[Bioc-devel] get_dcf_info failed and build intervals

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Sat Jun 15 02:02:01 CEST 2019 

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

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