mzR crashes R
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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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@laurent-gatto-5645
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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. 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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, 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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Laurent Gatto - http://proteome.sysbiol.cam.ac.uk/lgatto/ Cambridge Centre for Proteomics - http://www.bio.cam.ac.uk/proteomics
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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) 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. > [[elided Hotmail spam]] > > 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. > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Laurent Gatto > - http://proteome.sysbiol.cam.ac.uk/lgatto/ > Cambridge Centre for Proteomics > - http://www.bio.cam.ac.uk/proteomics
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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. >> >>> >> >>> _______________________________________________ >> >>> Bioconductor mailing list >> >>> Bioconductor at r-project.org >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> -- >> Laurent Gatto >> - http://proteome.sysbiol.cam.ac.uk/lgatto/ >> Cambridge Centre for Proteomics >> - http://www.bio.cam.ac.uk/proteomics >
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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. 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. > >> [[elided Hotmail spam]] > >> > >> 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. > >> >>> > >> >>> _______________________________________________ > >> >>> Bioconductor mailing list > >> >>> Bioconductor at r-project.org > >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> > >> >> _______________________________________________ > >> >> Bioconductor mailing list > >> >> Bioconductor at r-project.org > >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > >> > >> -- > >> Laurent Gatto > >> - http://proteome.sysbiol.cam.ac.uk/lgatto/ > >> Cambridge Centre for Proteomics > >> - http://www.bio.cam.ac.uk/proteomics > >
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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. >> >> >>> >> >> >>> _______________________________________________ >> >> >>> Bioconductor mailing list >> >> >>> Bioconductor at r-project.org >> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> >> >> _______________________________________________ >> >> >> Bioconductor mailing list >> >> >> Bioconductor at r-project.org >> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> >> >> >> >> -- >> >> Laurent Gatto >> >> - http://proteome.sysbiol.cam.ac.uk/lgatto/ >> >> Cambridge Centre for Proteomics >> >> - http://www.bio.cam.ac.uk/proteomics >> > >
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On Wed, Mar 27, 2013 at 7:42 AM, 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. The dual-architecture version is now available, so you should be able to install and load mzR. Sorry about that. Dan > 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. >>> >> >>> >>> >> >>> _______________________________________________ >>> >> >>> Bioconductor mailing list >>> >> >>> Bioconductor at r-project.org >>> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >>> >> >> _______________________________________________ >>> >> >> Bioconductor mailing list >>> >> >> Bioconductor at r-project.org >>> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >>> >> >>> >> >>> >> -- >>> >> Laurent Gatto >>> >> - http://proteome.sysbiol.cam.ac.uk/lgatto/ >>> >> Cambridge Centre for Proteomics >>> >> - http://www.bio.cam.ac.uk/proteomics >>> > >>
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On 27 March 2013 15:05, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > The dual-architecture version is now available, so you should be able > to install and load mzR. Works here. Thanks, Dan. Laurent > Sorry about that. > Dan > > >> 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. >>>> >> >>> >>>> >> >>> _______________________________________________ >>>> >> >>> Bioconductor mailing list >>>> >> >>> Bioconductor at r-project.org >>>> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >> >> >>>> >> >> _______________________________________________ >>>> >> >> Bioconductor mailing list >>>> >> >> Bioconductor at r-project.org >>>> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >> >>>> >> >>>> >> >>>> >> -- >>>> >> Laurent Gatto >>>> >> - http://proteome.sysbiol.cam.ac.uk/lgatto/ >>>> >> Cambridge Centre for Proteomics >>>> >> - http://www.bio.cam.ac.uk/proteomics >>>> > >>> -- Laurent Gatto - http://proteome.sysbiol.cam.ac.uk/lgatto/ Cambridge Centre for Proteomics - http://www.bio.cam.ac.uk/proteomics
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Works now. Thank you everyone for your quick help. Dan, thank you so much for pushing the mzR to the bioc repository. You've eliminated a lot of my headache. Lin ---------------------------------------- > Date: Wed, 27 Mar 2013 15:17:50 +0000 > Subject: Re: [BioC] mzR crashes R > From: lg390 at cam.ac.uk > To: dtenenba at fhcrc.org > CC: baccts at hotmail.com; bioconductor at r-project.org > > On 27 March 2013 15:05, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > > The dual-architecture version is now available, so you should be able > > to install and load mzR. > > Works here. Thanks, Dan. > > Laurent > > > Sorry about that. > > Dan > > > > > >> 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. > >>>> >> [[elided Hotmail spam]] > >>>> >> > >>>> >> 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. > >>>> >> >>> > >>>> >> >>> _______________________________________________ > >>>> >> >>> Bioconductor mailing list > >>>> >> >>> Bioconductor at r-project.org > >>>> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>> >> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>> >> >> > >>>> >> >> _______________________________________________ > >>>> >> >> Bioconductor mailing list > >>>> >> >> Bioconductor at r-project.org > >>>> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>> >> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>> >> > >>>> >> > >>>> >> > >>>> >> -- > >>>> >> Laurent Gatto > >>>> >> - http://proteome.sysbiol.cam.ac.uk/lgatto/ > >>>> >> Cambridge Centre for Proteomics > >>>> >> - http://www.bio.cam.ac.uk/proteomics > >>>> > > >>> > > > > -- > Laurent Gatto > - http://proteome.sysbiol.cam.ac.uk/lgatto/ > Cambridge Centre for Proteomics > - http://www.bio.cam.ac.uk/proteomics
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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. >>> >> >>> >>> >> >>> _______________________________________________ >>> >> >>> Bioconductor mailing list >>> >> >>> Bioconductor at r-project.org >>> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >>> >> >> _______________________________________________ >>> >> >> Bioconductor mailing list >>> >> >> Bioconductor at r-project.org >>> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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