[Bioc-devel] get_dcf_info failed and build intervals

Fri, Jun 14, 2019 5:02 PM

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 at 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 at fredhutch.org 
<mailto:hpages at 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 at fredhutch.org <mailto:hpages at fredhutch.org>

     > <mailto:hpages at fredhutch.org <mailto:hpages at 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
     >? ? ? >
     >
     >? ? ?--
     >? ? ?Herv? Pag?s
     >
     >? ? ?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 at fredhutch.org <mailto:hpages at fredhutch.org>

    <mailto:hpages at fredhutch.org <mailto:hpages at 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

    -- 
    Herv? Pag?s

    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 at fredhutch.org <mailto:hpages at 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

Herv? Pag?s

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 at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

[Bioc-devel] get_dcf_info failed and build intervals

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