error when loading mzR
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To whom it may concern: Here I get this error when I open new R session: "During startup - Warning messages: 1: In fun(libname, pkgname) : mzR has been built against a different Rcpp version than is installed on your system. 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. 2: Class "C++Object" is defined (with package slot ???Rcpp???) but no metadata object found to revise subclass information---not exported? Making a copy in package ???.GlobalEnv???" I have installed xcms and metaXCMS packages but I encounter several errors when I try to run metaXCMS. I installed/uninstall R several times. IS there a way of fixing mzR/Rcpp problem? I appreciate any help\ All Best, Monika -- output of sessionInfo(): > sessionInfo() R version 2.15.3 (2013-03-01) Platform: i386-w64-mingw32/i386 (32-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] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] Biobase_2.18.0 BiocGenerics_0.4.0 codetools_0.2-8 metaXCMS_0.1.20 [5] mzR_1.4.7 Rcpp_0.10.4 xcms_1.34.0 > -- Sent via the guest posting facility at bioconductor.org.
xcms mzR xcms mzR • 2.1k views
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@steve-lianoglou-2771
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Hi, On Wed, Jul 31, 2013 at 4:28 PM, Monika Lukaszewska [guest] <guest at="" bioconductor.org=""> wrote: > > To whom it may concern: > Here I get this error when I open new R session: > > "During startup - Warning messages: > 1: In fun(libname, pkgname) : > mzR has been built against a different Rcpp version > than is installed on your system. 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. > 2: Class "C++Object" is defined (with package slot ???Rcpp???) but no metadata object found to revise subclass information---not exported? Making a copy in package ???.GlobalEnv???" > > I have installed xcms and metaXCMS packages but I encounter several errors when I try to run metaXCMS. > > I installed/uninstall R several times. IS there a way of fixing mzR/Rcpp problem? You're installing an old(er) version of R (2.15.3), please install the latest version of R (3.0.1) and then reinstall your packages using biocLite. There was some chatter about mzR and Rcpp inconsistencies some time ago, which maybe what is biting you now, and I believe has since been resolved. The upgrade to R 3.0.1 will likely be all you need. You'll also get the added bonus of using the latest and greatest (and supported) versions of the Bionconductor packages you will be using for your analysis. HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
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On Wed, Jul 31, 2013 at 4:39 PM, Steve Lianoglou <lianoglou.steve at="" gene.com=""> wrote: > Hi, > > On Wed, Jul 31, 2013 at 4:28 PM, Monika Lukaszewska [guest] > <guest at="" bioconductor.org=""> wrote: >> >> To whom it may concern: >> Here I get this error when I open new R session: >> >> "During startup - Warning messages: >> 1: In fun(libname, pkgname) : >> mzR has been built against a different Rcpp version >> than is installed on your system. 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. >> 2: Class "C++Object" is defined (with package slot ???Rcpp???) but no metadata object found to revise subclass information---not exported? Making a copy in package ???.GlobalEnv???" >> >> I have installed xcms and metaXCMS packages but I encounter several errors when I try to run metaXCMS. >> >> I installed/uninstall R several times. IS there a way of fixing mzR/Rcpp problem? > > You're installing an old(er) version of R (2.15.3), please install the > latest version of R (3.0.1) and then reinstall your packages using > biocLite. > > There was some chatter about mzR and Rcpp inconsistencies some time > ago, which maybe what is biting you now, and I believe has since been > resolved. The upgrade to R 3.0.1 will likely be all you need. > > You'll also get the added bonus of using the latest and greatest (and > supported) versions of the Bionconductor packages you will be using > for your analysis. > And when you're done with all that, make sure you have Rcpp 0.10.4 installed. > HTH, > -steve > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > > _______________________________________________ > 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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Steve, Dan, Thank you guys for your comments. Unfortunately, the problem started when we installed R 3.0.1 version-metaXCMS package is build under lower version and does not work at all (our fault, we should have checked that before updating R). So we went back to R (2.15.3) version and to our surprise we got this error after opening the new session. Now, even more packages are not functional and there is no use of the software on this computer at the moment. Should we try to install Rcpp 0.10.4, or it works only with 3.0 version? We tried Rcpp 0.9.10 but got error.... All best, Monika On Wed, Jul 31, 2013 at 6:34 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Wed, Jul 31, 2013 at 4:39 PM, Steve Lianoglou > <lianoglou.steve@gene.com> wrote: > > Hi, > > > > On Wed, Jul 31, 2013 at 4:28 PM, Monika Lukaszewska [guest] > > <guest@bioconductor.org> wrote: > >> > >> To whom it may concern: > >> Here I get this error when I open new R session: > >> > >> "During startup - Warning messages: > >> 1: In fun(libname, pkgname) : > >> mzR has been built against a different Rcpp version > >> than is installed on your system. 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. > >> 2: Class "C++Object" is defined (with package slot ‘Rcpp’) but no > metadata object found to revise subclass information---not exported? > Making a copy in package ‘.GlobalEnv’" > >> > >> I have installed xcms and metaXCMS packages but I encounter several > errors when I try to run metaXCMS. > >> > >> I installed/uninstall R several times. IS there a way of fixing > mzR/Rcpp problem? > > > > You're installing an old(er) version of R (2.15.3), please install the > > latest version of R (3.0.1) and then reinstall your packages using > > biocLite. > > > > There was some chatter about mzR and Rcpp inconsistencies some time > > ago, which maybe what is biting you now, and I believe has since been > > resolved. The upgrade to R 3.0.1 will likely be all you need. > > > > You'll also get the added bonus of using the latest and greatest (and > > supported) versions of the Bionconductor packages you will be using > > for your analysis. > > > > And when you're done with all that, make sure you have Rcpp 0.10.4 > installed. > > > > > HTH, > > -steve > > > > -- > > Steve Lianoglou > > Computational Biologist > > Bioinformatics and Computational Biology > > Genentech > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Monika Lukaszewska Postdoctoral Fellow Chemistry & Biochemistry Department Montana State University Bozeman MT, 59717 lab: (406) 994 5418 tokminalukas@chemistry.montana.edu [[alternative HTML version deleted]]
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On Thu, Aug 1, 2013 at 8:02 AM, Monika Tokmina-Lukaszewska <tokminalukas at="" gmail.com=""> wrote: > Steve, Dan, > > Thank you guys for your comments. Unfortunately, the problem started when we > installed R 3.0.1 version-metaXCMS package is build under lower version and > does not work at all (our fault, we should have checked that before updating > R). So we went back to R (2.15.3) version and to our surprise we got this > error after opening the new session. Now, even more packages are not > functional and there is no use of the software on this computer at the > moment. > Should we try to install Rcpp 0.10.4, or it works only with 3.0 version? We > tried Rcpp 0.9.10 but got error.... > When you reinstall R you should always do a fresh install; don't reinstall R and then expect previously installed packages to work. Similarly, don't mix and match packages from different versions of Bioconductor. If you follow these rules and always install packages with biocLite(), everything should work. So, recommendation: Do a clean install of R 3.0.1 (removing previous installations or installing in a different directory), then use biocLite() to install all the packages you need. Dan > All best, Monika > > > On Wed, Jul 31, 2013 at 6:34 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Wed, Jul 31, 2013 at 4:39 PM, Steve Lianoglou >> <lianoglou.steve at="" gene.com=""> wrote: >> > Hi, >> > >> > On Wed, Jul 31, 2013 at 4:28 PM, Monika Lukaszewska [guest] >> > <guest at="" bioconductor.org=""> wrote: >> >> >> >> To whom it may concern: >> >> Here I get this error when I open new R session: >> >> >> >> "During startup - Warning messages: >> >> 1: In fun(libname, pkgname) : >> >> mzR has been built against a different Rcpp version >> >> than is installed on your system. 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. >> >> 2: Class "C++Object" is defined (with package slot ???Rcpp???) but no >> >> metadata object found to revise subclass information---not exported? Making >> >> a copy in package ???.GlobalEnv???" >> >> >> >> I have installed xcms and metaXCMS packages but I encounter several >> >> errors when I try to run metaXCMS. >> >> >> >> I installed/uninstall R several times. IS there a way of fixing >> >> mzR/Rcpp problem? >> > >> > You're installing an old(er) version of R (2.15.3), please install the >> > latest version of R (3.0.1) and then reinstall your packages using >> > biocLite. >> > >> > There was some chatter about mzR and Rcpp inconsistencies some time >> > ago, which maybe what is biting you now, and I believe has since been >> > resolved. The upgrade to R 3.0.1 will likely be all you need. >> > >> > You'll also get the added bonus of using the latest and greatest (and >> > supported) versions of the Bionconductor packages you will be using >> > for your analysis. >> > >> >> And when you're done with all that, make sure you have Rcpp 0.10.4 >> installed. >> >> >> >> > HTH, >> > -steve >> > >> > -- >> > Steve Lianoglou >> > Computational Biologist >> > Bioinformatics and Computational Biology >> > Genentech >> > >> > _______________________________________________ >> > 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 > > > > > -- > Monika Lukaszewska > > Postdoctoral Fellow > Chemistry & Biochemistry Department > Montana State University > Bozeman MT, 59717 > lab: (406) 994 5418 > tokminalukas at chemistry.montana.edu
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Dear Monika, In case you could not implement 'the right way', as per Dan's email, here are a few hints/clarifications regarding mzR. The first thing to do when switching back to R 2.15.3 is to run biocLite to update (actually downgrade) the Bioconductor packages to match the R version. This should also downgrade mzR to version 1.4.6, I believe. The matching Rcpp version should then be 0.10.3. Note that based on your first email, it does not seem that you have an actual error but just a warning. When loading the package, mzR checks whether the Rcpp version used to build the binary package that you have and the actual installed Rcpp version are the same and warns if there is a mismatch. This does not mean that things will go wrong (although things have gone wrong in the past, resulting in the warning message you see): mzR 1.4.6 (originally built using Rcpp 0.10.3) does work with 0.10.3 and _might_ also work with the latest Rcpp 0.10.4. Hope this helps. Best wishes, Laurent On 1 August 2013 16:02, Monika Tokmina-Lukaszewska <tokminalukas at="" gmail.com=""> wrote: > Steve, Dan, > > Thank you guys for your comments. Unfortunately, the problem started when > we installed R 3.0.1 version-metaXCMS package is build under lower version > and does not work at all (our fault, we should have checked that before > updating R). So we went back to R (2.15.3) version and to our surprise we > got this error after opening the new session. Now, even more packages are > not functional and there is no use of the software on this computer at the > moment. > Should we try to install Rcpp 0.10.4, or it works only with 3.0 version? We > tried Rcpp 0.9.10 but got error.... > > All best, Monika > > On Wed, Jul 31, 2013 at 6:34 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > >> On Wed, Jul 31, 2013 at 4:39 PM, Steve Lianoglou >> <lianoglou.steve at="" gene.com=""> wrote: >> > Hi, >> > >> > On Wed, Jul 31, 2013 at 4:28 PM, Monika Lukaszewska [guest] >> > <guest at="" bioconductor.org=""> wrote: >> >> >> >> To whom it may concern: >> >> Here I get this error when I open new R session: >> >> >> >> "During startup - Warning messages: >> >> 1: In fun(libname, pkgname) : >> >> mzR has been built against a different Rcpp version >> >> than is installed on your system. 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. >> >> 2: Class "C++Object" is defined (with package slot ?Rcpp?) but no >> metadata object found to revise subclass information---not exported? >> Making a copy in package ?.GlobalEnv?" >> >> >> >> I have installed xcms and metaXCMS packages but I encounter several >> errors when I try to run metaXCMS. >> >> >> >> I installed/uninstall R several times. IS there a way of fixing >> mzR/Rcpp problem? >> > >> > You're installing an old(er) version of R (2.15.3), please install the >> > latest version of R (3.0.1) and then reinstall your packages using >> > biocLite. >> > >> > There was some chatter about mzR and Rcpp inconsistencies some time >> > ago, which maybe what is biting you now, and I believe has since been >> > resolved. The upgrade to R 3.0.1 will likely be all you need. >> > >> > You'll also get the added bonus of using the latest and greatest (and >> > supported) versions of the Bionconductor packages you will be using >> > for your analysis. >> > >> >> And when you're done with all that, make sure you have Rcpp 0.10.4 >> installed. >> >> >> >> > HTH, >> > -steve >> > >> > -- >> > Steve Lianoglou >> > Computational Biologist >> > Bioinformatics and Computational Biology >> > Genentech >> > >> > _______________________________________________ >> > 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 >> > > > > -- > Monika Lukaszewska > > Postdoctoral Fellow > Chemistry & Biochemistry Department > Montana State University > Bozeman MT, 59717 > lab: (406) 994 5418 > tokminalukas at chemistry.montana.edu > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 Using R/Bioconductor for proteomics data analysis - http://lgatto.github.io/RforProteomics/
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Dear Colleagues, thank you very much for you comments. Indeed, there was still other R version "lingering" in the directory I did not expect. After we removed all versions and did clean install R works beautifully, no errors, no warring :) All Best, Monika On Thu, Aug 1, 2013 at 9:40 AM, Laurent Gatto <lg390@cam.ac.uk> wrote: > Dear Monika, > > In case you could not implement 'the right way', as per Dan's email, > here are a few hints/clarifications regarding mzR. > > The first thing to do when switching back to R 2.15.3 is to run > biocLite to update (actually downgrade) the Bioconductor packages to > match the R version. This should also downgrade mzR to version 1.4.6, > I believe. The matching Rcpp version should then be 0.10.3. > > Note that based on your first email, it does not seem that you have an > actual error but just a warning. When loading the package, mzR checks > whether the Rcpp version used to build the binary package that you > have and the actual installed Rcpp version are the same and warns if > there is a mismatch. This does not mean that things will go wrong > (although things have gone wrong in the past, resulting in the warning > message you see): mzR 1.4.6 (originally built using Rcpp 0.10.3) does > work with 0.10.3 and _might_ also work with the latest Rcpp 0.10.4. > > Hope this helps. > > Best wishes, > > Laurent > > > On 1 August 2013 16:02, Monika Tokmina-Lukaszewska > <tokminalukas@gmail.com> wrote: > > Steve, Dan, > > > > Thank you guys for your comments. Unfortunately, the problem started when > > we installed R 3.0.1 version-metaXCMS package is build under lower > version > > and does not work at all (our fault, we should have checked that before > > updating R). So we went back to R (2.15.3) version and to our surprise we > > got this error after opening the new session. Now, even more packages are > > not functional and there is no use of the software on this computer at > the > > moment. > > Should we try to install Rcpp 0.10.4, or it works only with 3.0 version? > We > > tried Rcpp 0.9.10 but got error.... > > > > All best, Monika > > > > On Wed, Jul 31, 2013 at 6:34 PM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > > > >> On Wed, Jul 31, 2013 at 4:39 PM, Steve Lianoglou > >> <lianoglou.steve@gene.com> wrote: > >> > Hi, > >> > > >> > On Wed, Jul 31, 2013 at 4:28 PM, Monika Lukaszewska [guest] > >> > <guest@bioconductor.org> wrote: > >> >> > >> >> To whom it may concern: > >> >> Here I get this error when I open new R session: > >> >> > >> >> "During startup - Warning messages: > >> >> 1: In fun(libname, pkgname) : > >> >> mzR has been built against a different Rcpp version > >> >> than is installed on your system. 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. > >> >> 2: Class "C++Object" is defined (with package slot ‘Rcpp’) but no > >> metadata object found to revise subclass information---not exported? > >> Making a copy in package ‘.GlobalEnv’" > >> >> > >> >> I have installed xcms and metaXCMS packages but I encounter several > >> errors when I try to run metaXCMS. > >> >> > >> >> I installed/uninstall R several times. IS there a way of fixing > >> mzR/Rcpp problem? > >> > > >> > You're installing an old(er) version of R (2.15.3), please install the > >> > latest version of R (3.0.1) and then reinstall your packages using > >> > biocLite. > >> > > >> > There was some chatter about mzR and Rcpp inconsistencies some time > >> > ago, which maybe what is biting you now, and I believe has since been > >> > resolved. The upgrade to R 3.0.1 will likely be all you need. > >> > > >> > You'll also get the added bonus of using the latest and greatest (and > >> > supported) versions of the Bionconductor packages you will be using > >> > for your analysis. > >> > > >> > >> And when you're done with all that, make sure you have Rcpp 0.10.4 > >> installed. > >> > >> > >> > >> > HTH, > >> > -steve > >> > > >> > -- > >> > Steve Lianoglou > >> > Computational Biologist > >> > Bioinformatics and Computational Biology > >> > Genentech > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor@r-project.org > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > > > -- > > Monika Lukaszewska > > > > Postdoctoral Fellow > > Chemistry & Biochemistry Department > > Montana State University > > Bozeman MT, 59717 > > lab: (406) 994 5418 > > tokminalukas@chemistry.montana.edu > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@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 > Using R/Bioconductor for proteomics data analysis > - http://lgatto.github.io/RforProteomics/ > -- Monika Lukaszewska Postdoctoral Fellow Chemistry & Biochemistry Department Montana State University Bozeman MT, 59717 lab: (406) 994 5418 tokminalukas@chemistry.montana.edu [[alternative HTML version deleted]]
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