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 <hpa...@fredhutch.org > <mailto:hpa...@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 > <hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> > > <mailto:hpa...@fredhutch.org <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 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 <mailto:hpa...@fredhutch.org> > <mailto:hpa...@fredhutch.org <mailto: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=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: hpa...@fredhutch.org <mailto: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=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: 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