[Bioc-devel] Build ERRORS caused by unable to be find dependencies

[Obenchain, Valerie]

Marcin,

I'm traveling this week and don't have a stable internet connection.
I've done some preliminary testing and can do more when I'm back next
week if necessary. I was able to reproduce the error with
library(RTCGA.rnaseq) on the release build machine. I then tried to
re-install with biocLite() and my session locked up.

One potential problem (thanks Herve for noticing) is that you use
LazyData=TRUE. This significantly slows down installation especially if
the data are big. This should be changed to 'FALSE' or just omitted.

I did spot check a few files and it looks like you've saved the data
with compress='xz' (which is good). If that isn't the case for all,
please re-save with save(..., compress='xz').

The last thing, just housekeeping, is the version:

Version: 20151101.6.0

The usual approach is to include the date, genome, build, etc.
information in the title, not the package version. If you feel you can't
change this now, please keep it in mind for future packages.

Please remove LazyData and re-save the data objects (if necessary). If
we still see an error after those changes I'll look into it further.

Valerie



On 06/14/2017 09:20 AM, Marcin Kosiński wrote:
> Hello bioc developers,
>
> The same error appeard for RTCGA as the one year ago.
> It is impossible to find dependent RTCGA.rnaseq package.
> http://bioconductor.org/checkResults/release/bioc-LATEST/RTCGA/tokay2-checksrc.html
> This is the only platform that has such an error. It appeared frequently 
> recently in RTCGA.
>
> It would be terrific if you might help somehow,
>
> Cheers,
> Marcin
>
>
>
> 2016-06-19 16:54 GMT+02:00 Obenchain, Valerie <Valerie.Obenchain at roswellpark.org 
> <mailto:Valerie.Obenchain at roswellpark.org>>:
>
>     Hi Marcin,
>
>     Dan is out for a few days and can give a more detailed answer when he's
>     back.
>
>     This looks like a problem on our end with the windows builder. Several
>     other packages are failing with similar error messages, re: missing
>     dependencies on packages that successfully built.
>
>     Thanks for keeping an eye on the build report.
>
>     Valerie
>
>
>     On 06/19/2016 07:40 AM, Marcin Kosiński wrote:
>      > Hello bioc developers,
>      >
>      > Do you maybe know what is the cause of this error?
>      >
>     http://bioconductor.org/checkResults/release/bioc-LATEST/RTCGA/moscato2-checksrc.html
>     <http://bioconductor.org/checkResults/release/bioc-LATEST/RTCGA/moscato2-checksrc.html>
>      > This is the only platform that has such an error. It appeared frequently
>      > recently in RTCGA.
>      >
>      > Cheers,
>      > Marcin
>      >
>      >       [[alternative HTML version deleted]]
>      >
>      > _______________________________________________
>      > Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
>      > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>      >
>
>
>
>     This email message may contain legally privileged and/or confidential
>     information.  If you are not the intended recipient(s), or the employee or
>     agent responsible for the delivery of this message to the intended
>     recipient(s), you are hereby notified that any disclosure, copying,
>     distribution, or use of this email message is prohibited.  If you have
>     received this message in error, please notify the sender immediately by
>     e-mail and delete this email message from your computer. Thank you.
>
>



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.