Re: [Bioc-devel] Error loading rtracklayer

[Shepherd, Lori]

For the single package builder: Once the issue is resolved you could kick off a 
new build by bumping the version number; it is probably the fastest way. I will 
also try to check and manually build packages that encountered this error and 
haven't kicked off a new build.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Malcolm Perry 
<mgperr...@gmail.com>
Sent: Wednesday, March 29, 2017 12:45:43 PM
To: Jurat Shayidin
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Error loading rtracklayer

Thanks for the quick reply. Will i need to bump the version to trigger a
rebuild once the changes are made?

On 29 Mar 2017 5:17 pm, "Jurat Shayidin" <juratb...@gmail.com> wrote:

> Hi:
>
> This happened to me several times, and I figured out the issue. I tried to
> remove `rtracklayer` package completely from `R` home directory; you can
> try: remove.packages("rtracklayer"). Don't  be panic, if this problem
> still bumps up again, try to reboot your PC (you may need to restart your
> PC several times), I am sure this could help you out. Cheers :)
>
>

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Re: [Bioc-devel] Error loading rtracklayer

[Malcolm Perry]

Thanks for the quick reply. Will i need to bump the version to trigger a
rebuild once the changes are made?

On 29 Mar 2017 5:17 pm, "Jurat Shayidin"  wrote:

> Hi:
>
> This happened to me several times, and I figured out the issue. I tried to
> remove `rtracklayer` package completely from `R` home directory; you can
> try: remove.packages("rtracklayer"). Don't  be panic, if this problem
> still bumps up again, try to reboot your PC (you may need to restart your
> PC several times), I am sure this could help you out. Cheers :)
>
>

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Re: [Bioc-devel] Error loading rtracklayer

[Shepherd, Lori]

This is an ERROR with rtracklayer until the ERROR is resolved in rtracklayer 
you will continue to see this ERROR in your package. We are in the processes of 
resolving and should be correctly shortly.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Malcolm Perry 
<mgperr...@gmail.com>
Sent: Wednesday, March 29, 2017 10:49:48 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Error loading rtracklayer

Hi all,

I receive this error when loading rtracklayer in my vignette which is
stopping my package from building:

Loading required package: IRanges
Loading required package: GenomeInfoDb
Quitting from lines 39-50 (heatmaps.Rmd)
Error: processing vignette 'heatmaps.Rmd' failed with diagnostics:
package or namespace load failed for 'rtracklayer':
 object 'inverted' is not exported by 'namespace:Biostrings'
Execution halted

The full build report is here:
http://bioconductor.org/spb_reports/heatmaps_buildreport_20170328102656.html

I have no idea what is causing this, so any help would be appreciated. The
package is building fine on my system.

Thanks,

Malcolm

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Re: [Bioc-devel] Error loading rtracklayer

[Jurat Shayidin]

Hi:

This happened to me several times, and I figured out the issue. I tried to
remove `rtracklayer` package completely from `R` home directory; you can
try: remove.packages("rtracklayer"). Don't  be panic, if this problem still
bumps up again, try to reboot your PC (you may need to restart your PC
several times), I am sure this could help you out. Cheers :)

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Re: [Bioc-devel] Error loading rtracklayer

[Michael Lawrence]

It looks like things got out of sync with some recent shuffling. A
change to Biostrings made it through to the latest builds, but not the
change to rtracklayer. There should be a fixed version of rtracklayer
available soon, or you could grab it from svn.

On Wed, Mar 29, 2017 at 7:49 AM, Malcolm Perry  wrote:
> Hi all,
>
> I receive this error when loading rtracklayer in my vignette which is
> stopping my package from building:
>
> Loading required package: IRanges
> Loading required package: GenomeInfoDb
> Quitting from lines 39-50 (heatmaps.Rmd)
> Error: processing vignette 'heatmaps.Rmd' failed with diagnostics:
> package or namespace load failed for 'rtracklayer':
>  object 'inverted' is not exported by 'namespace:Biostrings'
> Execution halted
>
> The full build report is here:
> http://bioconductor.org/spb_reports/heatmaps_buildreport_20170328102656.html
>
> I have no idea what is causing this, so any help would be appreciated. The
> package is building fine on my system.
>
> Thanks,
>
> Malcolm
>
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>
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[Bioc-devel] Error loading rtracklayer

[Malcolm Perry]

Hi all,

I receive this error when loading rtracklayer in my vignette which is
stopping my package from building:

Loading required package: IRanges
Loading required package: GenomeInfoDb
Quitting from lines 39-50 (heatmaps.Rmd)
Error: processing vignette 'heatmaps.Rmd' failed with diagnostics:
package or namespace load failed for 'rtracklayer':
 object 'inverted' is not exported by 'namespace:Biostrings'
Execution halted

The full build report is here:
http://bioconductor.org/spb_reports/heatmaps_buildreport_20170328102656.html

I have no idea what is causing this, so any help would be appreciated. The
package is building fine on my system.

Thanks,

Malcolm

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