[R-pkg-devel] Checking on Debian on RHub

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

I still have problems with checking one of my packages on RHub running Debian,  
as the Preprocessing fails in building in some of the needed spatial packages.  
This problem was reported quite awhile ago,  and never appears to have been 
completely fixed.  Is there an alternate place I can test a package under 
Debian that is consistent with CRAN.

Thanks,

-Roy

**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] how to address CRAN FAIL on r-devel-windows-x86_64-gcc10-UCRT?

[David Winsemius]

On 4/2/21 1:08 PM, David Winsemius wrote:


On 4/2/21 4:05 AM, Daniel Kelley wrote:
The "oce" package for oceanographic analysis is failing a check on 
the r-devel-windows-x86_64-gcc10-UCRT system (see
https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64-gcc10-UCRT/oce-00check.html). 
The problem seems to relate to the checking vignette outputs.


According to 
https://www.r-project.org/nosvn/winutf8/ucrt3/CRAN/checks/gcc10-UCRT/README.txt, 
that test setup is experimental.  Does that mean that I ought to I 
ignore the FAIL status for this machine, perhaps checking it once in 
a while to see if it changes?

Hello Daniel;

I'm not speaking for CRAN. I'm another maintainer whose current status 
page has a FAIL for that platform. But the FAIL notation is due at 
least in part to the fact that apparently the UCRT platform is less 
frequently run on the full CRAN package holdings. The note refers to a 
package that was updated a few days ago. The log file however has two 
other reports of failure relating to compiler warnings.


All the other platforms passed the newer versions. There is no mention 
of the UCRT platform at the CRAN Policies page: 
https://cran.r-project.org/web/packages/policies.html


I'm waiting to see whether the aging fortran code generates warnings 
whenever the UCRT platform gets fired up again.



Follow-up on UCRT package checks for muhaz package. When the version 
that corrected R code errors was eventually run, it now has a status of 
"OK". Apparently the warnings about the Fortran code are not 
sufficiently worrisome. It still have an LTO link but the status page 
doesn't even consider the warnings contained therein to be worthy of 
being called warnings or notes.



--

David Winsemius

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Package Rejection Error Help

[Duncan Murdoch]

On 07/04/2021 10:50 a.m., Andrew Dhawan wrote:

Thank you again Uwe,

So, to clarify - is the error occurring because RankProd is not found in
BioC 3.13 (current release is 3.12)?  If so, I'm not sure how I can fix
this...


I suspect the only thing you could do in the short term is to remove 
that dependency (or move it to Suggests, and check for it before using). 
 If that's not feasible, then you just need to wait for it to become 
available.  Based on its status page, it shouldn't be long.  Try 
submitting again tomorrow?


Duncan Murdoch




Thanks
Andrew


On Wed, Apr 7, 2021 at 5:45 AM Uwe Ligges 
wrote:




On 06.04.2021 19:26, Robert M. Flight wrote:

Andrew,

I think if you want to include a Bioconductor dependency, then I think

you

add the "biocViews:" line to your description file to enable bioconductor


Not needed for CRAN.

You simply need to declare the dependency, but BioC 3.13 is what we
should use to check with R-devel and that was recetnly still pretty
iunstable.

Best,
Uwe Ligges


package installation.

See this answer on Bioinformatics stackexchange:
https://bioinformatics.stackexchange.com/a/3375/51

Hope that helps!

-Robert

On Tue, Apr 6, 2021 at 1:14 PM Andrew Dhawan  wrote:


Thank you both very kindly - I have addressed both notes. I am still
wondering though about the RankProd dependency error - any insight into
this?

Thanks!
Andrew

On Tue, Apr 6, 2021 at 11:58 AM Uwe Ligges <
lig...@statistik.tu-dortmund.de>
wrote:




On 06.04.2021 17:39, Patrick Giraudoux wrote:

I had a similar problem with intepreting "notes" in pgirmess checks.
Some are lethal and lead to rejection and some not (just informative
comments). Fortunately Uwe has been kind enough to tell me what I

missed

(I thought that all notes were just "informative").
Would it be possible to call lethal notes "errors" to keep us aware

that

we must really do something with them and fix what is actually a

problem?


These are Notes as it may not be a serious issue or may be a false
positive, nevertheless, we like to get clean packages to CRAN.

WARNINGs and ERRORs will never be accepted.

The policies clearly say that significant Notes have to be addressed.
The only Note that is always acceptable is the CRAN maintainer Note
about the package maintainer's address. All other Notes should be fixed
generally or need manual attention in case of the really very few
exceptions.

Best,
Uwe Ligges





Best,
Patrick


Le 06/04/2021 à 17:33, Uwe Ligges a écrit :

Two Notes:


Found the following (possibly) invalid URLs:
   URL: http://imagemagick.org/script/download.php (moved to
https://imagemagick.org/script/download.php)
 From: inst/doc/vignette.html
 Status: 200
 Message: OK


Please change http --> https, add trailing slashes, or follow moved
content as appropriate.

* checking LazyData ... NOTE
   'LazyData' is specified without a 'data' directory

Simply omit the field if you have no data.

Best,
Uwe Ligges



On 06.04.2021 16:27, Andrew Dhawan wrote:

Dear all,

I am a bit puzzled by this error for the sigQC package being

uploaded

to

CRAN. Checks on my end pass without issue. There is one error
regarding the
bioConductor dependency RankProd that comes up only on the Debian OS
when
checking. See here for further details:






https://win-builder.r-project.org/incoming_pretest/sigQC_0.1.22_20210406_110708/



I am not sure how to resolve this - it seems to me that the

dependency

*should* be available across platforms, and short of removing the
dependency (which we rely on a fair bit), I'm not sure what  we can

do.


Any thoughts or suggestions would be massively appreciated.

Thank you so kindly!
Andrew

  [[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel







  [[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



   [[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel





[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Package Rejection Error Help

[Andrew Dhawan]

Thank you again Uwe,

So, to clarify - is the error occurring because RankProd is not found in
BioC 3.13 (current release is 3.12)?  If so, I'm not sure how I can fix
this...

Thanks
Andrew


On Wed, Apr 7, 2021 at 5:45 AM Uwe Ligges 
wrote:

>
>
> On 06.04.2021 19:26, Robert M. Flight wrote:
> > Andrew,
> >
> > I think if you want to include a Bioconductor dependency, then I think
> you
> > add the "biocViews:" line to your description file to enable bioconductor
>
> Not needed for CRAN.
>
> You simply need to declare the dependency, but BioC 3.13 is what we
> should use to check with R-devel and that was recetnly still pretty
> iunstable.
>
> Best,
> Uwe Ligges
>
> > package installation.
> >
> > See this answer on Bioinformatics stackexchange:
> > https://bioinformatics.stackexchange.com/a/3375/51
> >
> > Hope that helps!
> >
> > -Robert
> >
> > On Tue, Apr 6, 2021 at 1:14 PM Andrew Dhawan  wrote:
> >
> >> Thank you both very kindly - I have addressed both notes. I am still
> >> wondering though about the RankProd dependency error - any insight into
> >> this?
> >>
> >> Thanks!
> >> Andrew
> >>
> >> On Tue, Apr 6, 2021 at 11:58 AM Uwe Ligges <
> >> lig...@statistik.tu-dortmund.de>
> >> wrote:
> >>
> >>>
> >>>
> >>> On 06.04.2021 17:39, Patrick Giraudoux wrote:
>  I had a similar problem with intepreting "notes" in pgirmess checks.
>  Some are lethal and lead to rejection and some not (just informative
>  comments). Fortunately Uwe has been kind enough to tell me what I
> >> missed
>  (I thought that all notes were just "informative").
>  Would it be possible to call lethal notes "errors" to keep us aware
> >> that
>  we must really do something with them and fix what is actually a
> >> problem?
> >>>
> >>> These are Notes as it may not be a serious issue or may be a false
> >>> positive, nevertheless, we like to get clean packages to CRAN.
> >>>
> >>> WARNINGs and ERRORs will never be accepted.
> >>>
> >>> The policies clearly say that significant Notes have to be addressed.
> >>> The only Note that is always acceptable is the CRAN maintainer Note
> >>> about the package maintainer's address. All other Notes should be fixed
> >>> generally or need manual attention in case of the really very few
> >>> exceptions.
> >>>
> >>> Best,
> >>> Uwe Ligges
> >>>
> >>>
> >>>
> >>>
>  Best,
>  Patrick
> 
> 
>  Le 06/04/2021 à 17:33, Uwe Ligges a écrit :
> > Two Notes:
> >
> >
> > Found the following (possibly) invalid URLs:
> >   URL: http://imagemagick.org/script/download.php (moved to
> > https://imagemagick.org/script/download.php)
> > From: inst/doc/vignette.html
> > Status: 200
> > Message: OK
> >
> >
> > Please change http --> https, add trailing slashes, or follow moved
> > content as appropriate.
> >
> > * checking LazyData ... NOTE
> >   'LazyData' is specified without a 'data' directory
> >
> > Simply omit the field if you have no data.
> >
> > Best,
> > Uwe Ligges
> >
> >
> >
> > On 06.04.2021 16:27, Andrew Dhawan wrote:
> >> Dear all,
> >>
> >> I am a bit puzzled by this error for the sigQC package being
> uploaded
> >>> to
> >> CRAN. Checks on my end pass without issue. There is one error
> >> regarding the
> >> bioConductor dependency RankProd that comes up only on the Debian OS
> >> when
> >> checking. See here for further details:
> >>
> >>>
> >>
> https://win-builder.r-project.org/incoming_pretest/sigQC_0.1.22_20210406_110708/
> >>
> >>
> >> I am not sure how to resolve this - it seems to me that the
> >> dependency
> >> *should* be available across platforms, and short of removing the
> >> dependency (which we rely on a fair bit), I'm not sure what  we can
> >> do.
> >>
> >> Any thoughts or suggestions would be massively appreciated.
> >>
> >> Thank you so kindly!
> >> Andrew
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> 
> >>>
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org 

Re: [R-pkg-devel] R package depends on Bioconductor packages RTIGER

[Uwe Ligges]

Reason is that BioC 3.13 does not offer a new rtracklayer binary which 
the winbuilder machine typically uses.
As this also does not install from sources for me. So this seems hard to 
set up.



Best,
Uwe Ligges








On 07.04.2021 12:18, Rafael CM wrote:

Dear all,
I am trying to submit a package to CRAN that depends on Bioconductor
packages. On debian, I do not have any problems so far. But when checking
for windows I get several errors:

Error: package or namespace load failed for 'Gviz' in loadNamespace(j
<- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
  namespace 'rtracklayer' 1.48.0 is already loaded, but >= 1.51.5 is required
Error: package 'Gviz' could not be loaded
In addition: Warning message:
multiple methods tables found for 'export'
Execution halted
ERROR: lazy loading failed for package 'RTIGER'
* removing 'd:/RCompile/CRANincoming/R-devel/lib/RTIGER'
* restoring previous 'd:/RCompile/CRANincoming/R-devel/lib/RTIGER'

Could someone help me?

Thank you very much,

Rafael

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] rtracklayer installation problems

[Martin Morgan]

(sorry, too quick on the return key)

From the Bioconductor 'devel' (3.13, used with R-devel) 'landing page' for 
rtracklayer

https://bioconductor.org/packages/devel/rtracklayer

The 'build' badge is red; clicking on it shows a build system problem with 
rtracklayer on Windows. Scrolling on the landing page to the bottom shows

Source Package  rtracklayer_1.51.5.tar.gz
Windows Binary  
macOS 10.13 (High Sierra)   rtracklayer_1.51.5.tgz

so there is currently no Windows binary available. This is in the hands of the 
rtracklayer maintainer; there is a very high likelihood that it will be fixed, 
so either be patient or ask the rtracklayer maintainer directly to address this 
by, e.g., opening an issue at https://github.com/lawremi/rtracklayer

Martin Morgan


On 4/7/21, 6:32 AM, "R-package-devel on behalf of Gordon Brown" 
 wrote:

Hi, Rosario,

The message is telling you that you need to install the development header 
files for glibc on your computer.  This is a set of files that are needed for 
building some kinds of software, but are not installed by default.  Are you 
working on some sort of Linux machine?  On Centos 8, the relevant package to 
install is called "glibc-headers".  On Ubuntu 20.04 it's "libc6-dev".  You'd 
need to run a command in the shell, something like:

Centos:
> sudo dnf install glibc-headers
or
> sudo yum install glibc-headers

Ubuntu/Debian:
> sudo apt install libc6-dev

If it's Windows or Mac, I can't help...

If you don't have root access on your host, or the above doesn't make sense 
to you, you will need to talk to whoever administers your computing 
environment, asking them to install the relevant package.

Hope this helps.

 - Gord


On 20210407, 11:03, "R-package-devel on behalf of rosario.avo...@unina.it" 
 
wrote:

Hi everyone,



I hope this is the right e-mail I should have used; this is the first 
time
that I ask for help with R!

Yesterday, I installed the devel version of R (4.1) as I need to use a
package (RiboDiPa) which only works for this version.

The package requires, among the others, the package "rtracklayer". Since
yesterday I am struggling trying to install rtracklayer for devel 
version
without success.

Below you can find the final message I got before the installation 
stops.
Any idea of what might be the reason why I cannot install rtracklayer? 



ucsc/udc.c:46:10: fatal error: sys/mman.h: No such file or directory

#include 

  ^~~~

compilation terminated.

make: *** 
[https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fMakevars.win%3a16=E,1,aB4mtmdcaXh3y_rFcDWiXKtEvYZoLA3GcTOtz2EAwNVyTaBV0cLYVfIMvPNYj-c9QK7LiaHqut3FcMfCLlVShgqSAdXj_xGXP8nS49zX7vVKE9rNPhmLmWDTnyU,=1:
 ucsc/udc.o] Error 1

ERROR: compilation failed for package 'rtracklayer'

* removing 'C:/Users/Rosario/Documents/R/win-library/4.1/rtracklayer'



If you need any other information please, do not hesitate to ask.

Thank you in advance for your help!



Best,

Rosario





Rosario Avolio, PhD

Researcher

Department of Molecular Medicine and Medical Biotechnology

Via Pansini, 5

19/A Building

80131 Napoli, Italy

email:  <mailto:rosario.avo...@unina.it> rosario.avo...@unina.it

phone: +39 081 746 31 39




[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] rtracklayer installation problems

[Martin Morgan]

From the Bioconductor 'devel' (3.13, used with R-devel) 'landing page' for 
rtracklayer

https://bioconductor.org/packages/devel/rtracklayer

The 'build' badge is red; clicking on it shows a build system problem with 
rtracklayer on Windows. Scrolling on the landing page to the bottom shows

Source Package  rtracklayer_1.51.5.tar.gz
Windows Binary  
macOS 10.13 (High Sierra)   rtracklayer_1.51.5.tgz
Source Repository   



On 4/7/21, 6:32 AM, "R-package-devel on behalf of Gordon Brown" 
 wrote:

Hi, Rosario,

The message is telling you that you need to install the development header 
files for glibc on your computer.  This is a set of files that are needed for 
building some kinds of software, but are not installed by default.  Are you 
working on some sort of Linux machine?  On Centos 8, the relevant package to 
install is called "glibc-headers".  On Ubuntu 20.04 it's "libc6-dev".  You'd 
need to run a command in the shell, something like:

Centos:
> sudo dnf install glibc-headers
or
> sudo yum install glibc-headers

Ubuntu/Debian:
> sudo apt install libc6-dev

If it's Windows or Mac, I can't help...

If you don't have root access on your host, or the above doesn't make sense 
to you, you will need to talk to whoever administers your computing 
environment, asking them to install the relevant package.

Hope this helps.

 - Gord


On 20210407, 11:03, "R-package-devel on behalf of rosario.avo...@unina.it" 
 
wrote:

Hi everyone,



I hope this is the right e-mail I should have used; this is the first 
time
that I ask for help with R!

Yesterday, I installed the devel version of R (4.1) as I need to use a
package (RiboDiPa) which only works for this version.

The package requires, among the others, the package "rtracklayer". Since
yesterday I am struggling trying to install rtracklayer for devel 
version
without success.

Below you can find the final message I got before the installation 
stops.
Any idea of what might be the reason why I cannot install rtracklayer? 



ucsc/udc.c:46:10: fatal error: sys/mman.h: No such file or directory

#include 

  ^~~~

compilation terminated.

make: *** 
[https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fMakevars.win%3a16=E,1,aB4mtmdcaXh3y_rFcDWiXKtEvYZoLA3GcTOtz2EAwNVyTaBV0cLYVfIMvPNYj-c9QK7LiaHqut3FcMfCLlVShgqSAdXj_xGXP8nS49zX7vVKE9rNPhmLmWDTnyU,=1:
 ucsc/udc.o] Error 1

ERROR: compilation failed for package 'rtracklayer'

* removing 'C:/Users/Rosario/Documents/R/win-library/4.1/rtracklayer'



If you need any other information please, do not hesitate to ask.

Thank you in advance for your help!



Best,

Rosario





Rosario Avolio, PhD

Researcher

Department of Molecular Medicine and Medical Biotechnology

Via Pansini, 5

19/A Building

80131 Napoli, Italy

email:  <mailto:rosario.avo...@unina.it> rosario.avo...@unina.it

phone: +39 081 746 31 39




[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] R package depends on Bioconductor packages RTIGER

[Rafael CM]

Dear all,
I am trying to submit a package to CRAN that depends on Bioconductor
packages. On debian, I do not have any problems so far. But when checking
for windows I get several errors:

Error: package or namespace load failed for 'Gviz' in loadNamespace(j
<- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'rtracklayer' 1.48.0 is already loaded, but >= 1.51.5 is required
Error: package 'Gviz' could not be loaded
In addition: Warning message:
multiple methods tables found for 'export'
Execution halted
ERROR: lazy loading failed for package 'RTIGER'
* removing 'd:/RCompile/CRANincoming/R-devel/lib/RTIGER'
* restoring previous 'd:/RCompile/CRANincoming/R-devel/lib/RTIGER'

Could someone help me?

Thank you very much,

Rafael

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] rtracklayer installation problems

[Gordon Brown]

Hi, Rosario,

The message is telling you that you need to install the development header 
files for glibc on your computer.  This is a set of files that are needed for 
building some kinds of software, but are not installed by default.  Are you 
working on some sort of Linux machine?  On Centos 8, the relevant package to 
install is called "glibc-headers".  On Ubuntu 20.04 it's "libc6-dev".  You'd 
need to run a command in the shell, something like:

Centos:
> sudo dnf install glibc-headers
or
> sudo yum install glibc-headers

Ubuntu/Debian:
> sudo apt install libc6-dev

If it's Windows or Mac, I can't help...

If you don't have root access on your host, or the above doesn't make sense to 
you, you will need to talk to whoever administers your computing environment, 
asking them to install the relevant package.

Hope this helps.

 - Gord


On 20210407, 11:03, "R-package-devel on behalf of rosario.avo...@unina.it" 
 
wrote:

Hi everyone,



I hope this is the right e-mail I should have used; this is the first time
that I ask for help with R!

Yesterday, I installed the devel version of R (4.1) as I need to use a
package (RiboDiPa) which only works for this version.

The package requires, among the others, the package "rtracklayer". Since
yesterday I am struggling trying to install rtracklayer for devel version
without success.

Below you can find the final message I got before the installation stops.
Any idea of what might be the reason why I cannot install rtracklayer? 



ucsc/udc.c:46:10: fatal error: sys/mman.h: No such file or directory

#include 

  ^~~~

compilation terminated.

make: *** 
[https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fMakevars.win%3a16=E,1,aB4mtmdcaXh3y_rFcDWiXKtEvYZoLA3GcTOtz2EAwNVyTaBV0cLYVfIMvPNYj-c9QK7LiaHqut3FcMfCLlVShgqSAdXj_xGXP8nS49zX7vVKE9rNPhmLmWDTnyU,=1:
 ucsc/udc.o] Error 1

ERROR: compilation failed for package 'rtracklayer'

* removing 'C:/Users/Rosario/Documents/R/win-library/4.1/rtracklayer'



If you need any other information please, do not hesitate to ask.

Thank you in advance for your help!



Best,

Rosario





Rosario Avolio, PhD

Researcher

Department of Molecular Medicine and Medical Biotechnology

Via Pansini, 5

19/A Building

80131 Napoli, Italy

email:  <mailto:rosario.avo...@unina.it> rosario.avo...@unina.it

phone: +39 081 746 31 39




[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] rtracklayer installation problems

[Duncan Murdoch]

On 07/04/2021 4:49 a.m., rosario.avo...@unina.it wrote:

Hi everyone,

  


I hope this is the right e-mail I should have used; this is the first time
that I ask for help with R!

Yesterday, I installed the devel version of R (4.1) as I need to use a
package (RiboDiPa) which only works for this version.

The package requires, among the others, the package "rtracklayer". Since
yesterday I am struggling trying to install rtracklayer for devel version
without success.

Below you can find the final message I got before the installation stops.
Any idea of what might be the reason why I cannot install rtracklayer?

  


ucsc/udc.c:46:10: fatal error: sys/mman.h: No such file or directory

#include 

   ^~~~

compilation terminated.

make: *** [Makevars.win:16: ucsc/udc.o] Error 1

ERROR: compilation failed for package 'rtracklayer'

* removing 'C:/Users/Rosario/Documents/R/win-library/4.1/rtracklayer'

  


If you need any other information please, do not hesitate to ask.

Thank you in advance for your help!


rtracklayer is a Bioconductor package, so you're probably better off 
asking on their support site https://support.bioconductor.org/.  When 
you do, please show the command you used for the install; it's possible 
a simple change there will fix things.


Duncan Murdoch

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] rtracklayer installation problems

[rosario.avolio]

Hi everyone,

 

I hope this is the right e-mail I should have used; this is the first time
that I ask for help with R!

Yesterday, I installed the devel version of R (4.1) as I need to use a
package (RiboDiPa) which only works for this version.

The package requires, among the others, the package "rtracklayer". Since
yesterday I am struggling trying to install rtracklayer for devel version
without success.

Below you can find the final message I got before the installation stops.
Any idea of what might be the reason why I cannot install rtracklayer? 

 

ucsc/udc.c:46:10: fatal error: sys/mman.h: No such file or directory

#include 

  ^~~~

compilation terminated.

make: *** [Makevars.win:16: ucsc/udc.o] Error 1

ERROR: compilation failed for package 'rtracklayer'

* removing 'C:/Users/Rosario/Documents/R/win-library/4.1/rtracklayer'

 

If you need any other information please, do not hesitate to ask.

Thank you in advance for your help!

 

Best,

Rosario

 

 

Rosario Avolio, PhD

Researcher

Department of Molecular Medicine and Medical Biotechnology

Via Pansini, 5

19/A Building

80131 Napoli, Italy

email:   rosario.avo...@unina.it

phone: +39 081 746 31 39

 


[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Package Rejection Error Help

[Uwe Ligges]

On 06.04.2021 19:26, Robert M. Flight wrote:

Andrew,

I think if you want to include a Bioconductor dependency, then I think you
add the "biocViews:" line to your description file to enable bioconductor


Not needed for CRAN.

You simply need to declare the dependency, but BioC 3.13 is what we 
should use to check with R-devel and that was recetnly still pretty 
iunstable.


Best,
Uwe Ligges


package installation.

See this answer on Bioinformatics stackexchange:
https://bioinformatics.stackexchange.com/a/3375/51

Hope that helps!

-Robert

On Tue, Apr 6, 2021 at 1:14 PM Andrew Dhawan  wrote:


Thank you both very kindly - I have addressed both notes. I am still
wondering though about the RankProd dependency error - any insight into
this?

Thanks!
Andrew

On Tue, Apr 6, 2021 at 11:58 AM Uwe Ligges <
lig...@statistik.tu-dortmund.de>
wrote:




On 06.04.2021 17:39, Patrick Giraudoux wrote:

I had a similar problem with intepreting "notes" in pgirmess checks.
Some are lethal and lead to rejection and some not (just informative
comments). Fortunately Uwe has been kind enough to tell me what I

missed

(I thought that all notes were just "informative").
Would it be possible to call lethal notes "errors" to keep us aware

that

we must really do something with them and fix what is actually a

problem?


These are Notes as it may not be a serious issue or may be a false
positive, nevertheless, we like to get clean packages to CRAN.

WARNINGs and ERRORs will never be accepted.

The policies clearly say that significant Notes have to be addressed.
The only Note that is always acceptable is the CRAN maintainer Note
about the package maintainer's address. All other Notes should be fixed
generally or need manual attention in case of the really very few
exceptions.

Best,
Uwe Ligges





Best,
Patrick


Le 06/04/2021 à 17:33, Uwe Ligges a écrit :

Two Notes:


Found the following (possibly) invalid URLs:
  URL: http://imagemagick.org/script/download.php (moved to
https://imagemagick.org/script/download.php)
From: inst/doc/vignette.html
Status: 200
Message: OK


Please change http --> https, add trailing slashes, or follow moved
content as appropriate.

* checking LazyData ... NOTE
  'LazyData' is specified without a 'data' directory

Simply omit the field if you have no data.

Best,
Uwe Ligges



On 06.04.2021 16:27, Andrew Dhawan wrote:

Dear all,

I am a bit puzzled by this error for the sigQC package being uploaded

to

CRAN. Checks on my end pass without issue. There is one error
regarding the
bioConductor dependency RankProd that comes up only on the Debian OS
when
checking. See here for further details:




https://win-builder.r-project.org/incoming_pretest/sigQC_0.1.22_20210406_110708/



I am not sure how to resolve this - it seems to me that the

dependency

*should* be available across platforms, and short of removing the
dependency (which we rely on a fair bit), I'm not sure what  we can

do.


Any thoughts or suggestions would be massively appreciated.

Thank you so kindly!
Andrew

 [[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel







 [[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Win-builder not finding binaries provided by LinkingTo: cargo?

[David Norris]

My DESCRIPTION has the same “SystemRequirements: …” line as salso—from which I 
probably copied it.

I had briefly reached out to ‘cargo’ author (who is also ‘salso’ author), who 
indicated I might need to supply binaries.
Indeed, on closer look, salso appears to include the binaries, rather than 
asking CRAN to do the build:
https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64-gcc10-UCRT/salso-00check.html

Thus, it seems ‘precautionary’ presents an opportunity to get Rust compilation 
working on Win-builder.
Rust is such a fine language that it would be a shame not to smooth this out 
for the community.

OTOH, crucial calculations in ‘precautionary’ parallelize so nicely with 
mclapply() that it would not be inappropriate to bypass (forkless) Win by 
setting OS_type to unix.

From: Kevin Ushey 
Date: Tuesday, April 6, 2021 at 6:41 PM
To: David Norris 
Cc: "r-package-devel@r-project.org" 
Subject: Re: [R-pkg-devel] Win-builder not finding binaries provided by 
LinkingTo: cargo?

I think this is the pertinent error:

make: cargo: Command not found

That is, make is assuming that the cargo utility is installed and
available on the PATH, but that doesn't appear to be true on the CRAN
winbuilder machine.

The salso package (https://cran.r-project.org/package=salso)
explicitly requires cargo to be already available, per
SystemRequirements:

SystemRequirements: Cargo (>= 1.42.0) for installation from sources:
see file INSTALL

so you probably need to do something similar. I'd also recommend
downloading the 'salso' package to see how they resolve this, or
contacting the 'salso' maintainer to see what steps they took to
ensure their package could build on CRAN.

Best,
Kevin

On Tue, Apr 6, 2021 at 12:10 PM David Norris
mailto:da...@precisionmethods.guru>> wrote:

For version 0.2-2 of my ‘precautionary’ package, I have added fast numerical 
routines implemented in Rust.
In my DESCRIPTION file, I am “LinkingTo: cargo (>= 0.1.28)”, but fail incoming 
check on Win-builder as follows:
https://win-builder.r-project.org/incoming_pretest/precautionary_0.2-2_20210406_142130/Windows/00install.out

* installing *source* package 'precautionary' ...
** using staged installation
** libs

*** arch - i386
rm -Rf precautionary.dll 
./rust/target/i686-pc-windows-gnu/release/libprecautionary.a entrypoint.o
d:/Compiler/rtools40/mingw32/bin/gcc  -I"D:/RCompile/recent/R/include" -DNDEBUG 
 -I'd:/RCompile/CRANpkg/lib/4.1/cargo/include'   
-I"d:/Compiler/gcc-4.9.3/local330/include" -pedantic -O2 -Wall  -std=gnu99 
-mfpmath=sse -msse2 -mstackrealign  -c entrypoint.c -o entrypoint.o
cargo build --target=i686-pc-windows-gnu --lib --release 
--manifest-path=./rust/Cargo.toml
make: cargo: Command not found
make: *** [Makevars.win:11: 
rust/target/-pc-windows-gnu/release/libprecautionary.a] Error 127
ERROR: compilation failed for package 'precautionary'
* removing 'd:/RCompile/CRANincoming/R-devel/lib/precautionary'

As I understand the intention of package cargo 
https://CRAN.R-project.org/package=cargo, it aims to solve precisely this 
problem.
Other platforms check my package just fine.
Is the solution to be found in configuration of Win-builder, in my 
Makevars.win, or elsewhere?
I have taken my Makevars.win straight from 
https://github.com/extendr/helloextendr/blob/main/src/Makevars.win as follows:


TARGET = $(subst 64,x86_64,$(subst 32,i686,$(WIN)))-pc-windows-gnu

LIBDIR = ./rust/target/$(TARGET)/release

STATLIB = $(LIBDIR)/libprecautionary.a

PKG_LIBS = -L$(LIBDIR) -lprecautionary -lws2_32 -ladvapi32 -luserenv



all: C_clean



$(SHLIB): $(STATLIB)



$(STATLIB):

 cargo build --target=$(TARGET) --lib --release 
--manifest-path=./rust/Cargo.toml



C_clean:

 rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)



clean:

 rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) rust/target


 [[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel


[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel