[Bioc-devel] ExperimentHub broken in bioc-devel?

It works for me when I have an existing cache, but not after removing the
cache:
unlink("~/.ExperimentHub", recursive=TRUE)
suppressPackageStartupMessages(library(curatedMetagenomicData))
ExperimentHub()
updating metadata: retrieving 1 resource

|=========================================================================|
100%
snapshotDate(): 2016-12-12
*Error in gzfile(file, "rb") : cannot open the connection*
In addition: Warning message:
In gzfile(file, "rb") :
  cannot open compressed file '/Users/lwaldron//.ExperimentHub/index.rds',
probable reason 'No such file or directory'
sessionInfo()
R version 3.4.0 Patched (2017-06-02 r72758)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
[1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11                  IRanges_2.11.3
 [3] digest_0.6.12                 mime_0.5
 [5] R6_2.2.1                      xtable_1.8-2
 [7] DBI_0.6-1                     stats4_3.4.0
 [9] RSQLite_1.1-2                 BiocInstaller_1.27.2
[11] httr_1.2.1                    curl_2.6
[13] S4Vectors_0.15.2              tools_3.4.0
[15] Biobase_2.37.2                shiny_1.0.3
[17] httpuv_1.3.3                  yaml_2.1.14
[19] compiler_3.4.0                AnnotationDbi_1.39.1
[21] memoise_1.1.0                 htmltools_0.3.6
[23] interactiveDisplayBase_1.15.0

Hi Levi,

Lori fixed this bug last week. You'll need AnnotationHub >= 2.9.4.

Val
It works for me when I have an existing cache, but not after removing the
cache:

unlink("~/.ExperimentHub", recursive=TRUE)
suppressPackageStartupMessages(library(curatedMetagenomicData))
ExperimentHub()
updating metadata: retrieving 1 resource

|=========================================================================|
100%
snapshotDate(): 2016-12-12
*Error in gzfile(file, "rb") : cannot open the connection*
In addition: Warning message:
In gzfile(file, "rb") :
  cannot open compressed file '/Users/lwaldron//.ExperimentHub/index.rds',
probable reason 'No such file or directory'
sessionInfo()
R version 3.4.0 Patched (2017-06-02 r72758)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
[1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11                  IRanges_2.11.3
 [3] digest_0.6.12                 mime_0.5
 [5] R6_2.2.1                      xtable_1.8-2
 [7] DBI_0.6-1                     stats4_3.4.0
 [9] RSQLite_1.1-2                 BiocInstaller_1.27.2
[11] httr_1.2.1                    curl_2.6
[13] S4Vectors_0.15.2              tools_3.4.0
[15] Biobase_2.37.2                shiny_1.0.3
[17] httpuv_1.3.3                  yaml_2.1.14
[19] compiler_3.4.0                AnnotationDbi_1.39.1
[21] memoise_1.1.0                 htmltools_0.3.6
[23] interactiveDisplayBase_1.15.0
	[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
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.
Thanks Val! 2.9.4 isn't in bioc-devel yet, but I got it through Subversion
and am up and running again.

On Sat, Jun 3, 2017 at 11:26 AM, Obenchain, Valerie <

Hi Levi,

Lori fixed this bug last week. You'll need AnnotationHub >= 2.9.4.

Val

On 06/03/2017 05:55 AM, Levi Waldron wrote:
It works for me when I have an existing cache, but not after removing the
cache:

unlink("~/.ExperimentHub", recursive=TRUE)
suppressPackageStartupMessages(library(curatedMetagenomicData))
ExperimentHub()
updating metadata: retrieving 1 resource

|===========================================================
==============|
100%
snapshotDate(): 2016-12-12
*Error in gzfile(file, "rb") : cannot open the connection*
In addition: Warning message:
In gzfile(file, "rb") :
  cannot open compressed file '/Users/lwaldron//.
ExperimentHub/index.rds',
probable reason 'No such file or directory'
sessionInfo()
R version 3.4.0 Patched (2017-06-02 r72758)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/
A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.4/
Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
[1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11                  IRanges_2.11.3
 [3] digest_0.6.12                 mime_0.5
 [5] R6_2.2.1                      xtable_1.8-2
 [7] DBI_0.6-1                     stats4_3.4.0
 [9] RSQLite_1.1-2                 BiocInstaller_1.27.2
[11] httr_1.2.1                    curl_2.6
[13] S4Vectors_0.15.2              tools_3.4.0
[15] Biobase_2.37.2                shiny_1.0.3
[17] httpuv_1.3.3                  yaml_2.1.14
[19] compiler_3.4.0                AnnotationDbi_1.39.1
[21] memoise_1.1.0                 htmltools_0.3.6
[23] interactiveDisplayBase_1.15.0
      [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
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.

Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics     CUNY School of Public Health
US: +1 646-364-9616                                           Skype:
levi.waldron

	[[alternative HTML version deleted]]
It should be up in bioc-devel soon.  It failed to build last night do to other package dependencies failing.  All should be remedied by tomorrows build.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Thanks Val! 2.9.4 isn't in bioc-devel yet, but I got it through Subversion
and am up and running again.

On Sat, Jun 3, 2017 at 11:26 AM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Hi Levi,
>
> Lori fixed this bug last week. You'll need AnnotationHub >= 2.9.4.
>
> Val
>
>
> On 06/03/2017 05:55 AM, Levi Waldron wrote:
> > It works for me when I have an existing cache, but not after removing the
> > cache:
> >
> >> unlink("~/.ExperimentHub", recursive=TRUE)
> >> suppressPackageStartupMessages(library(curatedMetagenomicData))
> >> ExperimentHub()
> > updating metadata: retrieving 1 resource
> >
> > |===========================================================
> ==============|
> > 100%
> > snapshotDate(): 2016-12-12
> > *Error in gzfile(file, "rb") : cannot open the connection*
> > In addition: Warning message:
> > In gzfile(file, "rb") :
> >   cannot open compressed file '/Users/lwaldron//.
> ExperimentHub/index.rds',
> > probable reason 'No such file or directory'
> >> sessionInfo()
> > R version 3.4.0 Patched (2017-06-02 r72758)
> > Platform: x86_64-apple-darwin15.6.0 (64-bit)
> > Running under: macOS Sierra 10.12.4
> >
> > Matrix products: default
> > BLAS:
> > /System/Library/Frameworks/Accelerate.framework/Versions/
> A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> > LAPACK:
> > /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods
> > base
> >
> > other attached packages:
> > [1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0
> >
> > loaded via a namespace (and not attached):
> >  [1] Rcpp_0.12.11                  IRanges_2.11.3
> >  [3] digest_0.6.12                 mime_0.5
> >  [5] R6_2.2.1                      xtable_1.8-2
> >  [7] DBI_0.6-1                     stats4_3.4.0
> >  [9] RSQLite_1.1-2                 BiocInstaller_1.27.2
> > [11] httr_1.2.1                    curl_2.6
> > [13] S4Vectors_0.15.2              tools_3.4.0
> > [15] Biobase_2.37.2                shiny_1.0.3
> > [17] httpuv_1.3.3                  yaml_2.1.14
> > [19] compiler_3.4.0                AnnotationDbi_1.39.1
> > [21] memoise_1.1.0                 htmltools_0.3.6
> > [23] interactiveDisplayBase_1.15.0
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > 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.
>

--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics     CUNY School of Public Health
US: +1 646-364-9616                                           Skype:
levi.waldron

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
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.