[BioC] mzR crashes R

Laurent Gatto lg390 at cam.ac.uk
Wed Mar 27 16:07:03 CET 2013 

FYI.

Works fine using 2.15.2 on linux - architecture is 32 bit, OS is 64.
Trying on a 64 bit windows with R 2.15.2, I get a message that the
binary is not available, only source. Using biocLite("mzR", type =
"source") fails to build - probably because of configuration reasons
on the local machine.

Hope this helps.

Laurent

On 27 March 2013 14:42, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Wed, Mar 27, 2013 at 6:23 AM, C Lin <baccts at hotmail.com> wrote:
>>
>> Dan, I just tried again but still got the following error:
>>
>>> options(BioC_mirror="http://bioconductor.org")
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("mzR")
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>> Installing package(s) 'mzR'
>> Warning message:
>> package ‘mzR’ is not available (for R version 2.15.1)
>>
>> Here is the output for biocinstallRepos()
>>                                                BioCsoft
>>            "http://bioconductor.org/packages/2.11/bioc"
>>                                                 BioCann
>> "http://bioconductor.org/packages/2.11/data/annotation"
>>                                                 BioCexp
>> "http://bioconductor.org/packages/2.11/data/experiment"
>>                                               BioCextra
>>           "http://bioconductor.org/packages/2.11/extra"
>>                                                    CRAN
>>                                 "http://cran.fhcrc.org"
>>                                               CRANextra
>>                    "http://www.stats.ox.ac.uk/pub/RWin"
>>                                                    MBNI
>>             "http://brainarray.mbni.med.umich.edu/bioc"
>>
>> I am also on windows.
>
>
> The problem is that I built a 32-bit only version. I'll build a
> dual-architecture version.
> Dan
>
>
>> Thanks for your help.
>> Lin
>>
>> ----------------------------------------
>>> Date: Tue, 26 Mar 2013 13:44:39 -0700
>>> Subject: Re: [BioC] mzR crashes R
>>> From: dtenenba at fhcrc.org
>>> To: baccts at hotmail.com
>>> CC: lg390 at cam.ac.uk; bioconductor at r-project.org
>>>
>>> On Tue, Mar 26, 2013 at 1:00 PM, C Lin <baccts at hotmail.com> wrote:
>>> >
>>> > Thank you both for your quick response.
>>> > I tried to install mzR but got error saying the package is not available.
>>> > Maybe it takes time? I'll try again tomorrow.
>>> >
>>> >> source("http://bioconductor.org/biocLite.R")
>>> > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
>>> >> biocLite("mzR")
>>> > BioC_mirror: http://bioconductor.org
>>> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>>> > Installing package(s) 'mzR'
>>> > Warning message:
>>> > package ‘mzR’ is not available (for R version 2.15.1)
>>> >
>>>
>>> It works for me on windows.
>>> Which Bioconductor mirror are you using? If it's not bioconductor.org,
>>> try using bioconductor.org, as the package has probably not yet
>>> propagated to other mirrors.
>>>
>>> try:
>>> options(BioC_mirror="http://bioconductor.org")
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("mzR")
>>>
>>> If that doesn't work, send the output of
>>> biocinstallRepos()
>>>
>>> Thanks
>>> Dan
>>>
>>>
>>> > How do I downgrade my Rcpp on windows?
>>> >
>>> > Thanks,
>>> > Lin
>>> >
>>> > ----------------------------------------
>>> >> Date: Tue, 26 Mar 2013 19:15:24 +0000
>>> >> Subject: Re: [BioC] mzR crashes R
>>> >> From: lg390 at cam.ac.uk
>>> >> To: dtenenba at fhcrc.org
>>> >> CC: guest at bioconductor.org; baccts at hotmail.com; bioconductor at r-project.org
>>> >>
>>> >> On 26 March 2013 19:13, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>> >> > On Tue, Mar 26, 2013 at 9:07 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:
>>> >> >> Dear Lin,
>>> >> >>
>>> >> >> I forgot to update the release version of mzR to match Rcpp 0.10.3 and
>>> >> >> commits to Bioc 2.11 are now disabled. A new version of mzR addressing
>>> >> >> this will be available next week with the next Bioc release.
>>> >> >
>>> >> > I've pushed mzR 1.4.7 to the BioC 2.11 repository, so it can now be
>>> >> > installed with
>>> >> > biocLite("mzR")
>>> >> > on systems running R-2.15.x and Bioconductor 2.11.
>>> >>
>>> >> Thanks for this, Dan!
>>> >>
>>> >> Laurent
>>> >>
>>> >> > Thanks,
>>> >> > Dan
>>> >> >
>>> >> >
>>> >> >> In the
>>> >> >> mean time, you could either stick with Rcpp 0.10.2 or install mzR
>>> >> >> v1.5.9 [1], which is the current devel version (and will become the
>>> >> >> next stable release in one week). I have not tested the latter, so
>>> >> >> there might be other unexpected incompatibilities that show up.
>>> >> >>
>>> >> >> Let us know if this works of need any further help.
>>> >> >>
>>> >> >> Sorry for the inconvenience.
>>> >> >>
>>> >> >> Best wishes,
>>> >> >>
>>> >> >> Laurent
>>> >> >>
>>> >> >>
>>> >> >> [1] http://bioconductor.org/packages/2.12/bioc/html/mzR.html
>>> >> >>
>>> >> >>
>>> >> >> On 26 March 2013 15:39, Lin [guest] <guest at bioconductor.org> wrote:
>>> >> >>>
>>> >> >>> Hi all,
>>> >> >>>
>>> >> >>> Everytime I tried to run "library(mzR)" my R crashes. I tried to search through the mailing and found out that this seemed to be the problem of incompatibility between Rcpp and mzR. My Rcpp is 0.10.3 and the current mzR version is 1.4.6. How do I fix it?
>>> >> >>>
>>> >> >>> Alternatively, I think I should be able to install older version of Rcpp and mzR but I don't know which version I should install and how to install archieved version on windows.
>>> >> >>>
>>> >> >>> Thanks in advance for your help.
>>> >> >>> Lin
>>> >> >>>
>>> >> >>> -- output of sessionInfo():
>>> >> >>>
>>> >> >>> R version 2.15.1 (2012-06-22)
>>> >> >>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>> >> >>>
>>> >> >>> locale:
>>> >> >>> [1] LC_COLLATE=English_United States.1252
>>> >> >>> [2] LC_CTYPE=English_United States.1252
>>> >> >>> [3] LC_MONETARY=English_United States.1252
>>> >> >>> [4] LC_NUMERIC=C
>>> >> >>> [5] LC_TIME=English_United States.1252
>>> >> >>>
>>> >> >>> attached base packages:
>>> >> >>> [1] grDevices datasets splines graphics stats tcltk utils
>>> >> >>> [8] methods base
>>> >> >>>
>>> >> >>> other attached packages:
>>> >> >>> [1] Rcpp_0.10.3 svSocket_0.9-54 TinnR_1.0-5 R2HTML_2.2
>>> >> >>> [5] Hmisc_3.10-1 survival_2.37-4
>>> >> >>>
>>> >> >>> loaded via a namespace (and not attached):
>>> >> >>> [1] cluster_1.14.3 grid_2.15.1 lattice_0.20-15 svMisc_0.9-69
>>> >> >>> [5] tools_2.15.1
>>> >> >>>
>>> >> >>>
>>> >> >>> --
>>> >> >>> Sent via the guest posting facility at bioconductor.org.
>>> >> >>>
>>> >> >>> _______________________________________________
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>>> >> >>
>>> >> >> _______________________________________________
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