[Bioc-devel] get_dcf_info failed and build intervals
Shraddha Pai
@hr@ddh@p@|@neuro @end|ng |rom gm@||@com
Sat Jun 15 04:12:37 CEST 2019
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 <hpages using fredhutch.org> 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 using 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 <hpages using fredhutch.org
> > <mailto: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>
> > > <mailto: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=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 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>
> > <mailto: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=n8w1wItMGynoMpsXdHLiOPNHxuSHWWql2FMAMaO7eXg&s=KpLkTGxvlbQeWz1aamcVsvnCbJ63qn1XeBPtReZb-14&e=
> >
> >
> > >
> > <
> 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 <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=n8w1wItMGynoMpsXdHLiOPNHxuSHWWql2FMAMaO7eXg&s=KpLkTGxvlbQeWz1aamcVsvnCbJ63qn1XeBPtReZb-14&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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