DEP package: Problems installing on macOS
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jp • 0
@jp-23895
Last seen 14 months ago

I am trying to install the DEP package. I tried multiple machines without success. Using

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DEP")

Everything seems to download/install just fine, no error or warnings, but when I call the library I get the following:

> 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
In addition: Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.4.6)
than is installed on your system (1.0.5). 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.

Here is the system I am on:

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.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] Rcpp_1.0.5                  mvtnorm_1.1-1             
 [3] lattice_0.20-41             circlize_0.4.10           
 [5] zoo_1.8-8                   png_0.1-7                 
 [7] assertthat_0.2.1            digest_0.6.25             
 [9] foreach_1.5.0               R6_2.4.1                  
[11] GenomeInfoDb_1.24.2         plyr_1.8.6                
[13] mzID_1.26.0                 stats4_4.0.2              
[15] ggplot2_3.3.2               pillar_1.4.6              
[17] GlobalOptions_0.1.2         zlibbioc_1.34.0           
[19] rlang_0.4.7                 S4Vectors_0.26.1          
[21] GetoptLong_1.0.2            Matrix_1.2-18             
[23] preprocessCore_1.50.0       mzR_2.22.0                
[25] BiocParallel_1.22.0         ProtGenerics_1.20.0       
[27] RCurl_1.98-1.2              munsell_0.5.0             
[29] DelayedArray_0.14.1         compiler_4.0.2            
[31] pkgconfig_2.0.3             BiocGenerics_0.34.0       
[33] shape_1.4.4                 pcaMethods_1.80.0         
[35] tidyselect_1.1.0            SummarizedExperiment_1.18.2
[37] tibble_3.0.3                GenomeInfoDbData_1.2.3    
[39] matrixStats_0.56.0          IRanges_2.22.2            
[41] codetools_0.2-16            XML_3.99-0.4              
[43] crayon_1.3.4                dplyr_1.0.0               
[45] MASS_7.3-51.6               bitops_1.0-6              
[47] grid_4.0.2                  gtable_0.3.0              
[49] lifecycle_0.2.0             affy_1.66.0               
[51] magrittr_1.5                scales_1.1.1              
[53] ncdf4_1.17                  impute_1.62.0             
[55] XVector_0.28.0              affyio_1.58.0             
[57] doParallel_1.0.15           limma_3.44.3              
[59] ellipsis_0.3.1              generics_0.0.2            
[61] vctrs_0.3.2                 sandwich_2.5-1            
[63] rjson_0.2.20                RColorBrewer_1.1-2        
[65] iterators_1.0.12            tools_4.0.2               
[67] Biobase_2.48.0              MSnbase_2.14.2            
[69] glue_1.4.1                  purrr_0.3.4               
[71] parallel_4.0.2              clue_0.3-57               
[73] colorspace_1.4-1            cluster_2.1.0             
[75] BiocManager_1.30.10         vsn_3.56.0                
[77] GenomicRanges_1.40.0        MALDIquant_1.19.3         
[79] ComplexHeatmap_2.4.2

Any advice or suggestions would be appreciated. Thanks

software error DEP proteomics • 699 views
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@javan-okendo-22941
Last seen 4 months ago
University of Cape Town

Hi,

Where are you running this from? is it on HPC/server?

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Just my local machine: MacBook Pro.

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@laurent-gatto-5645
Last seen 2 days ago
Belgium

In your output, there's a warning about mzR that you can ignore, and an error about gmm that seems to be missing. Even though gmm isn't a direct dependency of DEP, DEP is trying to load shared objects from gmm. My suggestion would be to BiocManager::install("gmm") and try again.

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@Laurent thank you for the suggestion. I am not too concerned about the mzR package: mzR has been built against a different Rcpp version (1.0.4.6) than is installed on your system (1.0.5). gmm was installed, to be sure I unistalled and reinstalled following your suggestion.

> BiocManager::install("gmm")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'gmm'
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/gmm_1.6-5.tgz'
Content type 'application/x-gzip' length 1360675 bytes (1.3 MB)
==================================================
downloaded 1.3 MB


The downloaded binary packages are in
    /var/folders/bk/9r7m83613r51cwtpxmmf2nx80000gp/T//RtmpobCU3r/downloaded_packages
> library(gmm)
Loading required package: sandwich
Error: package or namespace load failed for ‘gmm’ 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

and received the same error. I checked the path and permission and it looks fine. -rwxr-xr-x 1 jp admin 26K Jul 15 01:02 gmm.so drwxr-xr-x 3 jp admin 96B Jul 15 01:02 gmm.so.dSYM

Any other suggestions?

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So the issue clearly lies with gmm.

One suggestion would be to check that you have a working fortran compiler and that you have the libgomp (GCC OpenMP support library) system requirement installed. On a Debian-based system, the latter wound be done with

sudo apt install libgomp1

but I have no idea how to do that on a Mac.

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After installing Xcode (via App Store) and GNU Fortan, gmm compiled correctly and so did DEP. Thank you

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