Error when loading MSnbase package "object 'vI' not found"

Question: Error when loading MSnbase package "object 'vI' not found"

3 months ago by

lmg • 0

lmg • 0 wrote:

I tried several times installing the MSnbase package using:

BiocManager::install("MSnbase")

BiocManager::install("MSnbase", dependencies= T)

When I try to load the MSnbase package using library(MSnbase) I get the following error:

> library(MSnbase)
Error: package or namespace load failed for ‘MSnbase’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 object 'vI' not found

I am having the same problem with another package, "pheatmap" I do not know what else to do. Help please!

> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocParallel_1.16.6 ProtGenerics_1.14.0 S4Vectors_0.20.1    mzR_2.16.2          Rcpp_1.0.1         
[6] Biobase_2.42.0      BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] impute_1.56.0      tools_3.5.3        grid_3.5.3         yaml_2.2.0         BiocManager_1.30.4 codetools_0.2-16  
[7] ncdf4_1.16.1       compiler_3.5.3

Thank you

xcms msnbase pheatmap • 166 views

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modified 3 months ago • written 3 months ago by lmg • 0

Answer: Error when loading MSnbase package "object 'vI' not found"

3 months ago by

Laurent Gatto ♦ 1.1k

United Kingdom

Laurent Gatto ♦ 1.1k wrote:

Strange, and unlikely to be an MSnbase issue. Could you

restart R altogether
re-install with BiocManager::install("MSnbase")
load library("MSnbase")

If the above fails, could you provide the end of the installation output.

ADD COMMENT • link written 3 months ago by Laurent Gatto ♦ 1.1k

Dear Laurent,

Unfortunately it does not work. This is the output after installation:

> BiocManager::install("MSnbase")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.3 (2019-03-11)
Installing package(s) 'MSnbase'
trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/MSnbase_2.8.3.zip'
Content type 'application/zip' length 7336239 bytes (7.0 MB)
downloaded 7.0 MB

package ‘MSnbase’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\lmartin3\AppData\Local\Temp\RtmpekQkTA\downloaded_packages
Update old packages: 'caret'
Update all/some/none? [a/s/n]: 
n
> library(MSnbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply,
    parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: ProtGenerics
Error: package or namespace load failed for ‘MSnbase’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 object 'vI' not found
In addition: Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.0)
than is installed on your system (1.0.1). 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 support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

The "caret" package new version 6.0-82 is not available as windows binary file, so it is not really updated even I choose so.

ADD REPLY • link written 3 months ago by lmg • 0

Weird... Could you try to remove.packages("MSnbase") and re-install it again. I wonder if this might not be related to packages and their dependencies being installed in different libraries. What's your output of .libPaths()?

ADD REPLY • link written 3 months ago by Laurent Gatto ♦ 1.1k

Dear Laurent,

I managed to solve the issue by re-installing all my packages from scratch. Given the BiocManager update probably I was dragging packages from older versions which were giving problems, as it was not only MSnbase that gave this error. I keep my packages in two directories but I always set this up at the start of the R session.

Anyway, I saw a lot of posts in forums with people having the "object 'vI' not found" error, so maybe this is useful for them too.

Thank you for your help!

ADD REPLY • link written 3 months ago by lmg • 0

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