Entering edit mode
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
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?
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()andBiocManager::valid()to help trouble shoot this.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:
I then tried I tried BiocManager::valid() and showed the following:
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.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 =)!