S4Vectors not loading
1
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@panos-balomenos-9147
Last seen 4.8 years ago
Greece/University of Patras

Hi,

I am receiving the following error when loading S4Vectors, after a clean installation of R-devel and the package:

require('S4Vectors')
Loading required package: S4Vectors
Loading required package: stats4
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, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Error: package or namespace load failed for 'S4Vectors':
 .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class

sessionInfo()

R Under development (unstable) (2020-02-26 r77861)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253   
[3] LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C                 
[5] LC_TIME=Greek_Greece.1253    

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

other attached packages:
[1] BiocGenerics_0.33.0

loaded via a namespace (and not attached):
[1] compiler_4.0.0

Any ideas? Thanks.
S4Vectors • 2.1k views
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No luck getting the package to load in multiple Win installations and machines. Luckily, no problems in Linux. Thanks for the responses.

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Not sure what kind of response you're hoping. You're not providing any useful information. Please check our posting guide. Thanks!

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Instead of installing the package with BiocManager::install, I installed it from its source and the problem was solved. Thanks again for the responses.

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This sounds to me like you have packages from different versions of Bioconductor. What does

BiocManager::valid()

have to say? (note: you can format code by selecting it and then pressing the 101010 button)

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 BiocManager::valid()
    [1] TRUE
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@michael-lawrence-3846
Last seen 3.0 years ago
United States

Due to some changes in the methods package, you will need to rebuild S4Vectors. Note that if you're using a binary from a repository, it will not work until the repository rebuilds the binary. Installing from source of course should work.
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I was also getting an error with the latest R-devel:

<font color="#DC322F"> But after re-installing S4Vectors the error went away... </font>

<font color="#BABDB6">Error: package or namespace load failed for 'S4Vectors':</font>
<font color="#BABDB6"> .onLoad failed in loadNamespace() for 'S4Vectors', details:</font>
<font color="#BABDB6">  call: validObject(.Object)</font>
<font color="#BABDB6">  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class</font>
> sessionInfo()
<font color="#00D700">R Under development (unstable) (</font><font color="#D7AF5F">2020-02-28</font><font color="#00D700"> r</font><font color="#FFAF00">77874</font><font color="#00D700">)</font>
<font color="#00D700">Platform: x</font><font color="#FFAF00">86</font><font color="#00D700">_</font><font color="#FFAF00">64</font><font color="#00D700">-pc-linux-gnu (</font><font color="#FFAF00">64</font><font color="#00D700">-bit)</font>
<font color="#00D700">Running under: Ubuntu </font><font color="#FFAF00">19.04</font>

<font color="#00D700">Matrix products: default</font>
<font color="#00D700">BLAS/LAPACK: /usr/lib/x</font><font color="#FFAF00">86</font><font color="#00D700">_</font><font color="#FFAF00">64</font><font color="#00D700">-linux-gnu/libopenblasp-r</font><font color="#FFAF00">0.3.5.</font><font color="#00D700">so</font>

<font color="#00D700">locale:</font>
<font color="#00D700"> </font><font color="#008787">[1]</font><font color="#00D700"> LC_CTYPE=en_US.UTF</font><font color="#FF875F">-8</font><font color="#00D700">       LC_NUMERIC=C              </font>
<font color="#00D700"> </font><font color="#008787">[3]</font><font color="#00D700"> LC_TIME=en_US.UTF</font><font color="#FF875F">-8</font><font color="#00D700">        LC_COLLATE=en_US.UTF</font><font color="#FF875F">-8</font><font color="#00D700">    </font>
<font color="#00D700"> </font><font color="#008787">[5]</font><font color="#00D700"> LC_MONETARY=en_US.UTF</font><font color="#FF875F">-8</font><font color="#00D700">    LC_MESSAGES=en_US.UTF</font><font color="#FF875F">-8</font><font color="#00D700">   </font>
<font color="#00D700"> </font><font color="#008787">[7]</font><font color="#00D700"> LC_PAPER=en_US.UTF</font><font color="#FF875F">-8</font><font color="#00D700">       LC_NAME=C                 </font>
<font color="#00D700"> </font><font color="#008787">[9]</font><font color="#00D700"> LC_ADDRESS=C               LC_TELEPHONE=C            </font>
<font color="#008787">[11]</font><font color="#00D700"> LC_MEASUREMENT=en_US.UTF</font><font color="#FF875F">-8</font><font color="#00D700"> LC_IDENTIFICATION=C       </font>

<font color="#00D700">attached base packages:</font>
<font color="#008787">[1]</font><font color="#00D700"> parallel  stats</font><font color="#FFAF00">4</font><font color="#00D700">    stats     graphics  grDevices utils     datasets </font>
<font color="#008787">[8]</font><font color="#00D700"> methods   base     </font>

<font color="#00D700">other attached packages:</font>
<font color="#008787">[1]</font><font color="#00D700"> BiocGenerics_</font><font color="#FFAF00">0.33.0</font><font color="#00D700"> colorout_</font><font color="#FFAF00">1.2</font><font color="#FF875F">-2</font><font color="#00D700">     </font>

<font color="#00D700">loaded via a namespace (and not attached):</font>
<font color="#008787">[1]</font><font color="#00D700"> compiler_</font><font color="#FFAF00">4.0.0</font>
> packageVersion("S4Vectors")
<font color="#008787">[1]</font><font color="#00D700"> '</font><font color="#FFAF00">0.25.12</font><font color="#00D700">'</font>
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Sorry for the unrendered HTML, here it is in plain text:

Error: package or namespace load failed for 'S4Vectors':
 .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
### sessionInfo()
R Under development (unstable) (2020-02-28 r77874)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.04

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocGenerics_0.33.0 colorout_1.2-2     

loaded via a namespace (and not attached):
[1] compiler_4.0.0
### packageVersion("S4Vectors")
[1] '0.25.12'
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Yes, a reinstall is likely necessary to refresh the metadata.

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