mzR installation
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@gtsilikibioacademygr-6397
Last seen 10.3 years ago
Hello, I'm trying to install the Risa package at R 3.0.2 but there seems to be a problem with mzR installation. Particularly, >library(mzR) produces the following error message: Loading required package: Rcpp Error : .onLoad failed in loadNamespace() for 'mzR', details: call: value[[3L]](cond) error: failed to load module Ramp from package mzR value of 'SET_ATTRIB' must be a pairlist or NULL, not a 'character' In addition: Warning message: In fun(libname, pkgname) : mzR has been built against a different Rcpp version (0.10.5) than is installed on your system (0.11.0). This might lead to errors when loading mzR. If you encounter such issues, please send a report, including the output of sessionInfo() to the Bioc mailing list -- http://www.bioconductor.org/help/mailing-list. Error: package or namespace load failed for ?mzR? > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rcpp_0.11.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] Biobase_2.22.0 BiocGenerics_0.8.0 parallel_3.0.2 tools_3.0.2 Installing Rcpp 0.10.5 is the way around this? Thanks in advance, Georgia
mzR Risa mzR Risa • 2.5k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 6 months ago
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Hi Georgia, ----- Original Message ----- > From: gtsiliki at bioacademy.gr > To: bioconductor at r-project.org > Sent: Monday, February 10, 2014 6:01:31 AM > Subject: [BioC] mzR installation > > Hello, > > I'm trying to install the Risa package at R 3.0.2 but there seems to > be a > problem with mzR installation. > Particularly, >library(mzR) produces the following error message: > > Loading required package: Rcpp > Error : .onLoad failed in loadNamespace() for 'mzR', details: > call: value[[3L]](cond) > error: failed to load module Ramp from package mzR > value of 'SET_ATTRIB' must be a pairlist or NULL, not a 'character' > In addition: Warning message: > In fun(libname, pkgname) : > mzR has been built against a different Rcpp version (0.10.5) > than is installed on your system (0.11.0). This might lead to errors > when loading mzR. If you encounter such issues, please send > a report, including the output of sessionInfo() to the Bioc > mailing list -- http://www.bioconductor.org/help/mailing-list. > Error: package or namespace load failed for ?mzR? > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Rcpp_0.11.0 BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.22.0 BiocGenerics_0.8.0 parallel_3.0.2 > tools_3.0.2 > > > Installing Rcpp 0.10.5 is the way around this? > What the error message is saying is that installing Rcpp 0.11.0 is the way around this. Unfortunately, that's not all. The latest version of mzR is currently not available for Mac because of an issue in Rcpp which needs to be fixed. Looks like it has been fixed in Github but not yet propagated to CRAN. So as soon as you see a version of Rcpp higher than 0.11.0 on this page: http://cran.r-project.org/web/packages/Rcpp/index.html ...try again. Thanks, Dan > Thanks in advance, > Georgia > > _______________________________________________ > 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 10 February 2014 at 10:21, Dan Tenenbaum wrote: | What the error message is saying is that installing Rcpp 0.11.0 is the way around this. | Unfortunately, that's not all. | | The latest version of mzR is currently not available for Mac because of an issue in Rcpp which needs to be | fixed. Looks like it has been fixed in Github but not yet propagated to CRAN. So as soon as you see a version of Rcpp higher than 0.11.0 on | this page: | | http://cran.r-project.org/web/packages/Rcpp/index.html | | ...try again. Or just install Rcpp from it current (and *very stable*) source repository: https://github.com/RcppCore/Rcpp Dirk -- Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 6 months ago
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----- Original Message ----- > From: "Dirk Eddelbuettel" <edd at="" debian.org=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: gtsiliki at bioacademy.gr, bioconductor at r-project.org, "Dirk Eddelbuettel" <edd at="" debian.org="">, "Kevin Ushey" > <kevinushey at="" gmail.com="">, "Steffen Neumann" <sneumann at="" ipb-="" halle.de=""> > Sent: Monday, February 10, 2014 6:36:56 PM > Subject: Re: [BioC] mzR installation > > > On 10 February 2014 at 10:21, Dan Tenenbaum wrote: > | What the error message is saying is that installing Rcpp 0.11.0 is > | the way around this. > | Unfortunately, that's not all. > | > | The latest version of mzR is currently not available for Mac > | because of an issue in Rcpp which needs to be > | fixed. Looks like it has been fixed in Github but not yet > | propagated to CRAN. So as soon as you see a version of Rcpp higher > | than 0.11.0 on > | this page: > | > | http://cran.r-project.org/web/packages/Rcpp/index.html > | > | ...try again. > > Or just install Rcpp from it current (and *very stable*) source > repository: > https://github.com/RcppCore/Rcpp > You can also do this: source("http://bioconductor.org/biocLite.R") biocLite("mzR", type="source") But this (and the github url that Dirk suggests) requires that you have the appropriate compilers installed, which on Mac requires that you install Xcode and its "command line tools" package. Dan > Dirk > > -- > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com >
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----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > To: "Dirk Eddelbuettel" <edd at="" debian.org=""> > Cc: "Kevin Ushey" <kevinushey at="" gmail.com="">, bioconductor at r-project.org, gtsiliki at bioacademy.gr > Sent: Monday, February 10, 2014 6:50:31 PM > Subject: Re: [BioC] mzR installation > > > > ----- Original Message ----- > > From: "Dirk Eddelbuettel" <edd at="" debian.org=""> > > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > > Cc: gtsiliki at bioacademy.gr, bioconductor at r-project.org, "Dirk > > Eddelbuettel" <edd at="" debian.org="">, "Kevin Ushey" > > <kevinushey at="" gmail.com="">, "Steffen Neumann" <sneumann at="" ipb-="" halle.de=""> > > Sent: Monday, February 10, 2014 6:36:56 PM > > Subject: Re: [BioC] mzR installation > > > > > > On 10 February 2014 at 10:21, Dan Tenenbaum wrote: > > | What the error message is saying is that installing Rcpp 0.11.0 > > | is > > | the way around this. > > | Unfortunately, that's not all. > > | > > | The latest version of mzR is currently not available for Mac > > | because of an issue in Rcpp which needs to be > > | fixed. Looks like it has been fixed in Github but not yet > > | propagated to CRAN. So as soon as you see a version of Rcpp > > | higher > > | than 0.11.0 on > > | this page: > > | > > | http://cran.r-project.org/web/packages/Rcpp/index.html > > | > > | ...try again. > > > > Or just install Rcpp from it current (and *very stable*) source > > repository: > > https://github.com/RcppCore/Rcpp > > > > You can also do this: > > source("http://bioconductor.org/biocLite.R") > biocLite("mzR", type="source") > > But this (and the github url that Dirk suggests) requires that you > have the appropriate compilers installed, which on Mac requires that > you install Xcode and its "command line tools" package. > And you may also need the clang compiler (since Rcpp won't compile with the version of g++ that is available by default on Mac OS X). I'm working with Dirk and Kevin to get a patched version out so you don't need to do all this. Thanks, Dan > Dan > > > > Dirk > > > > -- > > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com > > > > _______________________________________________ > 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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----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > To: "Dirk Eddelbuettel" <edd at="" debian.org=""> > Cc: "Kevin Ushey" <kevinushey at="" gmail.com="">, bioconductor at r-project.org, gtsiliki at bioacademy.gr > Sent: Monday, February 10, 2014 6:57:06 PM > Subject: Re: [BioC] mzR installation > > > > ----- Original Message ----- > > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > > To: "Dirk Eddelbuettel" <edd at="" debian.org=""> > > Cc: "Kevin Ushey" <kevinushey at="" gmail.com="">, > > bioconductor at r-project.org, gtsiliki at bioacademy.gr > > Sent: Monday, February 10, 2014 6:50:31 PM > > Subject: Re: [BioC] mzR installation > > > > > > > > ----- Original Message ----- > > > From: "Dirk Eddelbuettel" <edd at="" debian.org=""> > > > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > > > Cc: gtsiliki at bioacademy.gr, bioconductor at r-project.org, "Dirk > > > Eddelbuettel" <edd at="" debian.org="">, "Kevin Ushey" > > > <kevinushey at="" gmail.com="">, "Steffen Neumann" <sneumann at="" ipb-="" halle.de=""> > > > Sent: Monday, February 10, 2014 6:36:56 PM > > > Subject: Re: [BioC] mzR installation > > > > > > > > > On 10 February 2014 at 10:21, Dan Tenenbaum wrote: > > > | What the error message is saying is that installing Rcpp 0.11.0 > > > | is > > > | the way around this. > > > | Unfortunately, that's not all. > > > | > > > | The latest version of mzR is currently not available for Mac > > > | because of an issue in Rcpp which needs to be > > > | fixed. Looks like it has been fixed in Github but not yet > > > | propagated to CRAN. So as soon as you see a version of Rcpp > > > | higher > > > | than 0.11.0 on > > > | this page: > > > | > > > | http://cran.r-project.org/web/packages/Rcpp/index.html > > > | > > > | ...try again. > > > > > > Or just install Rcpp from it current (and *very stable*) source > > > repository: > > > https://github.com/RcppCore/Rcpp > > > > > > > You can also do this: > > > > source("http://bioconductor.org/biocLite.R") > > biocLite("mzR", type="source") > > > > But this (and the github url that Dirk suggests) requires that you > > have the appropriate compilers installed, which on Mac requires > > that > > you install Xcode and its "command line tools" package. > > > > And you may also need the clang compiler (since Rcpp won't compile > with the version of g++ that is available by default on Mac OS X). > I'm working with Dirk and Kevin to get a patched version out so you > don't need to do all this. > A new version of mzR (1.8.1.1) is now available via: source("http://bioconductor.org/biocLite.R") biocLite("mzR") This does not require any special tools to be installed. Sorry for the inconvenience. Let me know if you continue to have issues. Dan > Thanks, > Dan > > > > Dan > > > > > > > Dirk > > > > > > -- > > > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com > > > > > > > _______________________________________________ > > 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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Issue solved! Many thanks for your help! Georgia > > > ----- Original Message ----- >> From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> To: "Dirk Eddelbuettel" <edd at="" debian.org=""> >> Cc: "Kevin Ushey" <kevinushey at="" gmail.com="">, bioconductor at r-project.org, >> gtsiliki at bioacademy.gr >> Sent: Monday, February 10, 2014 6:57:06 PM >> Subject: Re: [BioC] mzR installation >> >> >> >> ----- Original Message ----- >> > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> > To: "Dirk Eddelbuettel" <edd at="" debian.org=""> >> > Cc: "Kevin Ushey" <kevinushey at="" gmail.com="">, >> > bioconductor at r-project.org, gtsiliki at bioacademy.gr >> > Sent: Monday, February 10, 2014 6:50:31 PM >> > Subject: Re: [BioC] mzR installation >> > >> > >> > >> > ----- Original Message ----- >> > > From: "Dirk Eddelbuettel" <edd at="" debian.org=""> >> > > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> > > Cc: gtsiliki at bioacademy.gr, bioconductor at r-project.org, "Dirk >> > > Eddelbuettel" <edd at="" debian.org="">, "Kevin Ushey" >> > > <kevinushey at="" gmail.com="">, "Steffen Neumann" <sneumann at="" ipb-="" halle.de=""> >> > > Sent: Monday, February 10, 2014 6:36:56 PM >> > > Subject: Re: [BioC] mzR installation >> > > >> > > >> > > On 10 February 2014 at 10:21, Dan Tenenbaum wrote: >> > > | What the error message is saying is that installing Rcpp 0.11.0 >> > > | is >> > > | the way around this. >> > > | Unfortunately, that's not all. >> > > | >> > > | The latest version of mzR is currently not available for Mac >> > > | because of an issue in Rcpp which needs to be >> > > | fixed. Looks like it has been fixed in Github but not yet >> > > | propagated to CRAN. So as soon as you see a version of Rcpp >> > > | higher >> > > | than 0.11.0 on >> > > | this page: >> > > | >> > > | http://cran.r-project.org/web/packages/Rcpp/index.html >> > > | >> > > | ...try again. >> > > >> > > Or just install Rcpp from it current (and *very stable*) source >> > > repository: >> > > https://github.com/RcppCore/Rcpp >> > > >> > >> > You can also do this: >> > >> > source("http://bioconductor.org/biocLite.R") >> > biocLite("mzR", type="source") >> > >> > But this (and the github url that Dirk suggests) requires that you >> > have the appropriate compilers installed, which on Mac requires >> > that >> > you install Xcode and its "command line tools" package. >> > >> >> And you may also need the clang compiler (since Rcpp won't compile >> with the version of g++ that is available by default on Mac OS X). >> I'm working with Dirk and Kevin to get a patched version out so you >> don't need to do all this. >> > > > A new version of mzR (1.8.1.1) is now available via: > source("http://bioconductor.org/biocLite.R") > biocLite("mzR") > > This does not require any special tools to be installed. Sorry for the > inconvenience. Let me know if you continue to have issues. > > Dan > > > >> Thanks, >> Dan >> >> >> > Dan >> > >> > >> > > Dirk >> > > >> > > -- >> > > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com >> > > >> > >> > _______________________________________________ >> > 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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