subject:"\[Bioc\-devel\] Data package timeouts"

Re: [Bioc-devel] Data package timeouts

2017-12-05 Thread Sean Davis

Thanks, Leo.

It turns out that that accession is not "public" yet; the "file" that
GEOquery gets is just an HTML page saying so.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1062236

I'll work on fix to catch such problems.

Sean


On Tue, Dec 5, 2017 at 1:48 PM, Leonardo Collado Torres 
wrote:

> Hi Sean,
>
> I'm still seeing some timeouts with GEOquery 2.46.10 on bioc-release.
> Here's a quick example:
>
> library('GEOquery')
> getGEO('GSM1062236', getGPL = FALSE)
>
> I found it from
> https://github.com/leekgroup/recount/blob/master/tests/
> testthat/test-misc.R#L19
>
> Best,
> Leo
>
>
> > library('GEOquery')
> Loading required package: Biobase
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, sd, var, xtabs
>
> The following objects are masked from ‘package:base’:
>
> anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
> colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
> grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
> mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
> rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
> table, tapply, union, unique, unsplit, which, which.max, which.min
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material; view with
> 'browseVignettes()'. To cite Bioconductor, see
> 'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Setting options('download.file.method.GEOquery'='auto')
> Setting options('GEOquery.inmemory.gpl'=FALSE)
> > getGEO('GSM1062236', getGPL = FALSE)
> File stored at:
> /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//RtmpAyQR3U/
> GSM1062236.soft
> ## Force terminate after a long running time
> ^C
> > sessionInfo()
> R version 3.4.2 (2017-09-28)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.6
>
> Matrix products: default
> BLAS: /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRblas.0.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
> [8] base
>
> other attached packages:
> [1] GEOquery_2.46.10Biobase_2.38.0  BiocGenerics_0.24.0
> [4] colorout_1.1-2
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.14 tidyr_0.7.2  dplyr_0.7.4  assertthat_0.2.0
>  [5] R6_2.2.2 magrittr_1.5 rlang_0.1.4  bindrcpp_0.2
>  [9] limma_3.34.2 xml2_1.1.1   readr_1.1.1  glue_1.2.0
> [13] purrr_0.2.4  hms_0.4.0compiler_3.4.2   pkgconfig_2.0.1
> [17] bindr_0.1tibble_1.3.4
>
>
> On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres
>  wrote:
> >
> > Thanks Sean! I was seeing timeouts also in recount related to GEOquery
> which I just recently looked into.
> >
> > On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis  wrote:
> >>
> >>
> >> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith 
> wrote:
> >>
> >> > Thanks for the speedy response Sean.  I'll switch back to the version
> >> > using a file name shortly.
> >> >
> >>
> >> No problem. Let me know if it does not work as expected.
> >>
> >> Sean
> >>
> >>
> >>
> >> >
> >> > Cheers,
> >> > Mike
> >> >
> >> > On 30 November 2017 at 11:20, Sean Davis  wrote:
> >> >
> >> >> Thanks for the report, Mike.
> >> >>
> >> >> The problem was (specifically) in parsing a GSEMatrix file using a
> >> >> filename. This should be fixed in versions 2.46.10 (release) and
> 2.47.12
> >> >> (devel).
> >> >>
> >> >> Sean
> >> >>
> >> >>
> >> >> On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith 
> wrote:
> >> >>
> >> >>> Hi Mike,
> >> >>>
> >> >>> I was experiencing similar problems with the BeadArrayUseCases
> vignette,
> >> >>> where using getGEO() from GEOquery was getting stuck in a
> (seemingly)
> >> >>> infinite loop processing a GSE series matrix file.  It looks like
> both of
> >> >>> your examples try to do this too, so I suspect it's a similar
> issue.  I
> >> >>> think the format of those files has changed recently and it seems
> to be
> >> >>> causing a fair few issues with GEOquery.
> >> >>>
> >> >>> I temporarily settled a solution by getting querying GEO directly
> rather
> >> >>> than using a local file, but it would be nice to get it back
> working as
> >> >>> intended.
> >> >>>
> >> >>> Mike
> >> >>>
> >> >>> On 29 November 2017 at 18:56,

Re: [Bioc-devel] Data package timeouts

2017-12-05 Thread Leonardo Collado Torres

Hi Sean,

I'm still seeing some timeouts with GEOquery 2.46.10 on bioc-release.
Here's a quick example:

library('GEOquery')
getGEO('GSM1062236', getGPL = FALSE)

I found it from
https://github.com/leekgroup/recount/blob/master/tests/testthat/test-misc.R#L19

Best,
Leo


> library('GEOquery')
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> getGEO('GSM1062236', getGPL = FALSE)
File stored at:
/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//RtmpAyQR3U/GSM1062236.soft
## Force terminate after a long running time
^C
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.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
[8] base

other attached packages:
[1] GEOquery_2.46.10Biobase_2.38.0  BiocGenerics_0.24.0
[4] colorout_1.1-2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14 tidyr_0.7.2  dplyr_0.7.4  assertthat_0.2.0
 [5] R6_2.2.2 magrittr_1.5 rlang_0.1.4  bindrcpp_0.2
 [9] limma_3.34.2 xml2_1.1.1   readr_1.1.1  glue_1.2.0
[13] purrr_0.2.4  hms_0.4.0compiler_3.4.2   pkgconfig_2.0.1
[17] bindr_0.1tibble_1.3.4


On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres
 wrote:
>
> Thanks Sean! I was seeing timeouts also in recount related to GEOquery which 
> I just recently looked into.
>
> On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis  wrote:
>>
>>
>> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith  wrote:
>>
>> > Thanks for the speedy response Sean.  I'll switch back to the version
>> > using a file name shortly.
>> >
>>
>> No problem. Let me know if it does not work as expected.
>>
>> Sean
>>
>>
>>
>> >
>> > Cheers,
>> > Mike
>> >
>> > On 30 November 2017 at 11:20, Sean Davis  wrote:
>> >
>> >> Thanks for the report, Mike.
>> >>
>> >> The problem was (specifically) in parsing a GSEMatrix file using a
>> >> filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
>> >> (devel).
>> >>
>> >> Sean
>> >>
>> >>
>> >> On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith  wrote:
>> >>
>> >>> Hi Mike,
>> >>>
>> >>> I was experiencing similar problems with the BeadArrayUseCases vignette,
>> >>> where using getGEO() from GEOquery was getting stuck in a (seemingly)
>> >>> infinite loop processing a GSE series matrix file.  It looks like both of
>> >>> your examples try to do this too, so I suspect it's a similar issue.  I
>> >>> think the format of those files has changed recently and it seems to be
>> >>> causing a fair few issues with GEOquery.
>> >>>
>> >>> I temporarily settled a solution by getting querying GEO directly rather
>> >>> than using a local file, but it would be nice to get it back working as
>> >>> intended.
>> >>>
>> >>> Mike
>> >>>
>> >>> On 29 November 2017 at 18:56, Michael Love 
>> >>> wrote:
>> >>>
>> >>> > I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on
>> >>> > both release and devel machines (release was fine leading up to the
>> >>> > Bioc release).
>> >>> >
>> >>> > Not sure what's the issue, I haven't changed these packages in a
>> >>> > while. I checked these out and these both build fine and in ~30s on my
>> >>> > machine (devel branch).
>> >>> >
>> >>> > Here are the reports for release:
>> >>> >
>> >>> > http://bioconductor.org/checkResults/release/data-
>> >>> >

Re: [Bioc-devel] Data package timeouts

2017-11-30 Thread Leonardo Collado Torres

Thanks Sean! I was seeing timeouts also in recount related to GEOquery
which I just recently looked into.

On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis  wrote:

>
> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith  wrote:
>
> > Thanks for the speedy response Sean.  I'll switch back to the version
> > using a file name shortly.
> >
>
> No problem. Let me know if it does not work as expected.
>
> Sean
>
>
>
> >
> > Cheers,
> > Mike
> >
> > On 30 November 2017 at 11:20, Sean Davis  wrote:
> >
> >> Thanks for the report, Mike.
> >>
> >> The problem was (specifically) in parsing a GSEMatrix file using a
> >> filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
> >> (devel).
> >>
> >> Sean
> >>
> >>
> >> On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith 
> wrote:
> >>
> >>> Hi Mike,
> >>>
> >>> I was experiencing similar problems with the BeadArrayUseCases
> vignette,
> >>> where using getGEO() from GEOquery was getting stuck in a (seemingly)
> >>> infinite loop processing a GSE series matrix file.  It looks like both
> of
> >>> your examples try to do this too, so I suspect it's a similar issue.  I
> >>> think the format of those files has changed recently and it seems to be
> >>> causing a fair few issues with GEOquery.
> >>>
> >>> I temporarily settled a solution by getting querying GEO directly
> rather
> >>> than using a local file, but it would be nice to get it back working as
> >>> intended.
> >>>
> >>> Mike
> >>>
> >>> On 29 November 2017 at 18:56, Michael Love <
> michaelisaiahl...@gmail.com>
> >>> wrote:
> >>>
> >>> > I got simultaneous timeout notices for 'airway' and 'parathyroidSE'
> on
> >>> > both release and devel machines (release was fine leading up to the
> >>> > Bioc release).
> >>> >
> >>> > Not sure what's the issue, I haven't changed these packages in a
> >>> > while. I checked these out and these both build fine and in ~30s on
> my
> >>> > machine (devel branch).
> >>> >
> >>> > Here are the reports for release:
> >>> >
> >>> > http://bioconductor.org/checkResults/release/data-
> >>> > experiment-LATEST/airway/malbec1-buildsrc.html
> >>> > http://bioconductor.org/checkResults/release/data-experiment-LATEST/
> >>> > parathyroidSE/malbec1-buildsrc.html
> >>> >
> >>> > The vignettes are here:
> >>> >
> >>> > http://bioconductor.org/packages/3.6/data/experiment/
> >>> > vignettes/airway/inst/doc/airway.html
> >>> > http://bioconductor.org/packages/3.6/data/experiment/
> >>> > vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf
> >>> >
> >>> > best,
> >>> > Mike
> >>> >
> >>> > ___
> >>> > Bioc-devel@r-project.org mailing list
> >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>> >
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ___
> >>> Bioc-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >>
> >>
> >> --
> >> Sean Davis, MD, PhD
> >> Center for Cancer Research
> >> National Cancer Institute
> >> National Institutes of Health
> >> Bethesda, MD 20892
> >> https://seandavi.github.io/
> >> https://twitter.com/seandavis12
> >>
> >
> >
>
>
> --
> Sean Davis, MD, PhD
> Center for Cancer Research
> National Cancer Institute
> National Institutes of Health
> Bethesda, MD 20892
> https://seandavi.github.io/
> https://twitter.com/seandavis12
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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Re: [Bioc-devel] Data package timeouts

2017-11-30 Thread Martin Morgan


On 11/30/2017 06:05 AM, Mike Smith wrote:

Thanks for the speedy response Sean.  I'll switch back to the version using
a file name shortly.


Is there a use case for BiocFileCache in here -- check if the file is in 
the cache bfcquery(), if so, check whether it needs updating 
bfcneedsupdate() and perhaps bfcupdate() ? this might make the overall 
download process more robust, and would certainly save on build time.


Martin



Cheers,
Mike

On 30 November 2017 at 11:20, Sean Davis  wrote:


Thanks for the report, Mike.

The problem was (specifically) in parsing a GSEMatrix file using a
filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
(devel).

Sean


On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith  wrote:


Hi Mike,

I was experiencing similar problems with the BeadArrayUseCases vignette,
where using getGEO() from GEOquery was getting stuck in a (seemingly)
infinite loop processing a GSE series matrix file.  It looks like both of
your examples try to do this too, so I suspect it's a similar issue.  I
think the format of those files has changed recently and it seems to be
causing a fair few issues with GEOquery.

I temporarily settled a solution by getting querying GEO directly rather
than using a local file, but it would be nice to get it back working as
intended.

Mike

On 29 November 2017 at 18:56, Michael Love 
wrote:


I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on
both release and devel machines (release was fine leading up to the
Bioc release).

Not sure what's the issue, I haven't changed these packages in a
while. I checked these out and these both build fine and in ~30s on my
machine (devel branch).

Here are the reports for release:

http://bioconductor.org/checkResults/release/data-
experiment-LATEST/airway/malbec1-buildsrc.html
http://bioconductor.org/checkResults/release/data-experiment-LATEST/
parathyroidSE/malbec1-buildsrc.html

The vignettes are here:

http://bioconductor.org/packages/3.6/data/experiment/
vignettes/airway/inst/doc/airway.html
http://bioconductor.org/packages/3.6/data/experiment/
vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf

best,
Mike

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--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12



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Re: [Bioc-devel] Data package timeouts

2017-11-30 Thread Sean Davis

On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith  wrote:

> Thanks for the speedy response Sean.  I'll switch back to the version
> using a file name shortly.
>

No problem. Let me know if it does not work as expected.

Sean



>
> Cheers,
> Mike
>
> On 30 November 2017 at 11:20, Sean Davis  wrote:
>
>> Thanks for the report, Mike.
>>
>> The problem was (specifically) in parsing a GSEMatrix file using a
>> filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
>> (devel).
>>
>> Sean
>>
>>
>> On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith  wrote:
>>
>>> Hi Mike,
>>>
>>> I was experiencing similar problems with the BeadArrayUseCases vignette,
>>> where using getGEO() from GEOquery was getting stuck in a (seemingly)
>>> infinite loop processing a GSE series matrix file.  It looks like both of
>>> your examples try to do this too, so I suspect it's a similar issue.  I
>>> think the format of those files has changed recently and it seems to be
>>> causing a fair few issues with GEOquery.
>>>
>>> I temporarily settled a solution by getting querying GEO directly rather
>>> than using a local file, but it would be nice to get it back working as
>>> intended.
>>>
>>> Mike
>>>
>>> On 29 November 2017 at 18:56, Michael Love 
>>> wrote:
>>>
>>> > I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on
>>> > both release and devel machines (release was fine leading up to the
>>> > Bioc release).
>>> >
>>> > Not sure what's the issue, I haven't changed these packages in a
>>> > while. I checked these out and these both build fine and in ~30s on my
>>> > machine (devel branch).
>>> >
>>> > Here are the reports for release:
>>> >
>>> > http://bioconductor.org/checkResults/release/data-
>>> > experiment-LATEST/airway/malbec1-buildsrc.html
>>> > http://bioconductor.org/checkResults/release/data-experiment-LATEST/
>>> > parathyroidSE/malbec1-buildsrc.html
>>> >
>>> > The vignettes are here:
>>> >
>>> > http://bioconductor.org/packages/3.6/data/experiment/
>>> > vignettes/airway/inst/doc/airway.html
>>> > http://bioconductor.org/packages/3.6/data/experiment/
>>> > vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf
>>> >
>>> > best,
>>> > Mike
>>> >
>>> > ___
>>> > Bioc-devel@r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
>> --
>> Sean Davis, MD, PhD
>> Center for Cancer Research
>> National Cancer Institute
>> National Institutes of Health
>> Bethesda, MD 20892
>> https://seandavi.github.io/
>> https://twitter.com/seandavis12
>>
>
>


-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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Re: [Bioc-devel] Data package timeouts

2017-11-30 Thread Sean Davis

Thanks for the report, Mike.

The problem was (specifically) in parsing a GSEMatrix file using a
filename. This should be fixed in versions 2.46.10 (release) and 2.47.12
(devel).

Sean


On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith  wrote:

> Hi Mike,
>
> I was experiencing similar problems with the BeadArrayUseCases vignette,
> where using getGEO() from GEOquery was getting stuck in a (seemingly)
> infinite loop processing a GSE series matrix file.  It looks like both of
> your examples try to do this too, so I suspect it's a similar issue.  I
> think the format of those files has changed recently and it seems to be
> causing a fair few issues with GEOquery.
>
> I temporarily settled a solution by getting querying GEO directly rather
> than using a local file, but it would be nice to get it back working as
> intended.
>
> Mike
>
> On 29 November 2017 at 18:56, Michael Love 
> wrote:
>
> > I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on
> > both release and devel machines (release was fine leading up to the
> > Bioc release).
> >
> > Not sure what's the issue, I haven't changed these packages in a
> > while. I checked these out and these both build fine and in ~30s on my
> > machine (devel branch).
> >
> > Here are the reports for release:
> >
> > http://bioconductor.org/checkResults/release/data-
> > experiment-LATEST/airway/malbec1-buildsrc.html
> > http://bioconductor.org/checkResults/release/data-experiment-LATEST/
> > parathyroidSE/malbec1-buildsrc.html
> >
> > The vignettes are here:
> >
> > http://bioconductor.org/packages/3.6/data/experiment/
> > vignettes/airway/inst/doc/airway.html
> > http://bioconductor.org/packages/3.6/data/experiment/
> > vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf
> >
> > best,
> > Mike
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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Re: [Bioc-devel] Data package timeouts

2017-11-30 Thread Mike Smith

Hi Mike,

I was experiencing similar problems with the BeadArrayUseCases vignette,
where using getGEO() from GEOquery was getting stuck in a (seemingly)
infinite loop processing a GSE series matrix file.  It looks like both of
your examples try to do this too, so I suspect it's a similar issue.  I
think the format of those files has changed recently and it seems to be
causing a fair few issues with GEOquery.

I temporarily settled a solution by getting querying GEO directly rather
than using a local file, but it would be nice to get it back working as
intended.

Mike

On 29 November 2017 at 18:56, Michael Love 
wrote:

> I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on
> both release and devel machines (release was fine leading up to the
> Bioc release).
>
> Not sure what's the issue, I haven't changed these packages in a
> while. I checked these out and these both build fine and in ~30s on my
> machine (devel branch).
>
> Here are the reports for release:
>
> http://bioconductor.org/checkResults/release/data-
> experiment-LATEST/airway/malbec1-buildsrc.html
> http://bioconductor.org/checkResults/release/data-experiment-LATEST/
> parathyroidSE/malbec1-buildsrc.html
>
> The vignettes are here:
>
> http://bioconductor.org/packages/3.6/data/experiment/
> vignettes/airway/inst/doc/airway.html
> http://bioconductor.org/packages/3.6/data/experiment/
> vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf
>
> best,
> Mike
>
> ___
> Bioc-devel@r-project.org mailing list
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>

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