Re: [Bioc-devel] get_dcf_info failed and build intervals

[Shraddha Pai]

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  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@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  > > 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
> > 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 pac

Re: [Bioc-devel] get_dcf_info failed and build intervals

[Pages, Herve]

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  > 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
> mailto:hpa...@fredhutch.org>
>  > >> wrote:
>  >
>  >     Hi,
>  >
>  >       From the Linux command line:
>  >
>  >         git clone https://github.com/BaderLab/netDx
> 
> 
>  >   
>   
> 
>  >
>  >         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 mailin

Re: [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  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  > > 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: 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=o0CBZ3WzxQoXDkcx7BM5F01_54FXHluV0h8gFJ4rc_U&s=ektyUHYcdy2ZKNVyyJ1_LPdse92aiigZr59mL_yPgMo&e=
> >
> > The Donnelly Center, University of Toronto
> > @spaiglass on Twitter
>
> --
> Hervé Pagès
>
> Program in Computational Biology

Re: [Bioc-devel] get_dcf_info failed and build intervals

[Pages, Herve]

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  > wrote:
> 
> Hi,
> 
>   From the Linux command line:
> 
>     git clone https://github.com/BaderLab/netDx
> 
> 
> 
>     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 
> 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

-- 
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

Re: [Bioc-devel] get_dcf_info failed and build intervals

[Shraddha Pai]

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.

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  wrote:

> Hi,
>
>  From the Linux command line:
>
>git clone https://github.com/BaderLab/netDx
>
>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
> 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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Re: [Bioc-devel] get_dcf_info failed and build intervals

[Pages, Herve]

Hi,

 From the Linux command line:

   git clone https://github.com/BaderLab/netDx

   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
Phone:  (206) 667-5791
Fax:(206) 667-1319
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[Bioc-devel] get_dcf_info failed and build intervals

[Shraddha Pai]

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://github.com/Bioconductor/Contributions/issues/1149
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://stat.ethz.ch/pipermail/bioc-devel/
My apologies if these are trivial questions.

Thanks very much,
Shraddha

-- 
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
@spaiglass on Twitter

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Re: [Bioc-devel] updating package

[Turaga, Nitesh]

Hi,

It seems like the email is configured correctly on BiocCredentials app. It is 
because the account is not activated it doesn't work. You'd have to first 
activate your account before moving forward with setting a password.

I've added your GitHub credentials to the account. 

Best,

Nitesh 

> On Jun 14, 2019, at 11:01 AM, ostro...@mskcc.org wrote:
> 
> 
> Hi,
> I'd like to update my package Clonality 
> https://bioconductor.org/packages/release/bioc/html/Clonality.html
> I used to do it through svn but as I understand it's not possible now.
> 
> I can't connect it to my git page with updated package 
> https://github.com/IOstrovnaya/Clonality
> 
> When I enter my email  ostro...@mskcc.org here  
> https://git.bioconductor.org/BiocCredentials/account_activation/ I can't 
> login and resetting the password doesn't work.
> 
> Can you please help me establish my account on bioconductor and connect it to 
> my github?
> 
> Thank you!!!
> Irina
> 
> =
> 
> Please note that this e-mail and any files transmitted from
> Memorial Sloan Kettering Cancer Center may be privileged, confidential,
> and protected from disclosure under applicable law. If the reader of
> this message is not the intended recipient, or an employee or agent
> responsible for delivering this message to the intended recipient,
> you are hereby notified that any reading, dissemination, distribution,
> copying, or other use of this communication or any of its attachments
> is strictly prohibited.  If you have received this communication in
> error, please notify the sender immediately by replying to this message
> and deleting this message, any attachments, and all copies and backups
> from your computer.
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] updating package

[ostrovni]

Hi,
I'd like to update my package Clonality 
https://bioconductor.org/packages/release/bioc/html/Clonality.html
I used to do it through svn but as I understand it's not possible now.

I can't connect it to my git page with updated package 
https://github.com/IOstrovnaya/Clonality

When I enter my email  ostro...@mskcc.org here  
https://git.bioconductor.org/BiocCredentials/account_activation/ I can't login 
and resetting the password doesn't work.

Can you please help me establish my account on bioconductor and connect it to 
my github?

Thank you!!!
Irina

=

 Please note that this e-mail and any files transmitted from
 Memorial Sloan Kettering Cancer Center may be privileged, confidential,
 and protected from disclosure under applicable law. If the reader of
 this message is not the intended recipient, or an employee or agent
 responsible for delivering this message to the intended recipient,
 you are hereby notified that any reading, dissemination, distribution,
 copying, or other use of this communication or any of its attachments
 is strictly prohibited.  If you have received this communication in
 error, please notify the sender immediately by replying to this message
 and deleting this message, any attachments, and all copies and backups
 from your computer.

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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Shepherd, Lori]

Thank you. We will investigate further and let you know when we have a solution 
on our end.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Jianhong Ou, Ph.D. 
Sent: Friday, June 14, 2019 9:57:47 AM
To: Shepherd, Lori; Michael Lawrence via Bioc-devel
Subject: Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

It looks like for arch'x64', there is no package org.Hs.eg.db.

Following is the whole error message:

** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
 user system elapsed
trackViewer-package 22.44   0.07   24.88
viewTracks  13.97   0.02   14.84
parseWIG12.81   0.00   12.94
browseTracks12.04   0.00   12.69
geneModelFromTxdb7.30   0.319.28
viewGene 5.15   0.115.26
** running examples for arch 'x64' ... ERROR
Running examples in 'trackViewer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trackViewer-package
> ### Title: Minimal designed plotting tool for genomic data
> ### Aliases: trackViewer trackViewer-package
>
> ### ** Examples
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(org.Hs.eg.db)
Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'
Execution halted



On 6/14/19, 9:31 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D." 
 wrote:

It is for a long time. Since last development version (BioC 3.9).

Jianhong.

From: "Shepherd, Lori" 
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via 
Bioc-devel 
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10


How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with 
no issues.   Let's wait and see if it clears up on todays build report.  If not 
we will investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong 
Ou, Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


[[alternative HTML version deleted]]

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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Jianhong Ou, Ph.D.]

It looks like for arch'x64', there is no package org.Hs.eg.db.

Following is the whole error message:

** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
 user system elapsed
trackViewer-package 22.44   0.07   24.88
viewTracks  13.97   0.02   14.84
parseWIG12.81   0.00   12.94
browseTracks12.04   0.00   12.69
geneModelFromTxdb7.30   0.319.28
viewGene 5.15   0.115.26
** running examples for arch 'x64' ... ERROR
Running examples in 'trackViewer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trackViewer-package
> ### Title: Minimal designed plotting tool for genomic data
> ### Aliases: trackViewer trackViewer-package
> 
> ### ** Examples
> 
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(org.Hs.eg.db)
Error in library(org.Hs.eg.db) : 
  there is no package called 'org.Hs.eg.db'
Execution halted



On 6/14/19, 9:31 AM, "Bioc-devel on behalf of Jianhong Ou, Ph.D." 
 wrote:

It is for a long time. Since last development version (BioC 3.9).

Jianhong.

From: "Shepherd, Lori" 
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via 
Bioc-devel 
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10


How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with 
no issues.   Let's wait and see if it clears up on todays build report.  If not 
we will investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong 
Ou, Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


[[alternative HTML version deleted]]

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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Jianhong Ou, Ph.D.]

It is for a long time. Since last development version (BioC 3.9).

Jianhong.

From: "Shepherd, Lori" 
Date: Friday, June 14, 2019 at 9:29 AM
To: "Jianhong Ou, Ph.D." , Michael Lawrence via 
Bioc-devel 
Subject: Re: CHECK ERROR in tokay1 for BioC 3.10


How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with no 
issues.   Let's wait and see if it clears up on todays build report.  If not we 
will investigate further.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong Ou, 
Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


[[alternative HTML version deleted]]

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Re: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

[Shepherd, Lori]

How long as this ERROR occurred?

I just went onto tokay1 and was able to run library("org.Hs.eg.db")  with no 
issues.   Let's wait and see if it clears up on todays build report.  If not we 
will investigate further.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Jianhong Ou, 
Ph.D. 
Sent: Thursday, June 13, 2019 2:51:26 PM
To: Michael Lawrence via Bioc-devel
Subject: [Bioc-devel] CHECK ERROR in tokay1 for BioC 3.10

Hi,

The package trackViewer get check error in tokay1 (windows) say:

Error in library(org.Hs.eg.db) :
  there is no package called 'org.Hs.eg.db'

How could I debug this error? Thank you for your help.

Yours Sincerely,

Jianhong Ou


[[alternative HTML version deleted]]

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distribution, or use of this email message is prohibited.  If you have received 
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[Bioc-devel] scRNAseq upgrade: give us your single-cell data!

[Aaron Lun]

We have recently repurposed the scRNAseq package to serve as a general 
location for any publicly available single-cell count data. The aim of 
this package is to provide convenient functions that directly yield 
nicely formatted SingleCellExperiment objects containing count matrices 
and relevant metadata, via BioC's ExperimentHub system for easy and 
rapid access anywhere in your computer. Our USP compared to other 
single-cell data packages is that we'll take anything - and, in fact, 
the more customized the original data is, the more we want it!


So, if you find an interesting public dataset that has been - ahem - 
"imaginatively" formatted by the original authors, we would welcome a 
contribution to the scRNAseq package to make the count data nice and 
pretty. This will save other members of the R/Bioconductor community 
from pulling their hair out (there's not much left!) if they want to 
make use of that data. Contribution guidelines are described in the 
scRNAseq vignette at 
http://bioconductor.org/packages/devel/data/experiment/html/scRNAseq.html, 
and if you more-or-less follow the suggestions, we can do the rest 
pretty quickly.


So, give us your tired, your poor, your huddled datasets yearning to 
breathe free!


-A & D

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