/examples running fine on both R release and
> devel.
>
> https://github.com/BioPAX/paxtoolsr/actions/runs/1372348962
>
> At this point, I'm not debugging my code rather the Bioconductor build
> system. Tests/examples that do not run on Bioconductor are running
> fine elsewhere.
>
> More helpful to me would be instructions to some VM file or Docker
> container where I could mimic the Bioconductor setup. I'm at a loss
> for how to debug this problem or what is unique about the Bioconductor
> system.
>
> Searching through code from other packages is not helpful unless I
> know what I'm looking for. In this case, it means a package that had a
> "JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote"
> error and addressed it successfully.
>
> Stack Overflow only gives me hints regarding
> "CFMessagePortCreateRemote" errors in that there is a problem with the
> installation of Java:
>
>
> https://stackoverflow.com/questions/15289059/install-java-on-mac-osx-10-8-2-error-calling-cfmessageportcreateremote
>
> PS: I removed the "which java" call.
>
> Thanks,
> Augustin Luna
>
> On Mon, Oct 18, 2021 at 3:14 PM Hervé Pagès 
> wrote:
> >
> > Hi Augustin,
> >
> > Please don't rely on JAVA_HOME to detect Java. The JDK installer on
> > Windows doesn't set this variable so you shouldn't expect it to be set
> > on the user's machine. AFAIK the other Bioconductor packages that depend
> > on Java don't use their own code to detect Java. Instead I believe that
> > they run their Java code via rJava so they delegate to rJava the
> > responsibility to find Java for them.
> >
> > Here is the list of all Bioconductor packages that depend on rJava:
> >
> >ArrayExpressHTS
> >(not supported on Windows)
> >BridgeDbR
> >
> >CHRONOS
> >
> >debCAM
> >
> >esATAC
> >
> >gaggle
> >
> >Onassis
> >
> >ReQON
> >
> >RGMQL
> >
> >rmelting
> >
> >sarks
> >
> >SELEX
> >
> >
> > Feel free to take a look at how they handle this.
> >
> > Cheers,
> > H.
> >
> >
> > On 18/10/2021 10:13, Vincent Carey wrote:
> > > That should be fixable.  The build system needs to have a correct
> setting
> > > for JAVA_HOME.  But you have
> > > clearly nonportable code in .onLoad in paxtoolsr.R -- system("which
> java")
> > > ... this should not be
> > > necessary at all, just import rJava.
> > >
> > > On Mon, Oct 18, 2021 at 12:29 PM Augustin Luna 
> wrote:
> > >
> > >> I have the following error:
> > >>
> > >> "error: JAVA_HOME cannot be determined from the Registry"
> > >>
> > >> for this package:
> > >>
> > >>
> > >>
> https://bioconductor.org/checkResults/devel/bioc-LATEST/paxtoolsr/riesling1-install.html
> > >>
> > >> I have been given assurances that Java is present but given this
> > >> error, I am not so sure and I am unsure how to debug or fix it.
> > >>
> > >> Can anyone suggest how to proceed?
> > >>
> > >> Thanks,
> > >> Augustin Luna
> > >>
> > >> ___
> > >> Bioc-devel@r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >
> >
> > --
> > Hervé Pagès
> >
> > Bioconductor Core Team
> > hpages.on.git...@gmail.com
>

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Re: [Bioc-devel] Updating the vignette in the published package

2021-10-22 Thread Kern, Lori

The changes to the vignette did not include a valid version bump.  Could you 
please trying bumping the version of your description.  Regardless of if this 
is needed to update the website, it would be needed to propagate and have the 
correct version available from within R using the vignette() function.
If the issue persists after the version bump, please let us know and we can 
investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of matine rb 

Sent: Friday, October 22, 2021 1:17 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Updating the vignette in the published package

Dear Bioconductor community members,

I am wondering how to update the vignette after the package is available
from the Bioconductor website? As I have noticed, the available vignette
for my package (*https://bioconductor.org/packages/HPiP/
*) includes two introductions. I
have already pushed the changes, but I think the vignette can not be
updated once the package is available online.

I would appreciate it if you help me with this matter.

with thanks,
Matineh

[[alternative HTML version deleted]]

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[Bioc-devel] Updating the vignette in the published package

2021-10-22 Thread matine rb

Dear Bioconductor community members,

I am wondering how to update the vignette after the package is available
from the Bioconductor website? As I have noticed, the available vignette
for my package (*https://bioconductor.org/packages/HPiP/
*) includes two introductions. I
have already pushed the changes, but I think the vignette can not be
updated once the package is available online.

I would appreciate it if you help me with this matter.

with thanks,
Matineh

[[alternative HTML version deleted]]

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Re: [Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

2021-10-22 Thread Augustin Luna

Thanks for the responses. But they are not addressing my problem. I
have GitHub Actions checking the package on Windows/macOS/Linux using
Java OpenJDK 14 with tests/examples running fine on both R release and
devel.

https://github.com/BioPAX/paxtoolsr/actions/runs/1372348962

At this point, I'm not debugging my code rather the Bioconductor build
system. Tests/examples that do not run on Bioconductor are running
fine elsewhere.

More helpful to me would be instructions to some VM file or Docker
container where I could mimic the Bioconductor setup. I'm at a loss
for how to debug this problem or what is unique about the Bioconductor
system.

Searching through code from other packages is not helpful unless I
know what I'm looking for. In this case, it means a package that had a
"JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote"
error and addressed it successfully.

Stack Overflow only gives me hints regarding
"CFMessagePortCreateRemote" errors in that there is a problem with the
installation of Java:

https://stackoverflow.com/questions/15289059/install-java-on-mac-osx-10-8-2-error-calling-cfmessageportcreateremote

PS: I removed the "which java" call.

Thanks,
Augustin Luna

On Mon, Oct 18, 2021 at 3:14 PM Hervé Pagès  wrote:
>
> Hi Augustin,
>
> Please don't rely on JAVA_HOME to detect Java. The JDK installer on
> Windows doesn't set this variable so you shouldn't expect it to be set
> on the user's machine. AFAIK the other Bioconductor packages that depend
> on Java don't use their own code to detect Java. Instead I believe that
> they run their Java code via rJava so they delegate to rJava the
> responsibility to find Java for them.
>
> Here is the list of all Bioconductor packages that depend on rJava:
>
>ArrayExpressHTS
>(not supported on Windows)
>BridgeDbR
>
>CHRONOS
>
>debCAM
>
>esATAC
>
>gaggle
>
>Onassis
>
>ReQON
>
>RGMQL
>
>rmelting
>
>sarks
>
>SELEX
>
>
> Feel free to take a look at how they handle this.
>
> Cheers,
> H.
>
>
> On 18/10/2021 10:13, Vincent Carey wrote:
> > That should be fixable.  The build system needs to have a correct setting
> > for JAVA_HOME.  But you have
> > clearly nonportable code in .onLoad in paxtoolsr.R -- system("which java")
> > ... this should not be
> > necessary at all, just import rJava.
> >
> > On Mon, Oct 18, 2021 at 12:29 PM Augustin Luna  wrote:
> >
> >> I have the following error:
> >>
> >> "error: JAVA_HOME cannot be determined from the Registry"
> >>
> >> for this package:
> >>
> >>
> >> https://bioconductor.org/checkResults/devel/bioc-LATEST/paxtoolsr/riesling1-install.html
> >>
> >> I have been given assurances that Java is present but given this
> >> error, I am not so sure and I am unsure how to debug or fix it.
> >>
> >> Can anyone suggest how to proceed?
> >>
> >> Thanks,
> >> Augustin Luna
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com

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[Bioc-devel] methylclock error in vignette (windows build)

2021-10-22 Thread Dolors Pelegrí

Hello,

In an example of the methylclock package vignette we use a GEO dataset
(GSE58045). The data is downloaded during the vignette generation and now
in the windows build we get the error :

File stored at:
D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqS7RSx/GPL8490.soft.gz
Warning in readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) :
  invalid or incomplete compressed data

This error did not appear previously and does not appear in Linux and macOS
builds. I do not know what could be the reason for this error and how to
solve it

Best,

Dolors

-- 
-- 
Dolors Pelegrí
Bioinformatics
*IS**Global** (Barcelona Institute for Global Health*
*)*Barcelona Biomedical Research Park (PRBB), *Campus Mar*
Doctor Aiguader, 88, 08003 Barcelona, Spain
dolors.pele...@isglobal.org 
www.isglobal.org

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Re: [Bioc-devel] Package name

2021-10-22 Thread Henrik Bengtsson

For CRAN packages it's easy. Packages on CRAN are eternal. They may be
archived, but they are never removed, so in a sense they're always
"currently on CRAN". Archived packages may still be installed, but only
with some efforts of the user. Some packages go in an out of "archived"
status depending how quick the maintainer fixes issues. Because of this, I
cannot really see how a CRAN package name can be "reused" by anyone else
without a formal handover agreement between old and new maintainers. Even
so, I think CRAN needs to approve on the "update" in order to unarchive it.

Personally, I'd argue the same should apply to Bioconductor packages.
Reusing package names for other purposes/different APIs is just asking for
troubles, e.g. when it comes to future scientists trying to reproduce
legacy results.

/Henrik

On Fri, Oct 22, 2021, 03:02 Wolfgang Huber  wrote:

> This is probably a niche concern, but  I’d find it a pity if a good
> package name (*) became unavailable forever, esp. if it refers to a
> real-world concept not owned by the authors of the original package.
> Perhaps we could allow re-using a name after a grace period (say 1 or 2
> years)?
> To be extra safe, one could also require the first version number of the
> new package be much higher than the last version of the old (dead) package.
>
> (*) One example I have in mind where we re-used the name of an extinct
> project is rhdf5.
>
> Kind regards
> Wolfgang
>
> > Il giorno 21ott2021, alle ore 13:39, Kern, Lori
>  ha scritto:
> >
> > Good point.  I'll open an issue on the github to fix.
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > 
> > From: Bioc-devel  on behalf of
> Laurent Gatto 
> > Sent: Thursday, October 21, 2021 12:53 AM
> > To: bioc-devel@r-project.org 
> > Subject: [Bioc-devel] Package name
> >
> > The Package Guidelines for Developers and Reviewers say that:
> >
> > A package name should be descriptive and should not already exist as a
> current package (case-insensitive) in Bioconductor nor CRAN.
> >
> > The sentences says current packages - does that imply that names of
> packages that have been archived (on CRAN) or deprecated (on Bioconductor)
> are available? This is likely to lead to serious confusion.
> >
> > Laurent
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://secure-web.cisco.com/18tLjfrOdSZ-K_8neKbEy5VWz_fgbNJthSRI3zRVyXXtc-p9kCgNhG51wWXnY7UGhy4yP_imTwLGoP4BCIicB_fqzg9U937WF_IJiOPJh7NnfQXFLeEV-SiiJJ1eCyN2vaJFacWPvahAlN135mDHZNw_peW0Yl4BOq8m2QBMh4i952Nt6oghMQpSWSjaP_2bN4VKIBT2ZP-A7pDqddlOSeCCaMEKJZp_6w1WthdY69MB6lAbsF-i9uX3JVNSCmAlXW3YMNOfVEBijto4EJaGIUJMJwGX_vec9kTf9gtFiYztotSHNfquFZ4GlaHmXeHwPaBEtazOY5fPiuzLjzDK52Q/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
> >
> >
> > 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.
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
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Re: [Bioc-devel] Deprecation genphen

2021-10-22 Thread Kern, Lori

Thank you for letting us know. We will begin the deprecation process.  The 
package will be deprecated in 3.15 and removed in 3.16.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Simo 
Kitanovski 
Sent: Thursday, October 21, 2021 4:00 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Deprecation genphen

Dears,

we would like to deprecate genphen as its functionality has
been superseded by other R packages.

Would it be possible to begin the deprecation process?

Best,
Simo

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Re: [Bioc-devel] Package name

2021-10-22 Thread Wolfgang Huber

This is probably a niche concern, but  I’d find it a pity if a good package 
name (*) became unavailable forever, esp. if it refers to a real-world concept 
not owned by the authors of the original package.
Perhaps we could allow re-using a name after a grace period (say 1 or 2 years)?
To be extra safe, one could also require the first version number of the new 
package be much higher than the last version of the old (dead) package.

(*) One example I have in mind where we re-used the name of an extinct project 
is rhdf5.

Kind regards
Wolfgang

> Il giorno 21ott2021, alle ore 13:39, Kern, Lori 
>  ha scritto:
> 
> Good point.  I'll open an issue on the github to fix.
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Bioc-devel  on behalf of Laurent 
> Gatto 
> Sent: Thursday, October 21, 2021 12:53 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Package name
> 
> The Package Guidelines for Developers and Reviewers say that:
> 
> A package name should be descriptive and should not already exist as a 
> current package (case-insensitive) in Bioconductor nor CRAN.
> 
> The sentences says current packages - does that imply that names of packages 
> that have been archived (on CRAN) or deprecated (on Bioconductor) are 
> available? This is likely to lead to serious confusion.
> 
> Laurent
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://secure-web.cisco.com/18tLjfrOdSZ-K_8neKbEy5VWz_fgbNJthSRI3zRVyXXtc-p9kCgNhG51wWXnY7UGhy4yP_imTwLGoP4BCIicB_fqzg9U937WF_IJiOPJh7NnfQXFLeEV-SiiJJ1eCyN2vaJFacWPvahAlN135mDHZNw_peW0Yl4BOq8m2QBMh4i952Nt6oghMQpSWSjaP_2bN4VKIBT2ZP-A7pDqddlOSeCCaMEKJZp_6w1WthdY69MB6lAbsF-i9uX3JVNSCmAlXW3YMNOfVEBijto4EJaGIUJMJwGX_vec9kTf9gtFiYztotSHNfquFZ4GlaHmXeHwPaBEtazOY5fPiuzLjzDK52Q/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> 
> 
> 
> 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.
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

Re: [Bioc-devel] Updating the vignette in the published package

[Bioc-devel] Updating the vignette in the published package

Re: [Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

[Bioc-devel] methylclock error in vignette (windows build)

Re: [Bioc-devel] Package name

Re: [Bioc-devel] Deprecation genphen

Re: [Bioc-devel] Package name

8 matches

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