Martin Maechler
2019-Aug-20 10:31 UTC
[R] Cannot load vegan and vcd, "object vI not found"
>>>>> Jeff Newmiller >>>>> on Mon, 19 Aug 2019 17:38:19 -0700 writes:> Try closing all instances of R except for one and then run the update.packages() function. If that doesn't work then post the output of sessionInfo(). I also strongly suspect that some of the packages concerned were not correctly installed. > On August 19, 2019 5:11:11 AM PDT, Camilo Bernardo Garcia Ramirez <cbgarciar at unal.edu.co> wrote: >> Hi: Could you help me with the following issue?: >> >> I downloaded the packages vegan and vcd with R3.6.1. When I try to load >> them I got this error messages: >> >> > library(vegan) >> Loading required package: permute >> Loading required package: lattice >> Error: package or namespace load failed for ?vegan? in loadNamespace(j >> <- >> i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): >> objeto 'vI' no encontrado (translation: object vI not found - my R is >> in >> Spanish) The error message above comes from base R's function loadNamespace() [which calls itself recursively, when importing from other packages]. I think the error message is not really useful, and indeed I think should *not* happen at this time: 'vI' is not defined here, because earlier the 'pkgInfo' result was not really valid. So I think you may have touched on a "buglet" in R in the sense that for such semi-validly / invalidly installed packages, you should get a better error message. Martin Maechler ETH Zurich and R Core team. >>> library(vcd) >> Loading required package: grid >> Error: package or namespace load failed for ?vcd? in loadNamespace(j <- >> i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): >> objeto 'vI' no encontrado (translation: object vI not found - my R is >> in >> Spanish) >> >> Sofar no one knows what that means. I am not an R expert! Could you >> help >> me?. >> Regards, >> Camilo B. Garcia > -- > Sent from my phone. Please excuse my brevity. > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Camilo Bernardo Garcia Ramirez
2019-Aug-20 22:03 UTC
[R] Cannot load vegan and vcd, "object vI not found"
Hi again: First at all, thanks for your answer. My problem is still there. Here the session. I did remove and (re)install vegan and then called for update but no effect in the error. I included the sessionInfo() at the end. Camilo> remove.packages("vegan")Removing package from ?C:/Users/Camilo/Documents/R/win-library/3.6? (as ?lib? is unspecified)> install.packages("vegan", dependencies=TRUE)Installing package into ?C:/Users/Camilo/Documents/R/win-library/3.6? (as ?lib? is unspecified) --- Please select a CRAN mirror for use in this session --- probando la URL ' https://cran.wu.ac.at/bin/windows/contrib/3.6/vegan_2.5-5.zip' Content type 'application/zip' length 3862370 bytes (3.7 MB) downloaded 3.7 MB package ?vegan? successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Camilo\AppData\Local\Temp\Rtmpu0yOZa\downloaded_packages> update.packages("vegan") > library(vegan)Loading required package: permute Loading required package: lattice Error: package or namespace load failed for ?vegan? in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): objeto 'vI' no encontrado> sessionInfo()R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134) Matrix products: default locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lattice_0.20-38 permute_0.9-5 loaded via a namespace (and not attached): [1] compiler_3.6.1 parallel_3.6.1 tools_3.6.1 grid_3.6.1>El mar., 20 ago. 2019 a las 5:31, Martin Maechler (< maechler at stat.math.ethz.ch>) escribi?:> >>>>> Jeff Newmiller > >>>>> on Mon, 19 Aug 2019 17:38:19 -0700 writes: > > > Try closing all instances of R except for one and then run the > update.packages() function. If that doesn't work then post the output of > sessionInfo(). > > I also strongly suspect that some of the packages concerned were > not correctly installed. > > > On August 19, 2019 5:11:11 AM PDT, Camilo Bernardo Garcia Ramirez < > cbgarciar at unal.edu.co> wrote: > >> Hi: Could you help me with the following issue?: > >> > >> I downloaded the packages vegan and vcd with R3.6.1. When I try to > load > >> them I got this error messages: > >> > >> > library(vegan) > >> Loading required package: permute > >> Loading required package: lattice > >> Error: package or namespace load failed for ?vegan? in > loadNamespace(j > >> <- > >> i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): > >> objeto 'vI' no encontrado (translation: object vI not found - my R > is > >> in > >> Spanish) > > The error message above comes from base R's function > loadNamespace() [which calls itself recursively, when importing > from other packages]. > > I think the error message is not really useful, and indeed I think > should *not* happen at this time: 'vI' is not defined here, > because earlier the 'pkgInfo' result was not really valid. > > So I think you may have touched on a "buglet" in R in the sense > that for such semi-validly / invalidly installed packages, you > should get a better error message. > > Martin Maechler > ETH Zurich and R Core team. > > > >>> library(vcd) > >> Loading required package: grid > >> Error: package or namespace load failed for ?vcd? in > loadNamespace(j <- > >> i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): > >> objeto 'vI' no encontrado (translation: object vI not found - my R > is > >> in > >> Spanish) > >> > >> Sofar no one knows what that means. I am not an R expert! Could you > >> help > >> me?. > >> Regards, > >> Camilo B. Garcia > > > -- > > Sent from my phone. Please excuse my brevity. > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. >-- Camilo B. Garc?a, Dr. rer. nat Profesor Asociado, Departamento de Biolog?a Universidad Nacional de Colombia - Sede Bogot? [[alternative HTML version deleted]]
Hi, You misunderstood the suggestion, which was to run update.packages() to update all packages, not just vegan (which doesn't need updated because you just reinstalled it). To make your own life easier, I'd run it as: update.packages(ask=FALSE, checkBuilt = TRUE) You could also try reinstalling the packages that vegan requires, which seems to be where the error actually is. (lattice, perhaps, but I'd reinstall Sarah On Tue, Aug 20, 2019 at 6:27 PM Camilo Bernardo Garcia Ramirez <cbgarciar at unal.edu.co> wrote:> > Hi again: First at all, thanks for your answer. My problem is still there. > Here the session. I did remove and (re)install vegan and then called for > update but no effect in the error. I included the sessionInfo() at the end. > Camilo > > > remove.packages("vegan") > Removing package from ?C:/Users/Camilo/Documents/R/win-library/3.6? > (as ?lib? is unspecified) > > install.packages("vegan", dependencies=TRUE) > Installing package into ?C:/Users/Camilo/Documents/R/win-library/3.6? > (as ?lib? is unspecified) > --- Please select a CRAN mirror for use in this session --- > probando la URL ' > https://cran.wu.ac.at/bin/windows/contrib/3.6/vegan_2.5-5.zip' > Content type 'application/zip' length 3862370 bytes (3.7 MB) > downloaded 3.7 MB > > package ?vegan? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\Camilo\AppData\Local\Temp\Rtmpu0yOZa\downloaded_packages > > update.packages("vegan") > > library(vegan) > Loading required package: permute > Loading required package: lattice > Error: package or namespace load failed for ?vegan? in loadNamespace(j <- > i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): > objeto 'vI' no encontrado > > > sessionInfo() > R version 3.6.1 (2019-07-05) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 10 x64 (build 17134) > > Matrix products: default > > locale: > [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 > [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C > [5] LC_TIME=Spanish_Spain.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lattice_0.20-38 permute_0.9-5 > > loaded via a namespace (and not attached): > [1] compiler_3.6.1 parallel_3.6.1 tools_3.6.1 grid_3.6.1 > > > > El mar., 20 ago. 2019 a las 5:31, Martin Maechler (< > maechler at stat.math.ethz.ch>) escribi?: > > > >>>>> Jeff Newmiller > > >>>>> on Mon, 19 Aug 2019 17:38:19 -0700 writes: > > > > > Try closing all instances of R except for one and then run the > > update.packages() function. If that doesn't work then post the output of > > sessionInfo(). > > > > I also strongly suspect that some of the packages concerned were > > not correctly installed. > > > > > On August 19, 2019 5:11:11 AM PDT, Camilo Bernardo Garcia Ramirez < > > cbgarciar at unal.edu.co> wrote: > > >> Hi: Could you help me with the following issue?: > > >> > > >> I downloaded the packages vegan and vcd with R3.6.1. When I try to > > load > > >> them I got this error messages: > > >> > > >> > library(vegan) > > >> Loading required package: permute > > >> Loading required package: lattice > > >> Error: package or namespace load failed for ?vegan? in > > loadNamespace(j > > >> <- > > >> i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): > > >> objeto 'vI' no encontrado (translation: object vI not found - my R > > is > > >> in > > >> Spanish) > > > > The error message above comes from base R's function > > loadNamespace() [which calls itself recursively, when importing > > from other packages]. > > > > I think the error message is not really useful, and indeed I think > > should *not* happen at this time: 'vI' is not defined here, > > because earlier the 'pkgInfo' result was not really valid. > > > > So I think you may have touched on a "buglet" in R in the sense > > that for such semi-validly / invalidly installed packages, you > > should get a better error message. > > > > Martin Maechler > > ETH Zurich and R Core team. > > > > > > >>> library(vcd) > > >> Loading required package: grid > > >> Error: package or namespace load failed for ?vcd? in > > loadNamespace(j <- > > >> i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): > > >> objeto 'vI' no encontrado (translation: object vI not found - my R > > is > > >> in > > >> Spanish) > > >> > > >> Sofar no one knows what that means. I am not an R expert! Could you > > >> help > > >> me?. > > >> Regards, > > >> Camilo B. Garcia > > > > > --