[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 <hpages using fredhutch.org> 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 <hpages using fredhutch.org
> > <mailto:hpages using 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=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: hpages using fredhutch.org <mailto:hpages using 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
> 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: hpages using 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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