Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

[Dan Tenenbaum]

Actually it looks like it was a permissions issue with the directory 
/tmp/udcCache. I removed this directory (as superuser) and that error no longer 
happens.

Now I get a different error which seems unrelated:

...
* creating vignettes ... ERROR
Quitting from lines 2-32 (SRP009615-results.Rmd)
Error: processing vignette 'SRP009615-results.Rmd' failed with diagnostics:
object 'software' not found
Execution halted


Probably because of line 20:

Basic `r software` results exploration

`r software` is interpreted as a chunk of code to be executed by R.


Dan


- Original Message -
> From: "Dan Tenenbaum" 
> To: "lcollado" 
> Cc: "Jeff Leek" , "bioc-devel" , 
> "Andrew Jaffe" ,
> "Ben Langmead" , "Abhi Nellore" 
> Sent: Tuesday, August 9, 2016 11:46:32 AM
> Subject: Re: [Bioc-devel] Debugging build error on Linux machine: is it using 
> rtracklayer >= 1.33.11?

> 1.33.11 is the latest version in svn.
> 
> https://www.bioconductor.org/checkResults/3.4/bioc-LATEST/zin1-R-instpkgs.html
> will tell you (with a reasonable degree of accuracy) which version of which
> package is installed on zin1, it reports that it has version 1.33.11 
> installed.
> 
> The issue with recount looks like it's a (hopefully transient) UCSC connection
> problem.
> 
> Dan
> 
> 
> - Original Message -
>> From: "lcollado" 
>> To: "bioc-devel" 
>> Cc: "Jeff Leek" , "Andrew Jaffe" ,
>> "Ben Langmead" , "Abhi
>> Nellore" 
>> Sent: Tuesday, August 9, 2016 11:33:50 AM
>> Subject: [Bioc-devel] Debugging build error on Linux machine: is it using
>>  rtracklayer >= 1.33.11?
> 
>> Hi,
>> 
>> Currently the build for `recount` is failing in the Linux build
>> machine
>> http://www.bioconductor.org/checkResults/3.4/bioc-LATEST/recount/zin1-buildsrc.html.
>> It's been failing with the same error message for a while. The build
>> message ends with:
>> 
>> Setting options('download.file.method.GEOquery'='auto')
>> Setting options('GEOquery.inmemory.gpl'=FALSE)
>> trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata'
>> Content type 'application/octet-stream' length 1383643 bytes (1.3 MB)
>> ==
>> downloaded 1.3 MB
>> 
>> Quitting from lines 400-406 (recount-quickstart.Rmd)
>> Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
>> UCSC library operation failed
>> Execution halted
>> 
>> 
>> The lines of code from the recount vignette this refers to are:
>> 
>> ## Define expressed regions for study SRP009615, only for chromosome Y
>> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
>>maxClusterGap = 3000L)
>> 
>> ## Briefly explore the resulting regions
>> regions
>> 
>> 
>> 
>> The UCSC error is something I've seen in previous versions of
>> rtracklayer, which have been addressed in rtracklayer 1.33.11. recount
>> version 0.99.25 (which is the one from the build report) had under
>> suggests rtracklayer (>= 1.33.11). I thought that this would mean that
>> the build would fail if rtracklayer below version 1.33.11 was being
>> used. I'm no longer sure, which is why in recount version 0.99.27 I
>> moved rtracklayer to imports to test this. The latest build report
>> shows that rtracklayer 1.33.11 did build correctly in the Linux
>> machine.
>> 
>> 
>> Everything seems to be working fine in my local tests and in R Travis
>> https://travis-ci.org/leekgroup/recount/builds/150995800. Below is
>> some code showing that everything is working as expected in my local
>> Linux test. So I'm a tad confused and can't reproduce this issue when
>> using rtracklayer version 1.33.11. Which is why I'm guessing that
>> somehow the Linux build machine is not using rtracklayer >= 1.33.11.
>> 
>> 
>> 
>> 
>> ## The url redirects as expected to the correct url
>>> rtracklayer:::expandURL('http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata')
>> [1] "http://idies.jhu.edu/recount/data/SRP009615/rse_gene.Rdata;
>>> library('recount')
>> Loading required package: SummarizedExperiment
>> Loading required package: GenomicRanges
>> Loading required package: stats4
>> 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, xtabs
>> 
>> The following objects are masked from ‘package:base’:
>> 
>>anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
>>duplicated, eval, evalq, Filter, 

Re: [Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

[Dan Tenenbaum]

1.33.11 is the latest version in svn.

https://www.bioconductor.org/checkResults/3.4/bioc-LATEST/zin1-R-instpkgs.html 
will tell you (with a reasonable degree of accuracy) which version of which 
package is installed on zin1, it reports that it has version 1.33.11 installed.

The issue with recount looks like it's a (hopefully transient) UCSC connection 
problem.

Dan


- Original Message -
> From: "lcollado" 
> To: "bioc-devel" 
> Cc: "Jeff Leek" , "Andrew Jaffe" , 
> "Ben Langmead" , "Abhi
> Nellore" 
> Sent: Tuesday, August 9, 2016 11:33:50 AM
> Subject: [Bioc-devel] Debugging build error on Linux machine: is it using 
> rtracklayer >= 1.33.11?

> Hi,
> 
> Currently the build for `recount` is failing in the Linux build
> machine
> http://www.bioconductor.org/checkResults/3.4/bioc-LATEST/recount/zin1-buildsrc.html.
> It's been failing with the same error message for a while. The build
> message ends with:
> 
> Setting options('download.file.method.GEOquery'='auto')
> Setting options('GEOquery.inmemory.gpl'=FALSE)
> trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata'
> Content type 'application/octet-stream' length 1383643 bytes (1.3 MB)
> ==
> downloaded 1.3 MB
> 
> Quitting from lines 400-406 (recount-quickstart.Rmd)
> Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
> UCSC library operation failed
> Execution halted
> 
> 
> The lines of code from the recount vignette this refers to are:
> 
> ## Define expressed regions for study SRP009615, only for chromosome Y
> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
>maxClusterGap = 3000L)
> 
> ## Briefly explore the resulting regions
> regions
> 
> 
> 
> The UCSC error is something I've seen in previous versions of
> rtracklayer, which have been addressed in rtracklayer 1.33.11. recount
> version 0.99.25 (which is the one from the build report) had under
> suggests rtracklayer (>= 1.33.11). I thought that this would mean that
> the build would fail if rtracklayer below version 1.33.11 was being
> used. I'm no longer sure, which is why in recount version 0.99.27 I
> moved rtracklayer to imports to test this. The latest build report
> shows that rtracklayer 1.33.11 did build correctly in the Linux
> machine.
> 
> 
> Everything seems to be working fine in my local tests and in R Travis
> https://travis-ci.org/leekgroup/recount/builds/150995800. Below is
> some code showing that everything is working as expected in my local
> Linux test. So I'm a tad confused and can't reproduce this issue when
> using rtracklayer version 1.33.11. Which is why I'm guessing that
> somehow the Linux build machine is not using rtracklayer >= 1.33.11.
> 
> 
> 
> 
> ## The url redirects as expected to the correct url
>> rtracklayer:::expandURL('http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata')
> [1] "http://idies.jhu.edu/recount/data/SRP009615/rse_gene.Rdata;
>> library('recount')
> Loading required package: SummarizedExperiment
> Loading required package: GenomicRanges
> Loading required package: stats4
> 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, xtabs
> 
> The following objects are masked from ‘package:base’:
> 
>anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
>unique, unsplit, which, which.max, which.min
> 
> Loading required package: S4Vectors
> 
> Attaching package: ‘S4Vectors’
> 
> The following objects are masked from ‘package:base’:
> 
>colMeans, colSums, expand.grid, rowMeans, rowSums
> 
> Loading required package: IRanges
> Loading required package: GenomeInfoDb
> 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")'.
> 
> Setting options('download.file.method.GEOquery'='auto')
> Setting options('GEOquery.inmemory.gpl'=FALSE)
>>
>> ## Define expressed regions for study SRP009615, only for chromosome Y
>> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
> + maxClusterGap = 3000L)
> 2016-08-09 14:16:59 loadCoverage: loading BigWig file
> 

[Bioc-devel] Debugging build error on Linux machine: is it using rtracklayer >= 1.33.11?

[Leonardo Collado Torres]

Hi,

Currently the build for `recount` is failing in the Linux build
machine 
http://www.bioconductor.org/checkResults/3.4/bioc-LATEST/recount/zin1-buildsrc.html.
It's been failing with the same error message for a while. The build
message ends with:

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata'
Content type 'application/octet-stream' length 1383643 bytes (1.3 MB)
==
downloaded 1.3 MB

Quitting from lines 400-406 (recount-quickstart.Rmd)
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
UCSC library operation failed
Execution halted


The lines of code from the recount vignette this refers to are:

## Define expressed regions for study SRP009615, only for chromosome Y
regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
maxClusterGap = 3000L)

## Briefly explore the resulting regions
regions



The UCSC error is something I've seen in previous versions of
rtracklayer, which have been addressed in rtracklayer 1.33.11. recount
version 0.99.25 (which is the one from the build report) had under
suggests rtracklayer (>= 1.33.11). I thought that this would mean that
the build would fail if rtracklayer below version 1.33.11 was being
used. I'm no longer sure, which is why in recount version 0.99.27 I
moved rtracklayer to imports to test this. The latest build report
shows that rtracklayer 1.33.11 did build correctly in the Linux
machine.


Everything seems to be working fine in my local tests and in R Travis
https://travis-ci.org/leekgroup/recount/builds/150995800. Below is
some code showing that everything is working as expected in my local
Linux test. So I'm a tad confused and can't reproduce this issue when
using rtracklayer version 1.33.11. Which is why I'm guessing that
somehow the Linux build machine is not using rtracklayer >= 1.33.11.




## The url redirects as expected to the correct url
> rtracklayer:::expandURL('http://duffel.rail.bio/recount/SRP009615/rse_gene.Rdata')
[1] "http://idies.jhu.edu/recount/data/SRP009615/rse_gene.Rdata;
> library('recount')
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, xtabs

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

anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> ## Define expressed regions for study SRP009615, only for chromosome Y
> regions <- expressed_regions('SRP009615', 'chrY', cutoff = 5L,
+ maxClusterGap = 3000L)
2016-08-09 14:16:59 loadCoverage: loading BigWig file
http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw
2016-08-09 14:17:01 loadCoverage: applying the cutoff to the merged data
2016-08-09 14:17:02 filterData: originally there were 57227415 rows,
now there are 57227415 rows. Meaning that 0 percent was filtered.
2016-08-09 14:17:02 findRegions: identifying potential segments
2016-08-09 14:17:02 findRegions: segmenting information
2016-08-09 14:17:02 .getSegmentsRle: segmenting with cutoff(s) 5
2016-08-09 14:17:02 findRegions: identifying candidate regions
2016-08-09 14:17:03 findRegions: identifying region clusters
>
> ## Briefly explore the resulting regions
> regions
GRanges object with 808 ranges and 6 metadata columns:
  seqnames   ranges strand |value area
|
1 chrY   [2929794, 2929829]  * | 14.7265009482702 530.154034137726
2 chrY   [2956678, 2956701]  * | 12.8106340567271  307.45521736145
3 chrY   

Re: [Bioc-devel] Imports version that's only available on github?

[Laurent Gatto]

On  8 August 2016 21:29, Gabe Becker wrote:

> Alex (et al),
>
> Yihui is currently working towards a CRAN release for a modern version of
> DT, so sometime "soon" (I have no insight into what definition of soon is
> in use here) things should work in your particular case.

Soon actually means now - version 0.2.0 was just released on CRAN.

Laurent

> ~G
>
> On Fri, Aug 5, 2016 at 11:02 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
>> On 08/05/2016 01:55 PM, Alex Pickering wrote:
>>
>>> My package requires a version of 'DT' that's only available on github. I
>>> tried following the answer to this SO
>>> >> package-that-depends-on-another-r-package-located-on-github>
>>> (specifying 'Remotes' in the DESCRIPTION in addition to the version needed
>>> in 'Imports'). Build failed with "Package required and available but
>>> unsuitable version: 'DT'". How should this be handled? Thank you,
>>>
>>
>> Packages must be on CRAN or Bioconductor; the rationale is that these
>> represent stable, tested, and somehow mature packages, rather than an
>> arbitrary package of unknown stability. The StackOverflow question is a
>> solution for devtools, but biocLite() uses install.packages().
>>
>> Martin
>>
>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>> This email message may contain legally privileged and/or...{{dropped:2}}
>>
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>


-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/

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Re: [Bioc-devel] package not available (for R version 3.2.3)

[Obenchain, Valerie]

Hi Etienne,

The BiocInstaller package, which contains the biocLite() function, looks
in different Bioconductor repositories depending on what version of R is
being run. BiocInstaller 1.20.* (your code below) was looking in the
previous release repository (Bioconductor 3.1 and R 3.2) where the
biosigner package did not exist. The first version of BiocInstaller that
will 'find' your package is 1.22.* which is associated with the current
R 3.3 release.

biosigner is a new package in release which means it was developed
against R 3.3. While the package may work with earlier versions of R or
other dependencies there are no guarantees. Versions do matter.
BiocInstaller attempts to both minimize installation problems and
provide reproducible results by drawing from a repository tied to
particular version of R and Bioconductor.

Valerie

On 08/09/2016 06:03 AM, THEVENOT Etienne 207099 wrote:
> Dear Bioc team,
>
> A friend of mine had the following trouble to install the biosigner package 
> on R 3.2.3.
>
> I do not understand why the package would require a dedicated version of R 
> (in particular >3.2.3) except that it uses S4 methods, and if/how I have to 
> specify an R version within the package (note that the ropls package, which 
> biosigner depends upon, seemed to require also a recent version of R).
>
> I thank you very much in advance for your answer.
>
> Kind Regards,
>
> Etienne.
>
>
>> source("https://bioconductor.org/biocLite.R;)
> Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
> A new version of Bioconductor is available after installing the most recent
>   version of R; see http://bioconductor.org/install
>> biocLite("biosigner")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
> Installing package(s) 'biosigner'
> Old packages: 'AnnotationDbi', 'ape', 'BH', 'boot', 'car', 'caret', 'cluster',
>   'CORElearn', 'curl', 'DBI', 'devtools', 'digest', 'dplyr', 'evaluate',
>   'FactoMineR', 'formatR', 'ggplot2', 'git2r', 'gridExtra', 'gtable', 'highr',
>   'Hmisc', 'htmltools', 'httr', 'IRanges', 'jsonlite', 'knitr', 
> 'latticeExtra',
>   'lazyeval', 'lme4', 'maps', 'Matrix', 'memoise', 'mgcv', 'mime', 'mnormt',
>   'msm', 'mtbls2', 'mzR', 'nlme', 'nnet', 'phangorn', 'phytools', 'plotrix',
>   'plyr', 'quantreg', 'R6', 'Rcpp', 'RcppEigen', 'RCurl', 'rmarkdown',
>   'roxygen2', 'rstudioapi', 'rversions', 'S4Vectors', 'scales',
>   'scatterplot3d', 'stringi', 'survival', 'XML', 'xml2', 'xtable'
> Update all/some/none? [a/s/n]: n
> Warning message:
> package 'biosigner' is not available (for R version 3.2.3)
>
> When I updated my R version to the latest it worked. I'll check which version 
> is used in biosigner. But unless there is a good reason to have to use R > 
> 3.2.3, I would allow the package to install on older versions (people don't 
> update R on their desktops so often). I think you need to set that up on the 
> config files of the package that you upload to bioconductor.
>
>
>
> Etienne Th�venot
> Computational metabolomics
> CEA, 
> LIST, Laboratory for data analysis and 
> systems' 
> intelligence,
>  MetaboHUB
> B�t. 565 (Digiteo 
> Saclay),
>  PC 192
> F-91191 Gif-sur-Yvette Cedex, France
> Tel: +33 (0)1 69 08 79 23
> E-mail: etienne.theve...@cea.fr
> Workflow4metabolomics.org
> R�seau Francophone de M�tabolomique et Fluxomique
>
>
>   [[alternative HTML version deleted]]
>



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Re: [Bioc-devel] package not available (for R version 3.2.3)

[Laurent Gatto]

Dear Etienne,

Bioconductor versions are linked to R versions. As the biosigner package
is a recent addition to Bioconductor (Bioc version 3.3), it will require
a recent R version, i.e. the R version that was current when Bioc 3.3
was released. That is how things are, guaranteeing a coherent set of
functioning set of packages for a specific Bioc versions.

As a result, if a users want to use recent packages (as in newly added
to Bioc or new versions/features), they will have to install a recent R.

Best wishes,

Laurent

On  9 August 2016 14:02, THEVENOT Etienne 207099 wrote:

> Dear Bioc team,
>
> A friend of mine had the following trouble to install the biosigner package 
> on R 3.2.3.
>
> I do not understand why the package would require a dedicated version of R 
> (in particular >3.2.3) except that it uses S4 methods, and if/how I have to 
> specify an R version within the package (note that the ropls package, which 
> biosigner depends upon, seemed to require also a recent version of R).
>
> I thank you very much in advance for your answer.
>
> Kind Regards,
>
> Etienne.
>
>
>> source("https://bioconductor.org/biocLite.R;)
> Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
> A new version of Bioconductor is available after installing the most recent
>   version of R; see http://bioconductor.org/install
>> biocLite("biosigner")
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
> Installing package(s) 'biosigner'
> Old packages: 'AnnotationDbi', 'ape', 'BH', 'boot', 'car', 'caret', 'cluster',
>   'CORElearn', 'curl', 'DBI', 'devtools', 'digest', 'dplyr', 'evaluate',
>   'FactoMineR', 'formatR', 'ggplot2', 'git2r', 'gridExtra', 'gtable', 'highr',
>   'Hmisc', 'htmltools', 'httr', 'IRanges', 'jsonlite', 'knitr', 
> 'latticeExtra',
>   'lazyeval', 'lme4', 'maps', 'Matrix', 'memoise', 'mgcv', 'mime', 'mnormt',
>   'msm', 'mtbls2', 'mzR', 'nlme', 'nnet', 'phangorn', 'phytools', 'plotrix',
>   'plyr', 'quantreg', 'R6', 'Rcpp', 'RcppEigen', 'RCurl', 'rmarkdown',
>   'roxygen2', 'rstudioapi', 'rversions', 'S4Vectors', 'scales',
>   'scatterplot3d', 'stringi', 'survival', 'XML', 'xml2', 'xtable'
> Update all/some/none? [a/s/n]: n
> Warning message:
> package 'biosigner' is not available (for R version 3.2.3)
>
> When I updated my R version to the latest it worked. I'll check which version 
> is used in biosigner. But unless there is a good reason to have to use R > 
> 3.2.3, I would allow the package to install on older versions (people don't 
> update R on their desktops so often). I think you need to set that up on the 
> config files of the package that you upload to bioconductor.
>
>
>
> Etienne Thévenot
> Computational metabolomics
> CEA, 
> LIST, Laboratory for data analysis and 
> systems' 
> intelligence,
>  MetaboHUB
> Bât. 565 (Digiteo 
> Saclay),
>  PC 192
> F-91191 Gif-sur-Yvette Cedex, France
> Tel: +33 (0)1 69 08 79 23
> E-mail: etienne.theve...@cea.fr
> Workflow4metabolomics.org
> Réseau Francophone de Métabolomique et Fluxomique
>
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/

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[Bioc-devel] package not available (for R version 3.2.3)

[THEVENOT Etienne 207099]

Dear Bioc team,

A friend of mine had the following trouble to install the biosigner package on 
R 3.2.3.

I do not understand why the package would require a dedicated version of R (in 
particular >3.2.3) except that it uses S4 methods, and if/how I have to specify 
an R version within the package (note that the ropls package, which biosigner 
depends upon, seemed to require also a recent version of R).

I thank you very much in advance for your answer.

Kind Regards,

Etienne.


> source("https://bioconductor.org/biocLite.R;)
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("biosigner")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) 'biosigner'
Old packages: 'AnnotationDbi', 'ape', 'BH', 'boot', 'car', 'caret', 'cluster',
  'CORElearn', 'curl', 'DBI', 'devtools', 'digest', 'dplyr', 'evaluate',
  'FactoMineR', 'formatR', 'ggplot2', 'git2r', 'gridExtra', 'gtable', 'highr',
  'Hmisc', 'htmltools', 'httr', 'IRanges', 'jsonlite', 'knitr', 'latticeExtra',
  'lazyeval', 'lme4', 'maps', 'Matrix', 'memoise', 'mgcv', 'mime', 'mnormt',
  'msm', 'mtbls2', 'mzR', 'nlme', 'nnet', 'phangorn', 'phytools', 'plotrix',
  'plyr', 'quantreg', 'R6', 'Rcpp', 'RcppEigen', 'RCurl', 'rmarkdown',
  'roxygen2', 'rstudioapi', 'rversions', 'S4Vectors', 'scales',
  'scatterplot3d', 'stringi', 'survival', 'XML', 'xml2', 'xtable'
Update all/some/none? [a/s/n]: n
Warning message:
package 'biosigner' is not available (for R version 3.2.3)

When I updated my R version to the latest it worked. I'll check which version 
is used in biosigner. But unless there is a good reason to have to use R > 
3.2.3, I would allow the package to install on older versions (people don't 
update R on their desktops so often). I think you need to set that up on the 
config files of the package that you upload to bioconductor.



Etienne Th�venot
Computational metabolomics
CEA, 
LIST, Laboratory for data analysis and 
systems' 
intelligence,
 MetaboHUB
B�t. 565 (Digiteo 
Saclay),
 PC 192
F-91191 Gif-sur-Yvette Cedex, France
Tel: +33 (0)1 69 08 79 23
E-mail: etienne.theve...@cea.fr
Workflow4metabolomics.org
R�seau Francophone de M�tabolomique et Fluxomique


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[Bioc-devel] Git mirror out of sync

[Angerer, Philipp via Bioc-devel]

Hi, 

destiny ’s git mirror has been out of sync for quite some time. 

The currently latest SVN revision has bumped the version to 1.3.4 , but git 
master is still on 1.3.0 . 

Thanks for looking at it, 
Philipp 

 


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