Error when loading DEP in RStudio
2
2
Entering edit mode
hele7 ▴ 20
@hele7-15035
Last seen 11 weeks ago
Estonia

I would like to use DEP for differential expression analysis for mass spectometry data, but encountered an error when loading it (please see below). I have gone through some forums/posts describing similar issues, but no solution so far. Unfortunately not an expert user of R either...

Can someone please help me with fixing it? Details on the error and sessionInfo() can be found below.

Thanks in advance :)


    > if (!requireNamespace("BiocManager", quietly=TRUE))
    +     install.packages("BiocManager")
    > BiocManager::install("DEP")

Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'DEP'
trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/DEP_1.10.0.tgz'
Content type 'application/x-gzip' length 3096204 bytes (3.0 MB)
==================================================
downloaded 3.0 MB


The downloaded binary packages are in
    /var/folders/tt/yfpkjtyn32v1hj9xbbt4lsnsbbstt_/T//Rtmp2ej2mb/downloaded_packages

    > library("DEP")

Error: package or namespace load failed for ‘DEP’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gmm/libs/gmm.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gmm/libs/gmm.so, 6): Library not loaded: /usr/local/gfortran/lib/libgomp.1.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/gmm/libs/gmm.so
  Reason: image not found

    > sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
 [1] Biobase_2.48.0              vsn_3.56.0                 
 [3] foreach_1.5.0               assertthat_0.2.1           
 [5] BiocManager_1.30.10         affy_1.66.0                
 [7] stats4_4.0.2                GenomeInfoDbData_1.2.3     
 [9] impute_1.62.0               pillar_1.4.6               
[11] lattice_0.20-41             glue_1.4.2                 
[13] limma_3.44.3                digest_0.6.25              
[15] GenomicRanges_1.40.0        RColorBrewer_1.1-2         
[17] XVector_0.28.0              colorspace_1.4-1           
[19] sandwich_2.5-1              preprocessCore_1.50.0      
[21] Matrix_1.2-18               plyr_1.8.6                 
[23] MALDIquant_1.19.3           XML_3.99-0.5               
[25] pkgconfig_2.0.3             GetoptLong_1.0.2           
[27] zlibbioc_1.34.0             purrr_0.3.4                
[29] mvtnorm_1.1-1               scales_1.1.1               
[31] affyio_1.58.0               BiocParallel_1.22.0        
[33] tibble_3.0.3                generics_0.0.2             
[35] IRanges_2.22.2              ggplot2_3.3.2              
[37] ellipsis_0.3.1              SummarizedExperiment_1.18.2
[39] BiocGenerics_0.34.0         magrittr_1.5               
[41] crayon_1.3.4                ncdf4_1.17                 
[43] doParallel_1.0.15           MASS_7.3-53                
[45] mzR_2.22.0                  tools_4.0.2                
[47] GlobalOptions_0.1.2         lifecycle_0.2.0            
[49] matrixStats_0.56.0          ComplexHeatmap_2.4.3       
[51] MSnbase_2.14.2              S4Vectors_0.26.1           
[53] munsell_0.5.0               cluster_2.1.0              
[55] DelayedArray_0.14.1         pcaMethods_1.80.0          
[57] compiler_4.0.2              GenomeInfoDb_1.24.2        
[59] mzID_1.26.0                 rlang_0.4.7                
[61] grid_4.0.2                  RCurl_1.98-1.2             
[63] iterators_1.0.12            rstudioapi_0.11            
[65] rjson_0.2.20                circlize_0.4.10            
[67] bitops_1.0-6                gtable_0.3.0               
[69] codetools_0.2-16            R6_2.4.1                   
[71] zoo_1.8-8                   dplyr_1.0.2                
[73] clue_0.3-57                 ProtGenerics_1.20.0        
[75] shape_1.4.5                 parallel_4.0.2             
[77] Rcpp_1.0.5                  vctrs_0.3.4                
[79] png_0.1-7                   tidyselect_1.1.0 
dep • 1.2k views
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0
Entering edit mode
@martin-morgan-1513
Last seen 9 weeks ago
United States

This looks like a problem with the installation of the 'gmm' package. Try

library(gmm)

This probably fails, so try re-installing.

BiocManager::install("gmm")

By way of best practice, do this in a new R sessions with no unnecessary packages loaded.

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0
Entering edit mode

I have the same problem. But the solution didn't help me. The "gmn" package is not available for the latest version of R. Any other ideas?

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0
Entering edit mode

It is the 'gmm' package, but you wrote 'gmn'. gmm is a CRAN package. It is available on all operating systems, as shown on the page. Maybe post sessionInfo() and BiocManager::valid() to help trouble shoot this.

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0
Entering edit mode

Hi, I am having the same problem. I tried re-installing "gmm" package. It also ask to update old packages: 'rappdirs', 'shiny'. 'shiny' update is not available:

In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/shiny_1.6.0.tgz': HTTP status was '404 Not Found'

I then tried I tried BiocManager::valid() and showed the following:

BiocManager::valid()

* sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] sandwich_3.0-0      BiocManager_1.30.10

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.2.0        Biobase_2.50.0              vsn_3.58.0                 
 [4] foreach_1.5.1               assertthat_0.2.1            affy_1.68.0                
 [7] stats4_4.0.3                GenomeInfoDbData_1.2.4      impute_1.64.0              
[10] pillar_1.4.7                lattice_0.20-41             glue_1.4.2                 
[13] limma_3.46.0                digest_0.6.27               GenomicRanges_1.42.0       
[16] RColorBrewer_1.1-2          XVector_0.30.0              colorspace_2.0-0           
[19] preprocessCore_1.52.1       Matrix_1.3-2                plyr_1.8.6                 
[22] MALDIquant_1.19.3           XML_3.99-0.5                pkgconfig_2.0.3            
[25] GetoptLong_1.0.5            zlibbioc_1.36.0             mvtnorm_1.1-1              
[28] purrr_0.3.4                 scales_1.1.1                affyio_1.60.0              
[31] BiocParallel_1.24.1         tibble_3.0.5                generics_0.1.0             
[34] IRanges_2.24.1              ggplot2_3.3.3               ellipsis_0.3.1             
[37] SummarizedExperiment_1.20.0 BiocGenerics_0.36.0         magrittr_2.0.1             
[40] crayon_1.3.4                ncdf4_1.17                  doParallel_1.0.16          
[43] MASS_7.3-53                 mzR_2.24.1                  Cairo_1.5-12.2             
[46] tools_4.0.3                 GlobalOptions_0.1.2         lifecycle_0.2.0            
[49] matrixStats_0.57.0          ComplexHeatmap_2.6.2        MSnbase_2.16.1             
[52] S4Vectors_0.28.1            munsell_0.5.0               cluster_2.1.0              
[55] DelayedArray_0.16.1         pcaMethods_1.82.0           compiler_4.0.3             
[58] GenomeInfoDb_1.26.2         mzID_1.28.0                 rlang_0.4.10               
[61] grid_4.0.3                  RCurl_1.98-1.2              iterators_1.0.13           
[64] rstudioapi_0.13             rjson_0.2.20                circlize_0.4.12            
[67] bitops_1.0-6                gtable_0.3.0                codetools_0.2-18           
[70] DBI_1.1.1                   R6_2.5.0                    zoo_1.8-8                  
[73] dplyr_1.0.3                 clue_0.3-58                 ProtGenerics_1.22.0        
[76] shape_1.4.5                 parallel_4.0.3              Rcpp_1.0.6                 
[79] vctrs_0.3.6                 png_0.1-7                   tidyselect_1.1.0           

Bioconductor version '3.12'

  * 1 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install("shiny", update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
1 packages out-of-date; 0 packages too new
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0
Entering edit mode

Likely having the latest version of the shiny package does not break the functionality of the package you are using. If things are working for what you want to do, then you should just get to work... ;)

From here https://cran.r-project.org/web/checks/check_results_shiny.html it seems like the 1.6.0 version of the package built successfully, so it must just be delayed in propagating to a place where it can be installed; check back later.

If you'd really like the latest version, you could try BiocManager::install("shiny", type = "source") but this is often more trouble than it's worth.

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1
Entering edit mode

I found the source of my problem here. I am running R with Mojave (haven't updated my Mac for a while) and found a solution in a post in StackOverflow.

https://stackoverflow.com/questions/63511986/error-package-or-namespace-load-failed-for-gmm-in-dyn-loadfile-dllpath-dl

"The problem is caused because Library not loaded: /usr/local/gfortran/lib/libgomp.1.dylib is missed.

To solve it, I went to this Github release page, downloaded gfortran-10.2-Catalina.dmg, and installed it. Then I can finally load gmm package in R."

In my case I installed the one for Mojave OS.

DEP is now working =)!

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Entering edit mode
Krunal • 0
@Krunal-24460
Last seen 8 months ago

This happened to me when I updated yaml and yaml dependencies while, unknowingly, having an R notebook open.

What worked for me was going to the document folder that stores the packages, which you can locate by doing

.libPaths() and then simply deleting the yaml folder there. After that you should be able start a fresh RStudio session using Ctrl + Shift + F10 (or Cmd + Shift + F10 on mac) and simply reinstalling yaml.

install.packages("yaml")

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