Re: [Bioc-devel] get_dcf_info failed and build intervals

[Shraddha Pai]

Hi,
Sounds good- that's something I haven't run. I ran R CMD check after adding
the .Rcheck file with BioC flags but this sounds different.
But will look up how to run this.
Thanks, Herve.
Shraddha

On Fri, Jun 14, 2019 at 8:02 PM Pages, Herve  wrote:

> Sounds good. Also don't forget to run 'R CMD BiocCheck' on the source
> tarball of the package. Right now it reports a lot of problems:
>
>hpages@spectre:~$ R CMD BiocCheck netDx_0.99.0.tar.gz
>...
>Summary:
>ERROR count: 3
>WARNING count: 7
>NOTE count: 12
>
> Once everything is ready, don't forget to bump the version in order to
> trigger a new build by the Single Package Builder. Thanks!
>
> H.
>
>
> On 6/14/19 16:43, Shraddha Pai wrote:
> > Hi,
> > Ok thank you.
> > I should probably comment out some time-consuming steps in the vignettes
> > and just include the output in the companion data set, read those in.
> >
> > Thanks, will do that before next push to master.
> >
> > Best S
> >
> >
> > On Fri, Jun 14, 2019 at 7:37 PM Pages, Herve  > > wrote:
> >
> > On 6/14/19 15:58, Shraddha Pai wrote:
> >  > Hi,
> >  >
> >  > Thanks Herve. I have actually spent weeks making sure my packages
> > passed
> >  > check and build following guidelines. So I am actually doing my
> > best and
> >  > your snarky remark is not appreciated.
> >
> > OK maybe. But please note that our guidelines say that your package
> > should pass 'R CMD check' in less than 10 min. However in your case
> it
> > takes more than 20 min (on my laptop). This is the kind of problems
> that
> > should preferably be addressed before submission.
> >
> > Best,
> > H.
> >
> >  >
> >  > Then at the very end I expanded the DESCRIPTION file by putting
> > in line
> >  > breaks in the "description" field, which caused the build to
> > fail. My bad.
> >  >
> >  > Thank you for the feedback, I'm running the build on my machine
> > to make
> >  > sure there are no more trivial errors.
> >  >
> >  > Regards
> >  > Shraddha
> >  >
> >  > On Fri, Jun 14, 2019 at 6:35 PM Pages, Herve
> > mailto:hpa...@fredhutch.org>
> >  > >>
> wrote:
> >  >
> >  > Hi,
> >  >
> >  >   From the Linux command line:
> >  >
> >  > git clone https://github.com/BaderLab/netDx
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BaderLab_netDx=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n8w1wItMGynoMpsXdHLiOPNHxuSHWWql2FMAMaO7eXg=aCROvS-56IJNzoIZ2qid1WZLnCWMmaYHHUNphj522qc=
> >
> >  >
> >   <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BaderLab_netDx=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=o0CBZ3WzxQoXDkcx7BM5F01_54FXHluV0h8gFJ4rc_U=N-wWucRAP3w50kMnauxprPR4FvgiTQFJoMni50lmiIY=
> >
> >  >
> >  > R CMD INSTALL netDx
> >  > * installing to library
> ‘/home/hpages/R/R-3.6.r76454/library’
> >  > Error: error reading file
> > '/home/hpages/sandbox/netDx/DESCRIPTION'
> >  >
> >  > R CMD build netDx
> >  > * checking for file ‘netDx/DESCRIPTION’ ...Error : file
> >  > '/home/hpages/sandbox/netDx/DESCRIPTION' is not in valid DCF
> > format
> >  >  EXISTS but not correct format
> >  >
> >  >   From R:
> >  >
> >  > library(devtools)
> >  > remotes::install_github("BaderLab/netDx")
> >  > # Error in read.dcf(path) :
> >  > #   Line starting 'The method converts  ...' is malformed!
> >  >
> >  > How about making sure that your package is valid before
> > submitting?
> >  >
> >  > H.
> >  >
> >  > On 6/14/19 15:14, Shraddha Pai wrote:
> >  >  > Hello BioC dev community,
> >  >  >
> >  >  > I just submitted a package to BioC.
> >  >  >
> >  >  > 1) The automatic build gave it an "ABNORMAL" status with
> the
> >  > following
> >  >  > error " Accessing git_info complete. get_dcf_info failed;
> > could
> >  > not open."
> >  >  >
> >  >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1149=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA=
> >  >  > I've Googled a bit and cannot find the solution for what
> this
> >  > error means
> >  >  > and how to address it. Can someone please help me?
> >  >  >
> >  >  > 2) The package above was an AdditionalPackage to a
> companion
> >  > dataset. The
> >  >  > first build on the initial dataset package resulted in an
> > error.

Re: [Rd] Halfway through writing an "IDE" with support for R; Proof of concept, and request for suggestions.

[Abby Spurdle]

> What about Atom, VS Code and the like? Or what about taking a project
> that meets most of the constraints and pushing to cover all of them,
> or even forking it and modifying the part you don't like?

I'm not prepared to endorse GitHub affiliated software.

[[alternative HTML version deleted]]

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Re: [Bioc-devel] get_dcf_info failed and build intervals

[Pages, Herve]

Sounds good. Also don't forget to run 'R CMD BiocCheck' on the source
tarball of the package. Right now it reports a lot of problems:

   hpages@spectre:~$ R CMD BiocCheck netDx_0.99.0.tar.gz
   ...
   Summary:
   ERROR count: 3
   WARNING count: 7
   NOTE count: 12

Once everything is ready, don't forget to bump the version in order to
trigger a new build by the Single Package Builder. Thanks!

H.


On 6/14/19 16:43, Shraddha Pai wrote:
> Hi,
> Ok thank you.
> I should probably comment out some time-consuming steps in the vignettes 
> and just include the output in the companion data set, read those in.
> 
> Thanks, will do that before next push to master.
> 
> Best S
> 
> 
> On Fri, Jun 14, 2019 at 7:37 PM Pages, Herve  > wrote:
> 
> On 6/14/19 15:58, Shraddha Pai wrote:
>  > Hi,
>  >
>  > Thanks Herve. I have actually spent weeks making sure my packages
> passed
>  > check and build following guidelines. So I am actually doing my
> best and
>  > your snarky remark is not appreciated.
> 
> OK maybe. But please note that our guidelines say that your package
> should pass 'R CMD check' in less than 10 min. However in your case it
> takes more than 20 min (on my laptop). This is the kind of problems that
> should preferably be addressed before submission.
> 
> Best,
> H.
> 
>  >
>  > Then at the very end I expanded the DESCRIPTION file by putting
> in line
>  > breaks in the "description" field, which caused the build to
> fail. My bad.
>  >
>  > Thank you for the feedback, I'm running the build on my machine
> to make
>  > sure there are no more trivial errors.
>  >
>  > Regards
>  > Shraddha
>  >
>  > On Fri, Jun 14, 2019 at 6:35 PM Pages, Herve
> mailto:hpa...@fredhutch.org>
>  > >> wrote:
>  >
>  >     Hi,
>  >
>  >       From the Linux command line:
>  >
>  >         git clone https://github.com/BaderLab/netDx
> 
> 
>  >   
>   
> 
>  >
>  >         R CMD INSTALL netDx
>  >         * installing to library ‘/home/hpages/R/R-3.6.r76454/library’
>  >         Error: error reading file
> '/home/hpages/sandbox/netDx/DESCRIPTION'
>  >
>  >         R CMD build netDx
>  >         * checking for file ‘netDx/DESCRIPTION’ ...Error : file
>  >     '/home/hpages/sandbox/netDx/DESCRIPTION' is not in valid DCF
> format
>  >          EXISTS but not correct format
>  >
>  >       From R:
>  >
>  >         library(devtools)
>  >         remotes::install_github("BaderLab/netDx")
>  >         # Error in read.dcf(path) :
>  >         #   Line starting 'The method converts  ...' is malformed!
>  >
>  >     How about making sure that your package is valid before
> submitting?
>  >
>  >     H.
>  >
>  >     On 6/14/19 15:14, Shraddha Pai wrote:
>  >      > Hello BioC dev community,
>  >      >
>  >      > I just submitted a package to BioC.
>  >      >
>  >      > 1) The automatic build gave it an "ABNORMAL" status with the
>  >     following
>  >      > error " Accessing git_info complete. get_dcf_info failed;
> could
>  >     not open."
>  >      >
>  >
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1149=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA=
>  >      > I've Googled a bit and cannot find the solution for what this
>  >     error means
>  >      > and how to address it. Can someone please help me?
>  >      >
>  >      > 2) The package above was an AdditionalPackage to a companion
>  >     dataset. The
>  >      > first build on the initial dataset package resulted in an
> error.
>  >     I address
>  >      > the error and pushed a git commit 2-3 hours ago, but
> haven't seen
>  >     a second
>  >      > build attempt in response to that push. How often are builds
>  >     triggered?
>  >      > Obviously it would be great to do a series of builds and fix
>  >     errors in a
>  >      > short span of time.
>  >      >
>  >      > 3) Also how can I search the bioc-devel mailing list?
>  >      > I only see 

Re: [Bioc-devel] get_dcf_info failed and build intervals

[Shraddha Pai]

Hi,
Ok thank you.
I should probably comment out some time-consuming steps in the vignettes
and just include the output in the companion data set, read those in.

Thanks, will do that before next push to master.

Best S


On Fri, Jun 14, 2019 at 7:37 PM Pages, Herve  wrote:

> On 6/14/19 15:58, Shraddha Pai wrote:
> > Hi,
> >
> > Thanks Herve. I have actually spent weeks making sure my packages passed
> > check and build following guidelines. So I am actually doing my best and
> > your snarky remark is not appreciated.
>
> OK maybe. But please note that our guidelines say that your package
> should pass 'R CMD check' in less than 10 min. However in your case it
> takes more than 20 min (on my laptop). This is the kind of problems that
> should preferably be addressed before submission.
>
> Best,
> H.
>
> >
> > Then at the very end I expanded the DESCRIPTION file by putting in line
> > breaks in the "description" field, which caused the build to fail. My
> bad.
> >
> > Thank you for the feedback, I'm running the build on my machine to make
> > sure there are no more trivial errors.
> >
> > Regards
> > Shraddha
> >
> > On Fri, Jun 14, 2019 at 6:35 PM Pages, Herve  > > wrote:
> >
> > Hi,
> >
> >   From the Linux command line:
> >
> > git clone https://github.com/BaderLab/netDx
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BaderLab_netDx=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=o0CBZ3WzxQoXDkcx7BM5F01_54FXHluV0h8gFJ4rc_U=N-wWucRAP3w50kMnauxprPR4FvgiTQFJoMni50lmiIY=
> >
> >
> > R CMD INSTALL netDx
> > * installing to library ‘/home/hpages/R/R-3.6.r76454/library’
> > Error: error reading file
> '/home/hpages/sandbox/netDx/DESCRIPTION'
> >
> > R CMD build netDx
> > * checking for file ‘netDx/DESCRIPTION’ ...Error : file
> > '/home/hpages/sandbox/netDx/DESCRIPTION' is not in valid DCF format
> >  EXISTS but not correct format
> >
> >   From R:
> >
> > library(devtools)
> > remotes::install_github("BaderLab/netDx")
> > # Error in read.dcf(path) :
> > #   Line starting 'The method converts  ...' is malformed!
> >
> > How about making sure that your package is valid before submitting?
> >
> > H.
> >
> > On 6/14/19 15:14, Shraddha Pai wrote:
> >  > Hello BioC dev community,
> >  >
> >  > I just submitted a package to BioC.
> >  >
> >  > 1) The automatic build gave it an "ABNORMAL" status with the
> > following
> >  > error " Accessing git_info complete. get_dcf_info failed; could
> > not open."
> >  >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1149=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA=
> >  > I've Googled a bit and cannot find the solution for what this
> > error means
> >  > and how to address it. Can someone please help me?
> >  >
> >  > 2) The package above was an AdditionalPackage to a companion
> > dataset. The
> >  > first build on the initial dataset package resulted in an error.
> > I address
> >  > the error and pushed a git commit 2-3 hours ago, but haven't seen
> > a second
> >  > build attempt in response to that push. How often are builds
> > triggered?
> >  > Obviously it would be great to do a series of builds and fix
> > errors in a
> >  > short span of time.
> >  >
> >  > 3) Also how can I search the bioc-devel mailing list?
> >  > I only see this archive page:
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=sibCeuRBHi9h8oxdW9Wh6HJcxADJ7XxRY7CdSDhXgI4=
> >  > My apologies if these are trivial questions.
> >  >
> >  > Thanks very much,
> >  > Shraddha
> >  >
> >
> > --
> > Hervé Pagès
> >
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
> >
> > E-mail: hpa...@fredhutch.org 
> > Phone:  (206) 667-5791
> > Fax:(206) 667-1319
> >
> > --
> > Shraddha Pai
> > Post-doctoral Fellow, http://baderlab.org
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__baderlab.org=DwMFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=o0CBZ3WzxQoXDkcx7BM5F01_54FXHluV0h8gFJ4rc_U=ektyUHYcdy2ZKNVyyJ1_LPdse92aiigZr59mL_yPgMo=
> >
> > The Donnelly Center, University of Toronto
> > @spaiglass on Twitter
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred 

Re: [Rd] Halfway through writing an "IDE" with support for R; Proof of concept, and request for suggestions.

[Iñaki Ucar]

On Sat, 15 Jun 2019 at 01:24, Abby Spurdle  wrote:
>
> None of the tools that I've looked at satisfy these constraints.
> But if you know of some, I'd like to know... And I would consider 
> contributing...

What about Atom, VS Code and the like? Or what about taking a project
that meets most of the constraints and pushing to cover all of them,
or even forking it and modifying the part you don't like?

Iñaki

__
R-devel@r-project.org mailing list
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Re: [Bioc-devel] get_dcf_info failed and build intervals

[Pages, Herve]

On 6/14/19 15:58, Shraddha Pai wrote:
> Hi,
> 
> Thanks Herve. I have actually spent weeks making sure my packages passed 
> check and build following guidelines. So I am actually doing my best and 
> your snarky remark is not appreciated.

OK maybe. But please note that our guidelines say that your package
should pass 'R CMD check' in less than 10 min. However in your case it
takes more than 20 min (on my laptop). This is the kind of problems that
should preferably be addressed before submission.

Best,
H.

> 
> Then at the very end I expanded the DESCRIPTION file by putting in line 
> breaks in the "description" field, which caused the build to fail. My bad.
> 
> Thank you for the feedback, I'm running the build on my machine to make 
> sure there are no more trivial errors.
> 
> Regards
> Shraddha
> 
> On Fri, Jun 14, 2019 at 6:35 PM Pages, Herve  > wrote:
> 
> Hi,
> 
>   From the Linux command line:
> 
>     git clone https://github.com/BaderLab/netDx
> 
> 
> 
>     R CMD INSTALL netDx
>     * installing to library ‘/home/hpages/R/R-3.6.r76454/library’
>     Error: error reading file '/home/hpages/sandbox/netDx/DESCRIPTION'
> 
>     R CMD build netDx
>     * checking for file ‘netDx/DESCRIPTION’ ...Error : file
> '/home/hpages/sandbox/netDx/DESCRIPTION' is not in valid DCF format
>      EXISTS but not correct format
> 
>   From R:
> 
>     library(devtools)
>     remotes::install_github("BaderLab/netDx")
>     # Error in read.dcf(path) :
>     #   Line starting 'The method converts  ...' is malformed!
> 
> How about making sure that your package is valid before submitting?
> 
> H.
> 
> On 6/14/19 15:14, Shraddha Pai wrote:
>  > Hello BioC dev community,
>  >
>  > I just submitted a package to BioC.
>  >
>  > 1) The automatic build gave it an "ABNORMAL" status with the
> following
>  > error " Accessing git_info complete. get_dcf_info failed; could
> not open."
>  >
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1149=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA=
>  > I've Googled a bit and cannot find the solution for what this
> error means
>  > and how to address it. Can someone please help me?
>  >
>  > 2) The package above was an AdditionalPackage to a companion
> dataset. The
>  > first build on the initial dataset package resulted in an error.
> I address
>  > the error and pushed a git commit 2-3 hours ago, but haven't seen
> a second
>  > build attempt in response to that push. How often are builds
> triggered?
>  > Obviously it would be great to do a series of builds and fix
> errors in a
>  > short span of time.
>  >
>  > 3) Also how can I search the bioc-devel mailing list?
>  > I only see this archive page:
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=sibCeuRBHi9h8oxdW9Wh6HJcxADJ7XxRY7CdSDhXgI4=
>  > My apologies if these are trivial questions.
>  >
>  > Thanks very much,
>  > Shraddha
>  >
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org 
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 
> -- 
> Shraddha Pai
> Post-doctoral Fellow, http://baderlab.org 
> 
> The Donnelly Center, University of Toronto
> @spaiglass on Twitter

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
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Re: [Rd] Halfway through writing an "IDE" with support for R; Proof of concept, and request for suggestions.

[Abby Spurdle]

On Fri, Jun 14, 2019 at 7:24 PM Iñaki Ucar  wrote:
>
> There are many similar projects that are mature

I'm not sure what projects you're referring to.

If we create some constraints:

(1) Internal systems consoles (*plural*).
Rules out most things.
Noting that many tools are designed to bypass the console.

(2) Modern user interface.
Rules out Vim and Emacs.

(3) File system based rather than (IDE-dependent) project based.
Rules out Eclipse and many other IDEs.

(4) Multi-language focus.
Rules out RStudio and many other IDEs.

(5) Completely open source and completely free.
Also rules out RStudio, which limites many features to it's enterprise
edition.

(6) Cross platform desktop application, not web based.
(However, there is a need for web based tools).

None of the tools that I've looked at satisfy these constraints.
But if you know of some, I'd like to know... And I would consider
contributing...

[[alternative HTML version deleted]]

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Re: [Bioc-devel] get_dcf_info failed and build intervals

[Shraddha Pai]

Hi,

Thanks Herve. I have actually spent weeks making sure my packages passed
check and build following guidelines. So I am actually doing my best and
your snarky remark is not appreciated.

Then at the very end I expanded the DESCRIPTION file by putting in line
breaks in the "description" field, which caused the build to fail. My bad.

Thank you for the feedback, I'm running the build on my machine to make
sure there are no more trivial errors.

Regards
Shraddha

On Fri, Jun 14, 2019 at 6:35 PM Pages, Herve  wrote:

> Hi,
>
>  From the Linux command line:
>
>git clone https://github.com/BaderLab/netDx
>
>R CMD INSTALL netDx
>* installing to library ‘/home/hpages/R/R-3.6.r76454/library’
>Error: error reading file '/home/hpages/sandbox/netDx/DESCRIPTION'
>
>R CMD build netDx
>* checking for file ‘netDx/DESCRIPTION’ ...Error : file
> '/home/hpages/sandbox/netDx/DESCRIPTION' is not in valid DCF format
> EXISTS but not correct format
>
>  From R:
>
>library(devtools)
>remotes::install_github("BaderLab/netDx")
># Error in read.dcf(path) :
>#   Line starting 'The method converts  ...' is malformed!
>
> How about making sure that your package is valid before submitting?
>
> H.
>
> On 6/14/19 15:14, Shraddha Pai wrote:
> > Hello BioC dev community,
> >
> > I just submitted a package to BioC.
> >
> > 1) The automatic build gave it an "ABNORMAL" status with the following
> > error " Accessing git_info complete. get_dcf_info failed; could not
> open."
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1149=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA=
> > I've Googled a bit and cannot find the solution for what this error means
> > and how to address it. Can someone please help me?
> >
> > 2) The package above was an AdditionalPackage to a companion dataset. The
> > first build on the initial dataset package resulted in an error. I
> address
> > the error and pushed a git commit 2-3 hours ago, but haven't seen a
> second
> > build attempt in response to that push. How often are builds triggered?
> > Obviously it would be great to do a series of builds and fix errors in a
> > short span of time.
> >
> > 3) Also how can I search the bioc-devel mailing list?
> > I only see this archive page:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=sibCeuRBHi9h8oxdW9Wh6HJcxADJ7XxRY7CdSDhXgI4=
> > My apologies if these are trivial questions.
> >
> > Thanks very much,
> > Shraddha
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
-- 
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
@spaiglass on Twitter

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Re: [Bioc-devel] get_dcf_info failed and build intervals

[Pages, Herve]

Hi,

 From the Linux command line:

   git clone https://github.com/BaderLab/netDx

   R CMD INSTALL netDx
   * installing to library ‘/home/hpages/R/R-3.6.r76454/library’
   Error: error reading file '/home/hpages/sandbox/netDx/DESCRIPTION'

   R CMD build netDx
   * checking for file ‘netDx/DESCRIPTION’ ...Error : file 
'/home/hpages/sandbox/netDx/DESCRIPTION' is not in valid DCF format
EXISTS but not correct format

 From R:

   library(devtools)
   remotes::install_github("BaderLab/netDx")
   # Error in read.dcf(path) :
   #   Line starting 'The method converts  ...' is malformed!

How about making sure that your package is valid before submitting?

H.

On 6/14/19 15:14, Shraddha Pai wrote:
> Hello BioC dev community,
> 
> I just submitted a package to BioC.
> 
> 1) The automatic build gave it an "ABNORMAL" status with the following
> error " Accessing git_info complete. get_dcf_info failed; could not open."
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_1149=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA=
> I've Googled a bit and cannot find the solution for what this error means
> and how to address it. Can someone please help me?
> 
> 2) The package above was an AdditionalPackage to a companion dataset. The
> first build on the initial dataset package resulted in an error. I address
> the error and pushed a git commit 2-3 hours ago, but haven't seen a second
> build attempt in response to that push. How often are builds triggered?
> Obviously it would be great to do a series of builds and fix errors in a
> short span of time.
> 
> 3) Also how can I search the bioc-devel mailing list?
> I only see this archive page: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0=sibCeuRBHi9h8oxdW9Wh6HJcxADJ7XxRY7CdSDhXgI4=
> My apologies if these are trivial questions.
> 
> Thanks very much,
> Shraddha
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
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[Bioc-devel] get_dcf_info failed and build intervals

[Shraddha Pai]

Hello BioC dev community,

I just submitted a package to BioC.

1) The automatic build gave it an "ABNORMAL" status with the following
error " Accessing git_info complete. get_dcf_info failed; could not open."
https://github.com/Bioconductor/Contributions/issues/1149
I've Googled a bit and cannot find the solution for what this error means
and how to address it. Can someone please help me?

2) The package above was an AdditionalPackage to a companion dataset. The
first build on the initial dataset package resulted in an error. I address
the error and pushed a git commit 2-3 hours ago, but haven't seen a second
build attempt in response to that push. How often are builds triggered?
Obviously it would be great to do a series of builds and fix errors in a
short span of time.

3) Also how can I search the bioc-devel mailing list?
I only see this archive page: https://stat.ethz.ch/pipermail/bioc-devel/
My apologies if these are trivial questions.

Thanks very much,
Shraddha

-- 
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
@spaiglass on Twitter

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Re: [Rd] inappropriate warning in latticeExtra

[Richard M. Heiberger]

Yes. You identified it a while ago and Deepayan wrote that he fixed it on
r-forge a year ago.  It still isn't on cran.

On Fri, Jun 14, 2019 at 16:04 Duncan Murdoch 
wrote:

> On 14/06/2019 9:12 a.m., Richard M. Heiberger wrote:
> > This is still not repaired in
> >   R version 3.6.0 Patched (2019-05-17 r76528)
> >> library(latticeExtra)
> >>   a <- xyplot(1 ~ 1)
> >> c(a,a)
> > Warning message:
> > In formals(fun) : argument is not a function
> >
> > Can we have it in R-3.6.1 that Peter just announced?
>
> That looks like a bug in the latticeExtra package, not in base R.  In
> particular, the latticeExtra:::c.trellis function appears to be trying
> to take the formals of NULL, and that's why you get the warning.
>
> Duncan Murdoch
>
> >
> > Rich
> >
> > On Mon, Apr 2, 2018 at 4:08 AM Deepayan Sarkar
> >  wrote:
> >>
> >> On Fri, Mar 23, 2018 at 7:58 AM, Richard M. Heiberger 
> wrote:
> >>> The warning message in the last line of this email is incorrect.
> >>> This is behavior which Duncan Murdoch labeled a bug in
> >>> https://stat.ethz.ch/pipermail/r-help/2017-December/450494.html
> >>
> >> Yes, sorry, this has been fixed in the r-forge sources for a while
> >> now, but I haven't had the time to finish up some other fixes and push
> >> an update to CRAN.
> >>
> >> Hopefully over the summer break.
> >>
> >> Regards,
> >> -Deepayan
> >>
> >>
> >>> This is a fresh install of R-devel (2018-03-21 r74436)
> >>>
> >>>
> >>>
> >>>
> >>> R Under development (unstable) (2018-03-21 r74436) -- "Unsuffered
> Consequences"
> >>> Copyright (C) 2018 The R Foundation for Statistical Computing
> >>> Platform: x86_64-w64-mingw32/x64 (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.
> >>>
>  library(latticeExtra)
> >>> Error in library(latticeExtra) :
> >>>there is no package called ‘latticeExtra’
>  install.packages("latticeExtra")
> >>> Warning in install.packages("latticeExtra") :
> >>>'lib = "C:/Program Files/R/R-devel/library"' is not writable
> >>> --- Please select a CRAN mirror for use in this session ---
> >>> also installing the dependency ‘RColorBrewer’
> >>>
> >>> Warning: unable to access index for repository
> >>> http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.5:
> >>>cannot open URL
> >>> 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.5/PACKAGES'
> >>> trying URL '
> https://cran.wu.ac.at/bin/windows/contrib/3.5/RColorBrewer_1.1-2.zip'
> >>> Content type 'application/zip' length 55444 bytes (54 KB)
> >>> downloaded 54 KB
> >>>
> >>> trying URL '
> https://cran.wu.ac.at/bin/windows/contrib/3.5/latticeExtra_0.6-28.zip'
> >>> Content type 'application/zip' length 2191524 bytes (2.1 MB)
> >>> downloaded 2.1 MB
> >>>
> >>> package ‘RColorBrewer’ successfully unpacked and MD5 sums checked
> >>> package ‘latticeExtra’ successfully unpacked and MD5 sums checked
> >>>
> >>> The downloaded binary packages are in
> >>>
> C:\Users\rmh.DESKTOP-60G4CCO\AppData\Local\Temp\RtmpqA7Rqg\downloaded_packages
>  library(latticeExtra)
> >>> Loading required package: lattice
> >>> Loading required package: RColorBrewer
>  a <- xyplot(1 ~ 1)
>  c(a,a)
> >>> Warning message:
> >>> In formals(fun) : argument is not a function
> 
> >>>
> >>> __
> >>> R-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
>

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Re: [Rd] inappropriate warning in latticeExtra

[Duncan Murdoch]

On 14/06/2019 9:12 a.m., Richard M. Heiberger wrote:

This is still not repaired in
  R version 3.6.0 Patched (2019-05-17 r76528)

library(latticeExtra)
  a <- xyplot(1 ~ 1)
c(a,a)

Warning message:
In formals(fun) : argument is not a function

Can we have it in R-3.6.1 that Peter just announced?


That looks like a bug in the latticeExtra package, not in base R.  In 
particular, the latticeExtra:::c.trellis function appears to be trying 
to take the formals of NULL, and that's why you get the warning.


Duncan Murdoch



Rich

On Mon, Apr 2, 2018 at 4:08 AM Deepayan Sarkar
 wrote:


On Fri, Mar 23, 2018 at 7:58 AM, Richard M. Heiberger  wrote:

The warning message in the last line of this email is incorrect.
This is behavior which Duncan Murdoch labeled a bug in
https://stat.ethz.ch/pipermail/r-help/2017-December/450494.html


Yes, sorry, this has been fixed in the r-forge sources for a while
now, but I haven't had the time to finish up some other fixes and push
an update to CRAN.

Hopefully over the summer break.

Regards,
-Deepayan



This is a fresh install of R-devel (2018-03-21 r74436)




R Under development (unstable) (2018-03-21 r74436) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.


library(latticeExtra)

Error in library(latticeExtra) :
   there is no package called ‘latticeExtra’

install.packages("latticeExtra")

Warning in install.packages("latticeExtra") :
   'lib = "C:/Program Files/R/R-devel/library"' is not writable
--- Please select a CRAN mirror for use in this session ---
also installing the dependency ‘RColorBrewer’

Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.5:
   cannot open URL
'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.5/PACKAGES'
trying URL 
'https://cran.wu.ac.at/bin/windows/contrib/3.5/RColorBrewer_1.1-2.zip'
Content type 'application/zip' length 55444 bytes (54 KB)
downloaded 54 KB

trying URL 
'https://cran.wu.ac.at/bin/windows/contrib/3.5/latticeExtra_0.6-28.zip'
Content type 'application/zip' length 2191524 bytes (2.1 MB)
downloaded 2.1 MB

package ‘RColorBrewer’ successfully unpacked and MD5 sums checked
package ‘latticeExtra’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
 
C:\Users\rmh.DESKTOP-60G4CCO\AppData\Local\Temp\RtmpqA7Rqg\downloaded_packages

library(latticeExtra)

Loading required package: lattice
Loading required package: RColorBrewer

a <- xyplot(1 ~ 1)
c(a,a)

Warning message:
In formals(fun) : argument is not a function




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Re: [Bioc-devel] updating package

[Turaga, Nitesh]

Hi,

It seems like the email is configured correctly on BiocCredentials app. It is 
because the account is not activated it doesn't work. You'd have to first 
activate your account before moving forward with setting a password.

I've added your GitHub credentials to the account. 

Best,

Nitesh 

> On Jun 14, 2019, at 11:01 AM, ostro...@mskcc.org wrote:
> 
> 
> Hi,
> I'd like to update my package Clonality 
> https://bioconductor.org/packages/release/bioc/html/Clonality.html
> I used to do it through svn but as I understand it's not possible now.
> 
> I can't connect it to my git page with updated package 
> https://github.com/IOstrovnaya/Clonality
> 
> When I enter my email  ostro...@mskcc.org here  
> https://git.bioconductor.org/BiocCredentials/account_activation/ I can't 
> login and resetting the password doesn't work.
> 
> Can you please help me establish my account on bioconductor and connect it to 
> my github?
> 
> Thank you!!!
> Irina
> 
> =
> 
> Please note that this e-mail and any files transmitted from
> Memorial Sloan Kettering Cancer Center may be privileged, confidential,
> and protected from disclosure under applicable law. If the reader of
> this message is not the intended recipient, or an employee or agent
> responsible for delivering this message to the intended recipient,
> you are hereby notified that any reading, dissemination, distribution,
> copying, or other use of this communication or any of its attachments
> is strictly prohibited.  If you have received this communication in
> error, please notify the sender immediately by replying to this message
> and deleting this message, any attachments, and all copies and backups
> from your computer.
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] updating package

[ostrovni]

Hi,
I'd like to update my package Clonality 
https://bioconductor.org/packages/release/bioc/html/Clonality.html
I used to do it through svn but as I understand it's not possible now.

I can't connect it to my git page with updated package 
https://github.com/IOstrovnaya/Clonality

When I enter my email  ostro...@mskcc.org here  
https://git.bioconductor.org/BiocCredentials/account_activation/ I can't login 
and resetting the password doesn't work.

Can you please help me establish my account on bioconductor and connect it to 
my github?

Thank you!!!
Irina

=

 Please note that this e-mail and any files transmitted from
 Memorial Sloan Kettering Cancer Center may be privileged, confidential,
 and protected from disclosure under applicable law. If the reader of
 this message is not the intended recipient, or an employee or agent
 responsible for delivering this message to the intended recipient,
 you are hereby notified that any reading, dissemination, distribution,
 copying, or other use of this communication or any of its attachments
 is strictly prohibited.  If you have received this communication in
 error, please notify the sender immediately by replying to this message
 and deleting this message, any attachments, and all copies and backups
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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Shepherd, Lori]

Thank you. We will investigate further and let you know when we have a solution 
on our end.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Jianhong Ou, Ph.D. 
Sent: Friday, June 14, 2019 9:57:47 AM
To: Shepherd, Lori; Michael Lawrence via Bioc-devel
Subject: Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

It looks like for arch'x64', there is no package org.Hs.eg.db.

Following is the whole error message:

** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
 user system elapsed
trackViewer-package 22.44   0.07   24.88
viewTracks  13.97   0.02   14.84
parseWIG12.81   0.00   12.94
browseTracks12.04   0.00   12.69
geneModelFromTxdb7.30   0.319.28
viewGene 5.15   0.115.26
** running examples for arch 'x64' ... ERROR
Running examples in 'trackViewer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trackViewer-package
> ### Title: Minimal designed plotting tool for genomic data
> ### Aliases: trackViewer trackViewer-package
>
> ### ** Examples
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(org.Hs.eg.db)
Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'
Execution halted



On 6/14/19, 9:31 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D." 
 wrote:

It is for a long time. Since last development version (BioC 3.9).

Jianhong.

From: "Shepherd, Lori" 
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via 
Bioc-devel 
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10


How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with 
no issues.   Let's wait and see if it clears up on todays build report.  If not 
we will investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong 
Ou, Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


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Re: [R-pkg-devel] [External] Re: try() in R CMD check --as-cran

[Tomas Kalibera]

The advantage of "abort" (R_Suicide) over the default (R error) is that 
it cannot be caught accidentally, so that one can detect more errors, 
and it may be easier to find where the error happened. To make the 
default behavior less surprising/more user friendly, and to allow 
intentional catching of these errors, the default for R CMD check 
--as-cran was changed in R-devel so that the normal R error is thrown, 
and the documentation in R Internals updated accordingly. One thus has 
to set the variable explicitly to get the stricter checks.


Best
Tomas

On 6/7/19 8:51 PM, Tierney, Luke wrote:

A simplified version without a package:

Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_"="abort,verbose")
tryCatch(1:3 || 1, error = identity)

Running this aborts the session since it calls R_Suicide without first
signaling a condition to try any available handlers. Should be easy to
change, but I don't know if there are any downsides for the CRAN
workflow. I'll look into it.

Best,

luke


On Fri, 7 Jun 2019, William Dunlap wrote:


I've attached a package, ppp_0.1.tar.gz, which probably will not get
through to R-help, that illustrates this.
It contains one function which, by default, triggers a condition-length>1
issue:
   f <- function(x = 1:3)
   {
   if (x > 1) {
   x <- -x
   }
   stop("this function always gives an error")
   }
and the help file example is
   try(f())

Then
   env _R_CHECK_LENGTH_1_CONDITION_=abort,verbose R-3.6.0 CMD check
--as-cran ppp_0.1.tar.gz
results in
* checking examples ... ERROR
Running examples in ‘ppp-Ex.R’ failed
The error most likely occurred in:


base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: f
### Title: Cause an error
### Aliases: f
### Keywords: error

### ** Examples

try(f())

--- FAILURE REPORT --
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
ppp
--- call from context ---
f()
--- call from argument ---
if (x > 1) {
x <- -x
}
--- R stacktrace ---
where 1: f()
where 2: doTryCatch(return(expr), name, parentenv, handler)
where 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 4: tryCatchList(expr, classes, parentenv, handlers)
where 5: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
sm <- strsplit(conditionMessage(e), "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n  ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && isTRUE(getOption("show.error.messages"))) {
cat(msg, file = outFile)
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
where 6: try(f())

--- value of length: 3 type: logical ---
[1] FALSE  TRUE  TRUE
--- function from context ---
function (x = 1:3)
{
if (x > 1) {
x <- -x
}
stop("this function always gives an error")
}


--- function search by body ---
Function f in namespace ppp has this body.
--- END OF FAILURE REPORT --
Fatal error: the condition has length > 1
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/tmp/bill/ppp.Rcheck/00check.log’
for details.
Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Fri, Jun 7, 2019 at 10:21 AM Duncan Murdoch 
wrote:


On 07/06/2019 12:32 p.m., William Dunlap wrote:

The length-condition-not-equal-to-one checks will cause R to shutdown
even if the code in a tryCatch().

That's strange.  I'm unable to reproduce it with my tries, and John's
package is no longer online.  Do you have an example I could look at?

Duncan Murdoch


Bill Dunlap
TIBCO Software
wdunlap tibco.com 


On Fri, Jun 7, 2019 at 7:47 AM Duncan Murdoch mailto:murdoch.dun...@gmail.com>> wrote:

 On 07/06/2019 9:46 a.m., J C Nash wrote:
 > Should try() not stop those checks from forcing an error?

 try(stop("msg"))  will print the error message, but won't stop
 execution.  Presumably the printed message is what is causing you
 problems.  If you want to suppress that, use

 try(stop("msg"), silent = TRUE)

 Duncan Murdoch

 >
 > I recognize that this is the failure -- it is indeed the check
 I'm trying to
 > catch -- but I don't want tests of such checks to fail my package.
 >
 > JN
 >
 > On 2019-06-07 9:31 a.m., Sebastian Meyer wrote:
 >> The failure stated in the R CMD check failure report is:
 >>
 >>>   --- failure: length > 1 in coercion to logical ---
 >>
  

Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Jianhong Ou, Ph.D.]

It looks like for arch'x64', there is no package org.Hs.eg.db.

Following is the whole error message:

** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
 user system elapsed
trackViewer-package 22.44   0.07   24.88
viewTracks  13.97   0.02   14.84
parseWIG12.81   0.00   12.94
browseTracks12.04   0.00   12.69
geneModelFromTxdb7.30   0.319.28
viewGene 5.15   0.115.26
** running examples for arch 'x64' ... ERROR
Running examples in 'trackViewer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trackViewer-package
> ### Title: Minimal designed plotting tool for genomic data
> ### Aliases: trackViewer trackViewer-package
> 
> ### ** Examples
> 
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(org.Hs.eg.db)
Error in library(org.Hs.eg.db) : 
  there is no package called 'org.Hs.eg.db'
Execution halted



On 6/14/19, 9:31 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D." 
 wrote:

It is for a long time. Since last development version (BioC 3.9).

Jianhong.

From: "Shepherd, Lori" 
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via 
Bioc-devel 
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10


How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with 
no issues.   Let's wait and see if it clears up on todays build report.  If not 
we will investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong 
Ou, Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


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Re: [Rd] compiler flags for performance

[Dirk Eddelbuettel]

On 14 June 2019 at 15:22, arnaud gaboury wrote:
| I have build R with Intel MKL.The libraries are free for one year (maybe
| did it change). The build is far from being trivial. Please find on my
| github[0] some details

Gee, when oh when does this "meme" of "I built R with MKL" die?

BLAS/LAPACK are _an interface_ and once you tell R to configure with BLAS as
a shared library, _all_ matching BLAS/LAPACK libraries become _pluggable_. My
gcbd package and vignette demonstrated that a decade+ ago (then using Goto).
It also holds for MKL, and these days Intel tries harder with a) friendlier
licenses and b) better packaging -- they even give .deb (and I believe .rpm).

So now you just drop MKL in/out with a single script which you can find here
https://github.com/eddelbuettel/mkl4deb with supporting blog posts at
http://dirk.eddelbuettel.com/blog/2018/04/15#018_mkl_for_debian_ubuntu

So please, let's not repeat this 'you have to use Revolution / Microsoft /
$whatever R to get MKL' or 'you have to recompile R for MKL'.

Lastly, if it matters is up to the beholder. Because the optmization in the
MKL appears to come from _many_ explicit code paths for many Intel cpu
(micro-)architectures, the installed footprint is sizeable -- IIRC it was 2gb
when I wrote the blog post above.  My linear algebra use (at home) is light
so I just kept OpenBLAS which is almost as fast, and proper free software
with a smaller installation footprint. Your mileage, as they say, may vary.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Jianhong Ou, Ph.D.]

It is for a long time. Since last development version (BioC 3.9).

Jianhong.

From: "Shepherd, Lori" 
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via 
Bioc-devel 
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10


How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with no 
issues.   Let's wait and see if it clears up on todays build report.  If not we 
will investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong Ou, 
Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


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are hereby notified that any disclosure, copying, distribution, or use of this 
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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Shepherd, Lori]

How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with no 
issues.   Let's wait and see if it clears up on todays build report.  If not we 
will investigate further.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong Ou, 
Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


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Re: [Rd] compiler flags for performance

[arnaud gaboury]

On Fri, Jun 14, 2019 at 1:44 PM lejeczek via R-devel 
wrote:

> On 13/06/2019 16:14, Dirk Eddelbuettel wrote:
> > On 13 June 2019 at 16:05, lejeczek via R-devel wrote:
> > | I'd like to ask, and I believe this place here should be best as who
> can
> > | know better, if building R with different compilers and opt flags is
> > | something worth investing time into?
>
> |
> > | Or maybe this a subject that somebody has already investigated. If yes
> > | what then are the conclusion?
>

It is worth spending sometime,but all in all, you may end  disapointed.
There are other things you may try: new Intel Linux distro (optimized for
Intelprocessors); build with Clang compiler instead of GCC; use optimized
BLAS (that's indeed a very good idea,look for openblas).

I have build R with Intel MKL.The libraries are free for one year (maybe
did it change). The build is far from being trivial. Please find on my
github[0] some details


> |
> > | Reason I ask is such that, on Centos 7.6 with different compilers from
> > | stock repo but also from so called software collections, do not
> > | render(with flags for performance) an R binaries which would perform
> any
> > | better, according to R-benchmark-25 at least, then "vanilla" packages
> > | shipped from distro.
> > |
> > | And that makes me curious - is it because R is such a case which is
> > | prone to any compiler performance optimizations?
> > |
> > | Maybe there is more structured and organized way to conduct such
> > | different-compilers-optimizations benchmarks/test?
> > |
> > | What do devel can say and advise with regards to
> compile-for-performance
> > | subject?
> >
> > Of course you do that, and add those switches to ~/.R/Makeconf.  The
> > resulting binaries may become non-portable.
> >
> > E.g. "at work" we use -march=native quite a bit but it means can't share
> > libraries from a beefier dev box with skinnier deployment boxen as they
> don't
> > have the same chipset even thought the are both x86_64 and use the same
> Linux
> > distro.
> >
> > As for which switches help in which way on different compiler: that is
> > probably best seen as a black box.  Time and profile locally, I no
> longer try
> > to generalize.   The newer 'link-time-optimizations' can help too, they
> > certainly make builds longer ...
> >
> > Dirk
> >
> I've tried the "usual" tweaks and what puzzles me is the fact, that
> -march=native and -lto(s) + Os/3 do not help much, make almost invisible
> improvements (again, judging by results from R-benchmark-25) with gcc >=
> 7 as compared to distro's package which is built with -O2 -mtune=generic
> and no ltos.
>
> Would there be other(better) way to test core R?
>
> What king of R perf increases do you guys see with compiler's opt flags,
> if any?
>
> regards, L.
>
> [0] https://github.com/gabx/R-project/tree/master/R-mkl
>
>
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>

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Re: [Rd] inappropriate warning in latticeExtra

[Richard M. Heiberger]

This is still not repaired in
 R version 3.6.0 Patched (2019-05-17 r76528)
> library(latticeExtra)
>  a <- xyplot(1 ~ 1)
> c(a,a)
Warning message:
In formals(fun) : argument is not a function

Can we have it in R-3.6.1 that Peter just announced?

Rich

On Mon, Apr 2, 2018 at 4:08 AM Deepayan Sarkar
 wrote:
>
> On Fri, Mar 23, 2018 at 7:58 AM, Richard M. Heiberger  wrote:
> > The warning message in the last line of this email is incorrect.
> > This is behavior which Duncan Murdoch labeled a bug in
> >https://stat.ethz.ch/pipermail/r-help/2017-December/450494.html
>
> Yes, sorry, this has been fixed in the r-forge sources for a while
> now, but I haven't had the time to finish up some other fixes and push
> an update to CRAN.
>
> Hopefully over the summer break.
>
> Regards,
> -Deepayan
>
>
> > This is a fresh install of R-devel (2018-03-21 r74436)
> >
> >
> >
> >
> > R Under development (unstable) (2018-03-21 r74436) -- "Unsuffered 
> > Consequences"
> > Copyright (C) 2018 The R Foundation for Statistical Computing
> > Platform: x86_64-w64-mingw32/x64 (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.
> >
> >> library(latticeExtra)
> > Error in library(latticeExtra) :
> >   there is no package called ‘latticeExtra’
> >> install.packages("latticeExtra")
> > Warning in install.packages("latticeExtra") :
> >   'lib = "C:/Program Files/R/R-devel/library"' is not writable
> > --- Please select a CRAN mirror for use in this session ---
> > also installing the dependency ‘RColorBrewer’
> >
> > Warning: unable to access index for repository
> > http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.5:
> >   cannot open URL
> > 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.5/PACKAGES'
> > trying URL 
> > 'https://cran.wu.ac.at/bin/windows/contrib/3.5/RColorBrewer_1.1-2.zip'
> > Content type 'application/zip' length 55444 bytes (54 KB)
> > downloaded 54 KB
> >
> > trying URL 
> > 'https://cran.wu.ac.at/bin/windows/contrib/3.5/latticeExtra_0.6-28.zip'
> > Content type 'application/zip' length 2191524 bytes (2.1 MB)
> > downloaded 2.1 MB
> >
> > package ‘RColorBrewer’ successfully unpacked and MD5 sums checked
> > package ‘latticeExtra’ successfully unpacked and MD5 sums checked
> >
> > The downloaded binary packages are in
> > 
> > C:\Users\rmh.DESKTOP-60G4CCO\AppData\Local\Temp\RtmpqA7Rqg\downloaded_packages
> >> library(latticeExtra)
> > Loading required package: lattice
> > Loading required package: RColorBrewer
> >> a <- xyplot(1 ~ 1)
> >> c(a,a)
> > Warning message:
> > In formals(fun) : argument is not a function
> >>
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: [Rd] [R] Open a file which name contains a tilde

[Serguei Sokol]

On 14/06/2019 14:43, Frank Schwidom wrote:

Hi John,

First, the unix and linux filesystem allows the use of any nonzero character in 
its filesystem filenames
Well, even it's not the central point of the discussion let make this 
assertion more correct. It depends on file system. E.g. JFS 
(https://en.wikipedia.org/wiki/JFS_%28file_system%29) abides to this 
rule while very popular ext4 (https://en.wikipedia.org/wiki/Ext4) does 
not. In addition to NUL character, the latter forbids '/' as well.


Best,
Serguei.

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Re: [Rd] [R] Open a file which name contains a tilde

[Frank Schwidom]

Hi John,

First, the unix and linux filesystem allows the use of any nonzero character in 
its filesystem filenames and the c functions open / fopen, symlink. rename, 
chdir and so on  don't care about any tilde. If the open systemcall gets a file 
which begins with a tilde then it will try to open this filename without any 
preceding modification.

So the tilde expansion is not really a unix idiom. It is rather an idiom of its 
unix shells like bash. But beware, the bash treats the tilde as home path not 
in all cases.

Inside of quotes the tilde keeps unaltered. So bedides any cenvenience 
functionality which can lead to failing code the bash has a very clean way to 
access files in a unique way.

And here is the problem wirh R.

The R shell has no quoting mechanism for this use case. It provides the tilde 
expansion after a string has been defined. In the bash it is the opposite. 
First the string gets defined ( for instance ~"/abc.txt" would expand to 
"/home/user/abc.txt" or "~/abc.txt" keeps "~/abc.txt" and that means a 
directory named '~' with a directory entry named 'abc.txt' inside of it) and 
after it is defined it keeps consistent and can be passed to every function.

Actually R has already a clean string datatype. But by the transition to 
filesystem operations the expansion takes place. In my opinion at the wrong 
place. And additionally there exists no quoting mechanism which allows to keep 
tildes unaltered.  It would be better to clear distinguish between a string 
which is passed to the filesystem calls and some convenience expansion 
mechanisms.

But it is like it is. For my need I created a solution which takes strings 
unaltered and so I can fulfil my work.

And for whom who is interested in it, can take a look:

https://github.com/schwidom/simplefs

Suggestions are welcome.

Kind regards
Frank Schwidom



On 2019-06-12 12:50:12, John via R-help wrote:
> On Wed, 5 Jun 2019 18:07:15 +0200
> Frank Schwidom  wrote:
>
> In reading file names, names with spaces require escaping of the
> spaces, and you are using not only a tilde but the space as spell.  The
> tilde is conventionally read as wild card representing the leading
> portion of the file address, which is what you see here:
>
> The long standing convention in unix and linux is that a tilde is
> shorthand for your home directory, just as "./" is the local directory
> and "../" is one step back up the directory tree. The output of
> path.expand() varies in how your string is constructed:
>
> 1. > path.expand("ab")
>[1] "ab"
> 2. > path.expand("a b")
>[1] "a b"
> 3. > path.expand("a ~b")
>[1] "a ~b"
> 4. > path.expand("a ~ b")
>[1] "a /home/john b"
> 5. > path.expand("a ~/b")
>[1] "a /home/john/b"
> 6. > path.expand("~/a  b")
>[1] "/home/john/a  b"
>
> Notice that the spaces have an effect on how the tilde is parsed in
> the string.  The next to last case sees a string with three elements:
> "a", the local path, and "b".  The last expands the tilde as the "path"
> to a hypothetical file "b" in the home directory. In the sixth case the
> same behaviour occurs.
>
> If you read the help for path.expand(), the routine expects
> "leading" tildes, which explains the free floating "path in the fourth
> example.  In the third example, where the forward slash is omitted, the
> routine simply treats the tilde as part of a string.
>
> Also note this at http://www.linfo.org/file_name.html:
>
> "...file names only use alphanumeric characters (mostly lower case),
> underscores, hyphens and periods. Other characters, such as dollar
> signs, percentage signs and brackets, have special meanings to the
> shell and can be distracting to work with. File names should never
> begin with a hyphen."
>
> The probable "bug" is that none of the programmers imagined that anyone
> would use special characters within file names, "legal" or not, (just
> not done, don't y' know). In any case the simple solution, if you
> really, really need a tilde in a filename, is to avoid setting it off in
> spaces, or any other character that could mislead a routine into
> treating it conventionally as shorthand for you home directory.
>
> JWDougherty
>
> __
> r-h...@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [Rd] compiler flags for performance

[lejeczek via R-devel]

On 13/06/2019 16:14, Dirk Eddelbuettel wrote:
> On 13 June 2019 at 16:05, lejeczek via R-devel wrote:
> | I'd like to ask, and I believe this place here should be best as who can
> | know better, if building R with different compilers and opt flags is
> | something worth investing time into?
> | 
> | Or maybe this a subject that somebody has already investigated. If yes
> | what then are the conclusion?
> | 
> | Reason I ask is such that, on Centos 7.6 with different compilers from
> | stock repo but also from so called software collections, do not
> | render(with flags for performance) an R binaries which would perform any
> | better, according to R-benchmark-25 at least, then "vanilla" packages
> | shipped from distro.
> | 
> | And that makes me curious - is it because R is such a case which is
> | prone to any compiler performance optimizations?
> | 
> | Maybe there is more structured and organized way to conduct such
> | different-compilers-optimizations benchmarks/test?
> | 
> | What do devel can say and advise with regards to compile-for-performance
> | subject?
>
> Of course you do that, and add those switches to ~/.R/Makeconf.  The
> resulting binaries may become non-portable.
>
> E.g. "at work" we use -march=native quite a bit but it means can't share
> libraries from a beefier dev box with skinnier deployment boxen as they don't
> have the same chipset even thought the are both x86_64 and use the same Linux
> distro.  
>
> As for which switches help in which way on different compiler: that is
> probably best seen as a black box.  Time and profile locally, I no longer try
> to generalize.   The newer 'link-time-optimizations' can help too, they
> certainly make builds longer ...
>
> Dirk
>
I've tried the "usual" tweaks and what puzzles me is the fact, that
-march=native and -lto(s) + Os/3 do not help much, make almost invisible
improvements (again, judging by results from R-benchmark-25) with gcc >=
7 as compared to distro's package which is built with -O2 -mtune=generic
and no ltos.

Would there be other(better) way to test core R?

What king of R perf increases do you guys see with compiler's opt flags,
if any?

regards, L.




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[Rd] R 3.6.1 scheduled for July 5

[Peter Dalgaard via R-devel]

Full schedule is available on developer.r-project.org.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-pkg-devel] Installing conda dependecy onAttach

[Duncan Murdoch]

On 14/06/2019 5:04 a.m., Michael Gruenstaeudl wrote:

Assume an R package (`myRpackage`) that has a conda package
(`condaDependecy`) as a system requirement. The file `DESCRIPTION` of
the R package would read like:

  Package: myRpackage
  ...
  SystemRequirements: condaDependecy (>= 0.1)
  ...

How can I ensure the automatic installation of this condaDependecy (i.e.
`conda install condaDependency`) upon installing the R package itself
(i.e. `install.packages("myRpackage")`), assuming that myRpackage is
listed on CRAN?


You can't do that in a CRAN package.  You're not allowed to modify the 
user's system.


What you can do is include a function to install the dependency, and in 
your .onLoad (not .onAttach, which should rarely be used) try to detect 
if it is present.  If it is not, you can print a message telling the 
user what to do, and fail the load with a call to stop().


Duncan Murdoch



I would prefer a method less "clunky" as

  .onAttach = function(libname = find.package("myRpackage"), pkgname
= "myRpackage") {
  system("conda install -y condaDependency")
  }

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[R-pkg-devel] Installing conda dependecy onAttach

[Michael Gruenstaeudl]

Assume an R package (`myRpackage`) that has a conda package 
(`condaDependecy`) as a system requirement. The file `DESCRIPTION` of 
the R package would read like:


Package: myRpackage
...
SystemRequirements: condaDependecy (>= 0.1)
...

How can I ensure the automatic installation of this condaDependecy (i.e. 
`conda install condaDependency`) upon installing the R package itself 
(i.e. `install.packages("myRpackage")`), assuming that myRpackage is 
listed on CRAN?


I would prefer a method less "clunky" as

.onAttach = function(libname = find.package("myRpackage"), pkgname 
= "myRpackage") {

system("conda install -y condaDependency")
}

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Re: [Rd] Halfway through writing an "IDE" with support for R; Proof of concept, and request for suggestions.

[Iñaki Ucar]

Honestly, I don't see the motivation for this. There are many similar
projects that are mature, so my feedback would be: don't reinvent the wheel
and contribute to those.

Iñaki


El vie., 14 jun. 2019 3:18, Abby Spurdle  escribió:

> I thought that I'd get more feedback.
> But it's ok, I understand.
>
> I wanted to note that I've moved symbyont to GitLab, which is where I
> should have put it, in the first place.
>
> Also, I'm not planning to start another thread.
> However, if anyone has suggestions six months from now (or six years from
> now...), you're still welcome to email me, and I will try to listen...
>
> [[alternative HTML version deleted]]
>
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[[alternative HTML version deleted]]

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[Bioc-devel] scRNAseq upgrade: give us your single-cell data!

[Aaron Lun]

We have recently repurposed the scRNAseq package to serve as a general 
location for any publicly available single-cell count data. The aim of 
this package is to provide convenient functions that directly yield 
nicely formatted SingleCellExperiment objects containing count matrices 
and relevant metadata, via BioC's ExperimentHub system for easy and 
rapid access anywhere in your computer. Our USP compared to other 
single-cell data packages is that we'll take anything - and, in fact, 
the more customized the original data is, the more we want it!


So, if you find an interesting public dataset that has been - ahem - 
"imaginatively" formatted by the original authors, we would welcome a 
contribution to the scRNAseq package to make the count data nice and 
pretty. This will save other members of the R/Bioconductor community 
from pulling their hair out (there's not much left!) if they want to 
make use of that data. Contribution guidelines are described in the 
scRNAseq vignette at 
http://bioconductor.org/packages/devel/data/experiment/html/scRNAseq.html, 
and if you more-or-less follow the suggestions, we can do the rest 
pretty quickly.


So, give us your tired, your poor, your huddled datasets yearning to 
breathe free!


-A & D

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