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

2019-06-14 Thread 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&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=n8w1wItMGynoMpsXdHLiOPNHxuSHWWql2FMAMaO7eXg&s=aCROvS-56IJNzoIZ2qid1WZLnCWMmaYHHUNphj522qc&e=
> >
> >  >
> >   <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_BaderLab_netDx&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o0CBZ3WzxQoXDkcx7BM5F01_54FXHluV0h8gFJ4rc_U&s=N-wWucRAP3w50kMnauxprPR4FvgiTQFJoMni50lmiIY&e=
> >
> >  >
> >  > 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA&e=
> >  >  > 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 pac

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

2019-06-14 Thread 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA&e=
>  >      > 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 mailin

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

2019-06-14 Thread 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&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o0CBZ3WzxQoXDkcx7BM5F01_54FXHluV0h8gFJ4rc_U&s=N-wWucRAP3w50kMnauxprPR4FvgiTQFJoMni50lmiIY&e=
> >
> >
> > 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA&e=
> >  > 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_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=sibCeuRBHi9h8oxdW9Wh6HJcxADJ7XxRY7CdSDhXgI4&e=
> >  > 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&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o0CBZ3WzxQoXDkcx7BM5F01_54FXHluV0h8gFJ4rc_U&s=ektyUHYcdy2ZKNVyyJ1_LPdse92aiigZr59mL_yPgMo&e=
> >
> > The Donnelly Center, University of Toronto
> > @spaiglass on Twitter
>
> --
> Hervé Pagès
>
> Program in Computational Biology

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

2019-06-14 Thread 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA&e=
>  > 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_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=sibCeuRBHi9h8oxdW9Wh6HJcxADJ7XxRY7CdSDhXgI4&e=
>  > 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
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

2019-06-14 Thread 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA&e=
> > 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_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=sibCeuRBHi9h8oxdW9Wh6HJcxADJ7XxRY7CdSDhXgI4&e=
> > 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

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

2019-06-14 Thread 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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=OawuiEO9WE4oRyy8UOG-HzZ1XNKaDXntzuCSGADpetA&e=
> 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_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=e_D_8tgOJqRWkkntG6nT-DmtuDokbY-IAwP1G1LMyy0&s=sibCeuRBHi9h8oxdW9Wh6HJcxADJ7XxRY7CdSDhXgI4&e=
> 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
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] get_dcf_info failed and build intervals

2019-06-14 Thread 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

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel