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I am trying to use the DEP package, and I followed the installation instructions, and do not get error messages with the installation, but this is the message I get:
This error happens on both my computers (same R version, other computer has updated OS)
library("DEP")
Error: package or namespace load failed for ‘DEP’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/kathl/.RLibrary/gmm/libs/gmm.so':
dlopen(/Users/kath/.RLibrary/gmm/libs/gmm.so, 0x0006): Library not loaded: '/usr/local/gfortran/lib/libgomp.1.dylib'
Referenced from: '/Users/kath/.RLibrary/gmm/libs/gmm.so'
Reason: tried: '/usr/local/gfortran/lib/libgomp.1.dylib' (no such file), '/usr/local/lib/libgomp.1.dylib' (no such file), '/usr/lib/libgomp.1.dylib' (no such file)
In addition: Warning messages:
1: package ‘DEP’ was built under R version 4.2.1
2: In fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.9)
than is installed on your system (1.0.10). 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.
>
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] MatrixGenerics_1.10.0 Biobase_2.58.0 vsn_3.66.0 foreach_1.5.2
[5] assertthat_0.2.1 BiocManager_1.30.19 affy_1.76.0 stats4_4.2.0
[9] GenomeInfoDbData_1.2.8 norm_1.0-10.0 impute_1.72.3 pillar_1.8.1
[13] lattice_0.20-45 glue_1.6.2 limma_3.54.1 digest_0.6.31
[17] GenomicRanges_1.50.2 RColorBrewer_1.1-3 XVector_0.38.0 sandwich_3.0-2
[21] colorspace_2.1-0 preprocessCore_1.60.2 Matrix_1.5-3 plyr_1.8.8
[25] MALDIquant_1.22 XML_3.99-0.13 pkgconfig_2.0.3 GetoptLong_1.0.5
[29] zlibbioc_1.44.0 mvtnorm_1.1-3 scales_1.2.1 affyio_1.68.0
[33] BiocParallel_1.32.5 tibble_3.1.8 generics_0.1.3 IRanges_2.32.0
[37] ggplot2_3.4.0 SummarizedExperiment_1.28.0 BiocGenerics_0.44.0 cli_3.6.0
[41] magrittr_2.0.3 crayon_1.5.2 ncdf4_1.21 fansi_1.0.4
[45] doParallel_1.0.17 MASS_7.3-58.2 mzR_2.32.0 tools_4.2.0
[49] GlobalOptions_0.1.2 lifecycle_1.0.3 matrixStats_0.63.0 ComplexHeatmap_2.14.0
[53] MSnbase_2.24.2 S4Vectors_0.36.1 munsell_0.5.0 cluster_2.1.4
[57] DelayedArray_0.24.0 pcaMethods_1.90.0 compiler_4.2.0 GenomeInfoDb_1.34.9
[61] mzID_1.36.0 rlang_1.0.6 grid_4.2.0 RCurl_1.98-1.10
[65] iterators_1.0.14 rstudioapi_0.14 rjson_0.2.21 MsCoreUtils_1.10.0
[69] circlize_0.4.15 bitops_1.0-7 gtable_0.3.1 codetools_0.2-19
[73] DBI_1.1.3 R6_2.5.1 zoo_1.8-11 dplyr_1.1.0
[77] utf8_1.2.3 clue_0.3-64 ProtGenerics_1.30.0 shape_1.4.6
[81] parallel_4.2.0 Rcpp_1.0.10 vctrs_0.5.2 png_0.1-8
[85] tidyselect_1.2.0
>
Hi - I have followed these tips and am still getting the same error codes even after linking the files. Are there other things that can be causing it this error? I have Xcode, gfortran, and all dependents downloaded.