Error uploading deseq2
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@margaritabogorad-23345
Last seen 4.6 years ago

Hello,

Since yesterday I am facing an error uploading deseq2 package that has been installed for a long time and worked perfectly fine until yesterday. the error is

Error: package or namespace load failed for ‘DESeq2’:
 objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:S4Vectors'

I have restarted the R session, removed and installed again S4Vectors, IRanges, newest version of BiocGenerics but nothing helped. Do you know why all of the student I am facing this error?

Thank you in advance!

Rita

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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

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

other attached packages:
 [1] viridis_0.5.1               viridisLite_0.3.0           tidyr_1.0.2                
 [4] dendextend_1.13.4           ggplot2_3.3.0               vegan_2.5-6                
 [7] lattice_0.20-41             permute_0.9-5               phyloseq_1.28.0            
[10] SummarizedExperiment_1.14.1 DelayedArray_0.10.0         BiocParallel_1.18.1        
[13] matrixStats_0.56.0          Biobase_2.46.0              GenomicRanges_1.36.1       
[16] GenomeInfoDb_1.20.0         IRanges_2.18.3              S4Vectors_0.22.1           
[19] BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] nlme_3.1-147           bitops_1.0-6           RColorBrewer_1.1-2     tools_3.6.3           
 [5] backports_1.1.6        R6_2.4.1               rpart_4.1-15           Hmisc_4.4-0           
 [9] mgcv_1.8-31            colorspace_1.4-1       ade4_1.7-15            nnet_7.3-13           
[13] withr_2.1.2            tidyselect_1.0.0       gridExtra_2.3          compiler_3.6.3        
[17] cli_2.0.2              htmlTable_1.13.3       scales_1.1.0           checkmate_2.0.0       
[21] stringr_1.4.0          digest_0.6.25          foreign_0.8-76         XVector_0.26.0        
[25] base64enc_0.1-3        jpeg_0.1-8.1           pkgconfig_2.0.3        htmltools_0.4.0       
[29] htmlwidgets_1.5.1      rlang_0.4.5            rstudioapi_0.11        jsonlite_1.6.1        
[33] acepack_1.4.1          dplyr_0.8.5            RCurl_1.98-1.1         magrittr_1.5          
[37] GenomeInfoDbData_1.2.1 Formula_1.2-3          biomformat_1.14.0      Matrix_1.2-18         
[41] Rcpp_1.0.4.6           munsell_0.5.0          Rhdf5lib_1.8.0         fansi_0.4.1           
[45] ape_5.3                lifecycle_0.2.0        stringi_1.4.6          yaml_2.2.1            
[49] MASS_7.3-51.5          zlibbioc_1.32.0        rhdf5_2.30.1           plyr_1.8.6            
[53] grid_3.6.3             crayon_1.3.4           Biostrings_2.54.0      splines_3.6.3         
[57] multtest_2.42.0        knitr_1.28             pillar_1.4.3           igraph_1.2.5          
[61] reshape2_1.4.4         codetools_0.2-16       glue_1.4.0             latticeExtra_0.6-29   
[65] data.table_1.12.8      BiocManager_1.30.10    png_0.1-7              vctrs_0.2.4           
[69] foreach_1.5.0          gtable_0.3.0           purrr_0.3.3            assertthat_0.2.1      
[73] xfun_0.13              survival_3.1-12        tibble_3.0.0           iterators_1.0.12      
[77] cluster_2.1.0          ellipsis_0.3.0
deseq2 S4Vectors • 2.4k views
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@mikelove
Last seen 19 hours ago
United States

Can you check:

BiocManager::valid()
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Thank you for your reply,

0 packages out-of-date; 2 packages too new

Those packages are Biostrings and XVector. Creating a valid installation for those two fails, again because of the S4Vectors

 BiocManager::install(c(
    "Biostrings", "XVector"
  ), update = TRUE, ask = FALSE)

Error: package or namespace load failed for ‘S4Vectors’:
 Function found when exporting methods from the namespace ‘S4Vectors’ which is not S4 generic: ‘%in%’
Error: package ‘S4Vectors’ could not be loaded
Execution halted
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I'm not sure what the next step is. Do you know how you ended up with "too new" versions of these packages? Were you installing from .tar.gz packages downloaded from website?

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Can you please try again in a 'vanilla' R session with no packages loaded, just

BiocManager::install("S4Vectors")

Like Michael I don't really have a good explanation for this.

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installing S4Vectors in vanilla R helped to successfully load DESeq2, thank you for this suggestion.

But now I get an error with DESeq2 function (with the same input data) that was running well before yesterday.

DESeqDataSetFromMatrix(count_data, colData = data1_Prok, design = ~sample_type)

Error in validObject(.Object) : 
  invalid class “PartitioningByEnd” object: superclass "vector_OR_Vector" not defined in the environment of the object's class

The problem seems to be coming from IRanges package that by coincidence (or not) was updated yesterday. https://bioconductor.org/packages/release/bioc/manuals/IRanges/man/IRanges.pdf

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What do you have for valid()?

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do you mean BiocManager::valid() ? if so, then I still have 2 too new packages there ( "Biostrings", "XVector").

I did not install them from .tar.gz files and definitely did not get them recently (it was Easter holiday afterall..:)) everything was running just fine.

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Again in a vanilla R session, remove the previous installations, repeating the following command until R says that there are no packages to remove

remove.packages(c("Biostrings", "XVector"))

Quit R, start again in a vanilla session, and re-install

BiocManager::install(c("Biostrings", "XVector"))

Hopefully BiocManager::valid() is then happy? It's worth figuring out how you got the 'too new' packages installed. Maybe you have two different versions of R that share the same .libPaths()?

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Hmm, I guess I can't help much until you have an installation that passes valid() as it will likely lead to mis-matching code across versions of Bioc.

We take great care to make sure that all packages work within a release, so errors generated with versions of packages across releases are not really a developer concern (although we do want to make sure you can get to a correct installation of Bioconductor).

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I have followed the instructions in Martin's reply and now BiocManager::valid() seems to be happy, outputting just TRUE. I have cleared the environment, restarted the session, successfully loaded all the packages but the same error under DESeqDataSetFromMatrix the function appears.....

Error in validObject(.Object) : 
  invalid class “PartitioningByEnd” object: superclass "vector_OR_Vector" not defined in the environment of the object's class

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

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

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

other attached packages:
 [1] Biostrings_2.52.0           XVector_0.24.0              reshape_0.8.8              
 [4] viridis_0.5.1               viridisLite_0.3.0           tidyr_1.0.2                
 [7] dendextend_1.13.4           ggplot2_3.3.0               DESeq2_1.24.0              
[10] SummarizedExperiment_1.14.1 DelayedArray_0.10.0         BiocParallel_1.18.1        
[13] matrixStats_0.56.0          Biobase_2.44.0              GenomicRanges_1.36.1       
[16] GenomeInfoDb_1.20.0         IRanges_2.18.3              S4Vectors_0.22.1           
[19] BiocGenerics_0.30.0         vegan_2.5-6                 lattice_0.20-41            
[22] permute_0.9-5               phyloseq_1.28.0            

loaded via a namespace (and not attached):
 [1] nlme_3.1-147           bitops_1.0-6           bit64_0.9-7            RColorBrewer_1.1-2    
 [5] tools_3.6.3            backports_1.1.6        R6_2.4.1               rpart_4.1-15          
 [9] Hmisc_4.4-0            DBI_1.1.0              mgcv_1.8-31            colorspace_1.4-1      
[13] ade4_1.7-15            nnet_7.3-13            withr_2.1.2            tidyselect_1.0.0      
[17] gridExtra_2.3          bit_1.1-15.2           compiler_3.6.3         cli_2.0.2             
[21] htmlTable_1.13.3       scales_1.1.0           checkmate_2.0.0        genefilter_1.66.0     
[25] stringr_1.4.0          digest_0.6.25          foreign_0.8-76         base64enc_0.1-3       
[29] jpeg_0.1-8.1           pkgconfig_2.0.3        htmltools_0.4.0        htmlwidgets_1.5.1     
[33] rlang_0.4.5            rstudioapi_0.11        RSQLite_2.2.0          jsonlite_1.6.1        
[37] acepack_1.4.1          dplyr_0.8.5            RCurl_1.98-1.1         magrittr_1.5          
[41] GenomeInfoDbData_1.2.1 Formula_1.2-3          biomformat_1.12.0      Matrix_1.2-18         
[45] Rcpp_1.0.4.6           munsell_0.5.0          Rhdf5lib_1.6.3         fansi_0.4.1           
[49] ape_5.3                lifecycle_0.2.0        stringi_1.4.6          yaml_2.2.1            
[53] MASS_7.3-51.5          zlibbioc_1.30.0        rhdf5_2.28.1           plyr_1.8.6            
[57] blob_1.2.1             grid_3.6.3             crayon_1.3.4           splines_3.6.3         
[61] multtest_2.40.0        annotate_1.62.0        locfit_1.5-9.4         knitr_1.28            
[65] pillar_1.4.3           igraph_1.2.5           geneplotter_1.62.0     reshape2_1.4.4        
[69] codetools_0.2-16       XML_3.99-0.3           glue_1.4.0             latticeExtra_0.6-29   
[73] BiocManager_1.30.10    data.table_1.12.8      png_0.1-7              vctrs_0.2.4           
[77] foreach_1.5.0          gtable_0.3.0           purrr_0.3.3            assertthat_0.2.1      
[81] xfun_0.13              xtable_1.8-4           survival_3.1-12        tibble_3.0.0          
[85] iterators_1.0.12       memoise_1.1.0          AnnotationDbi_1.46.1   cluster_2.1.0         
[89] ellipsis_0.3.0
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I have managed to solve this issue - repeatedly installing and uninstalling all the packages involving vectors in R --vanilla mode helped to get DESeq2 functionalities back! I see that a similar issue previously occurred to another person as well so putting it here in case someone else gets stuck one day. https://support.bioconductor.org/p/115848/

Thank you very much, Michael and Martin, for all the help!

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