Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
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Jake • 0
@6426ec2d
Last seen 25 minutes ago
United States

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the "EnsDb.Mmusculus.v79" and "BSgenome.Mmusculus.UCSC.mm10" packages with bioconductor. The same ERROR has come up repeatedly whenever I try to install these packages or call on related packages I already have installed. See below:

Error: package or namespace load failed for ‘rtracklayer’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so': dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Symbol not found: ___darwin_check_fd_set_overflow Referenced from: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so Expected in: /usr/lib/libSystem.B.dylib in /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so Execution halted

Note that I have a limited bioinformatic background, but I have done all the basic fixes I can think of. I uninstalled and reinstalled R, Rstudio, and rtracklayer. I have updated any old packages. I tried a different computer with the same results and would try an earlier version of R if the signac package I am using didn't require R (≥ 4.0.0). All the details of the code and error messages can be seen below. Any insights are welcome help!

I have been referencing this vignette (https://stuartlab.org/signac/articles/pbmc_multiomic.html)


#Attempt install BSgenome.Mmusculus.UCSC.mm10
> if (!requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE))
+     BiocManager::install("BSgenome.Mmusculus.UCSC.mm10")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
Installing package(s) 'BSgenome.Mmusculus.UCSC.mm10'
cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'installing the source package ‘BSgenome.Mmusculus.UCSC.mm10’

trying URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.3.tar.gz'
Content type 'application/x-gzip' length 649827309 bytes (619.7 MB)
==================================================
downloaded 619.7 MB

* installing *source* package ‘BSgenome.Mmusculus.UCSC.mm10’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘rtracklayer’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Symbol not found: ___darwin_check_fd_set_overflow
  Referenced from: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so
  Expected in: /usr/lib/libSystem.B.dylib
 in /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so
Execution halted
ERROR: lazy loading failed for package ‘BSgenome.Mmusculus.UCSC.mm10’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BSgenome.Mmusculus.UCSC.mm10’
installation of package ‘BSgenome.Mmusculus.UCSC.mm10’ had non-zero exit status
The downloaded source packages are in
    ‘/private/var/folders/wz/v54x7v3n191dnzb4mq8t84tm0000gn/T/RtmpgzhuKZ/downloaded_packages’
Old packages: 'boot'
Update all/some/none? [a/s/n]: 
n

#Attempt to load rtracklayer
> library(rtracklayer)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘rtracklayer’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Symbol not found: ___darwin_check_fd_set_overflow
  Referenced from: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so
  Expected in: /usr/lib/libSystem.B.dylib
 in /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rtracklayer/libs/rtracklayer.so

# Session Info

sessionInfo( )
R version 4.2.2 (2022-10-31)
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/4.2/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     

other attached packages:
[1] Signac_1.8.0        BiocManager_1.30.19 SeuratObject_4.1.3  Seurat_4.3.0       

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  spatstat.explore_3.0-5      reticulate_1.26            
  [4] tidyselect_1.2.0            RSQLite_2.2.18              AnnotationDbi_1.60.0       
  [7] htmlwidgets_1.5.4           grid_4.2.2                  BiocParallel_1.32.1        
 [10] Rtsne_0.16                  munsell_0.5.0               codetools_0.2-18           
 [13] ica_1.0-3                   interp_1.1-3                future_1.29.0              
 [16] miniUI_0.1.1.1              withr_2.5.0                 spatstat.random_3.0-1      
 [19] colorspace_2.0-3            progressr_0.11.0            Biobase_2.58.0             
 [22] filelock_1.0.2              knitr_1.41                  rstudioapi_0.14            
 [25] stats4_4.2.2                ROCR_1.0-11                 tensor_1.5                 
 [28] listenv_0.8.0               MatrixGenerics_1.10.0       GenomeInfoDbData_1.2.9     
 [31] polyclip_1.10-4             bit64_4.0.5                 parallelly_1.32.1          
 [34] vctrs_0.5.1                 generics_0.1.3              xfun_0.35                  
 [37] BiocFileCache_2.6.0         R6_2.5.1                    GenomeInfoDb_1.34.3        
 [40] hdf5r_1.3.7                 AnnotationFilter_1.22.0     bitops_1.0-7               
 [43] spatstat.utils_3.0-1        cachem_1.0.6                DelayedArray_0.24.0        
 [46] assertthat_0.2.1            BiocIO_1.8.0                promises_1.2.0.1           
 [49] scales_1.2.1                nnet_7.3-18                 gtable_0.3.1               
 [52] globals_0.16.2              goftest_1.2-3               rlang_1.0.6                
 [55] RcppRoll_0.3.0              splines_4.2.2               lazyeval_0.2.2             
 [58] dichromat_2.0-0.1           spatstat.geom_3.0-3         checkmate_2.1.0            
 [61] yaml_2.3.6                  reshape2_1.4.4              abind_1.4-5                
 [64] backports_1.4.1             httpuv_1.6.6                SeuratDisk_0.0.0.9020      
 [67] Hmisc_4.7-2                 tools_4.2.2                 ggplot2_3.4.0              
 [70] ellipsis_0.3.2              RColorBrewer_1.1-3          BiocGenerics_0.44.0        
 [73] ggridges_0.5.4              Rcpp_1.0.9                  plyr_1.8.8                 
 [76] base64enc_0.1-3             progress_1.2.2              zlibbioc_1.44.0            
 [79] purrr_0.3.5                 RCurl_1.98-1.9              prettyunits_1.1.1          
 [82] rpart_4.1.19                deldir_1.0-6                pbapply_1.6-0              
 [85] cowplot_1.1.1               S4Vectors_0.36.0            zoo_1.8-11                 
 [88] SummarizedExperiment_1.28.0 ggrepel_0.9.2               cluster_2.1.4              
 [91] magrittr_2.0.3              data.table_1.14.6           scattermore_0.8            
 [94] lmtest_0.9-40               RANN_2.6.1                  fitdistrplus_1.1-8         
 [97] matrixStats_0.63.0          hms_1.1.2                   patchwork_1.1.2            
[100] mime_0.12                   xtable_1.8-4                XML_3.99-0.12              
[103] jpeg_0.1-9                  IRanges_2.32.0              gridExtra_2.3              
[106] compiler_4.2.2              biomaRt_2.54.0              tibble_3.1.8               
[109] KernSmooth_2.23-20          crayon_1.5.2                htmltools_0.5.3            
[112] later_1.3.0                 Formula_1.2-4               tidyr_1.2.1                
[115] DBI_1.1.3                   dbplyr_2.2.1                MASS_7.3-58.1              
[118] rappdirs_0.3.3              Matrix_1.5-3                cli_3.4.1                  
[121] parallel_4.2.2              igraph_1.3.5                GenomicRanges_1.50.1       
[124] pkgconfig_2.0.3             GenomicAlignments_1.34.0    foreign_0.8-83             
[127] sp_1.5-1                    plotly_4.10.1               spatstat.sparse_3.0-0      
[130] xml2_1.3.3                  XVector_0.38.0              stringr_1.4.1              
[133] digest_0.6.30               sctransform_0.3.5           RcppAnnoy_0.0.20           
[136] spatstat.data_3.0-0         Biostrings_2.66.0           fastmatch_1.1-3            
[139] leiden_0.4.3                htmlTable_2.4.1             uwot_0.1.14                
[142] restfulr_0.0.15             curl_4.3.3                  shiny_1.7.3                
[145] Rsamtools_2.14.0            rjson_0.2.21                lifecycle_1.0.3            
[148] nlme_3.1-160                jsonlite_1.8.3              viridisLite_0.4.1          
[151] fansi_1.0.3                 pillar_1.8.1                lattice_0.20-45            
[154] KEGGREST_1.38.0             fastmap_1.1.0               httr_1.4.4                 
[157] survival_3.4-0              remotes_2.4.2               glue_1.6.2                 
[160] png_0.1-7                   bit_4.0.5                   stringi_1.7.8              
[163] blob_1.2.3                  latticeExtra_0.6-30         memoise_2.0.1              
[166] dplyr_1.0.10                irlba_2.3.5.1               future.apply_1.10.0        
>
SingleCellMultiModal ensembldb rtracklayer Annotation • 39 views
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