Error when loading MSnbase package "object 'vI' not found"
Entering edit mode
lmg • 0
Last seen 2.1 years ago

I tried several times installing the MSnbase package using:



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

[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

msnbase xcms pheatmap • 911 views
Entering edit mode
Last seen 2 days ago

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

  1. restart R altogether
  2. re-install with BiocManager::install("MSnbase")
  3. load library("MSnbase")

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

Entering edit mode

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 ''
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
Update old packages: 'caret'
Update all/some/none? [a/s/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,, basename, cbind, colMeans, colnames, colSums, dirname,,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map,
    mapply, match, mget, order, paste, pmax,, pmin,, 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’:


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 For details see also

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.

Entering edit mode

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()?

Entering edit mode

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!


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