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rcavalcante / annotatr

Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=annotatr.
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No access to FANTOM #49

Closed jffpviana closed 1 year ago

jffpviana commented 1 year ago

I started getting an error this morning, which indicates the oaths in the FANTOM database have changed. Code:

library(annotatr)
annot <- builtin_annotations()[grep("mm10", builtin_annotations())]
annotations <- build_annotations(genome = 'mm10', annotations = annot)

Error:

Building enhancers...
snapshotDate(): 2022-10-31
loading from cache
require("rtracklayer")
Error in url(x, open = "rb") : 
  cannot open the connection to 'http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Enhancers/mouse_permissive_enhancers_phase_1_and_2.bed.gz'
 sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: AlmaLinux 8.5 (Arctic Sphynx)

Matrix products: default
BLAS:   /home/opt/R/4.2.2/lib64/R/lib/libRblas.so
LAPACK: /home/opt/R/4.2.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8          LC_NUMERIC=C                  LC_TIME=en_GB.UTF-8          
 [4] LC_COLLATE=en_GB.UTF-8        LC_MONETARY=en_GB.UTF-8       LC_MESSAGES=en_GB.UTF-8      
 [7] LC_PAPER=en_GB.UTF-8          LC_NAME=en_GB.UTF-8           LC_ADDRESS=en_GB.UTF-8       
[10] LC_TELEPHONE=en_GB.UTF-8      LC_MEASUREMENT=en_GB.UTF-8    LC_IDENTIFICATION=en_GB.UTF-8

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Mm.eg.db_3.16.0                                 TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0          
 [3] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2             rtracklayer_1.58.0                                 
 [5] introdataviz_0.0.0.9003                             annotatr_1.24.0                                    
 [7] forcats_0.5.2                                       stringr_1.5.0                                      
 [9] purrr_0.3.5                                         readr_2.1.3                                        
[11] tidyr_1.2.1                                         tibble_3.1.8                                       
[13] tidyverse_1.3.2                                     RnBeads.mm10_2.6.0                                 
[15] xlsx_0.6.5                                          karyoploteR_1.24.0                                 
[17] regioneR_1.30.0                                     RnBeads.hg19_1.30.0                                
[19] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 IlluminaHumanMethylationEPICmanifest_0.3.0         
[21] data.table_1.14.6                                   wateRmelon_2.4.0                                   
[23] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1  ROC_1.74.0                                         
[25] lumi_2.50.0                                         dplyr_1.0.10                                       
[27] pheatmap_1.0.12                                     RColorBrewer_1.1-3                                 
[29] ggrepel_0.9.2                                       RnBeads_2.16.0                                     
[31] plyr_1.8.8                                          methylumi_2.44.0                                   
[33] FDb.InfiniumMethylation.hg19_2.2.0                  org.Hs.eg.db_3.16.0                                
[35] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2             GenomicFeatures_1.50.0                             
[37] AnnotationDbi_1.60.0                                reshape2_1.4.4                                     
[39] scales_1.2.1                                        illuminaio_0.40.0                                  
[41] limma_3.54.0                                        gridExtra_2.3                                      
[43] gplots_3.1.3                                        ggplot2_3.4.0                                      
[45] fields_14.1                                         viridis_0.6.2                                      
[47] viridisLite_0.4.1                                   spam_2.9-1                                         
[49] ff_4.0.7                                            bit_4.0.5                                          
[51] cluster_2.1.4                                       MASS_7.3-58.1                                      
[53] readxl_1.4.1                                        minfi_1.44.0                                       
[55] bumphunter_1.40.0                                   locfit_1.5-9.6                                     
[57] iterators_1.0.14                                    foreach_1.5.2                                      
[59] Biostrings_2.66.0                                   XVector_0.38.0                                     
[61] SummarizedExperiment_1.28.0                         Biobase_2.58.0                                     
[63] MatrixGenerics_1.10.0                               matrixStats_0.63.0                                 
[65] GenomicRanges_1.50.2                                GenomeInfoDb_1.34.6                                
[67] IRanges_2.32.0                                      S4Vectors_0.36.1                                   
[69] BiocGenerics_0.44.0                                

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3                bamsignals_1.30.0             ragg_1.2.4                   
  [4] bezier_1.1.2                  bit64_4.0.5                   knitr_1.41                   
  [7] DelayedArray_0.24.0           rpart_4.1.19                  KEGGREST_1.38.0              
 [10] RCurl_1.98-1.9                GEOquery_2.66.0               AnnotationFilter_1.22.0      
 [13] generics_0.1.3                preprocessCore_1.60.1         RSQLite_2.2.19               
 [16] tzdb_0.3.0                    httpuv_1.6.6                  lubridate_1.9.0              
 [19] xml2_1.3.3                    assertthat_0.2.1              gargle_1.2.1                 
 [22] xfun_0.35                     hms_1.1.2                     rJava_1.0-6                  
 [25] promises_1.2.0.1              evaluate_0.18                 fansi_1.0.3                  
 [28] restfulr_0.0.15               scrime_1.3.5                  progress_1.2.2               
 [31] caTools_1.18.2                dbplyr_2.2.1                  DBI_1.1.3                    
 [34] htmlwidgets_1.5.4             reshape_0.8.9                 googledrive_2.0.0            
 [37] ellipsis_0.3.2                backports_1.4.1               annotate_1.76.0              
 [40] biomaRt_2.54.0                deldir_1.0-6                  sparseMatrixStats_1.10.0     
 [43] vctrs_0.5.0                   ensembldb_2.22.0              cachem_1.0.6                 
 [46] withr_2.5.0                   BSgenome_1.66.0               checkmate_2.1.0              
 [49] GenomicAlignments_1.34.0      prettyunits_1.1.1             mclust_6.0.0                 
 [52] dotCall64_1.0-2               lazyeval_0.2.2                crayon_1.5.2                 
 [55] genefilter_1.80.2             labeling_0.4.2                pkgconfig_2.0.3              
 [58] nlme_3.1-160                  ProtGenerics_1.30.0           nnet_7.3-18                  
 [61] rlang_1.0.6                   lifecycle_1.0.3               nleqslv_3.3.3                
 [64] filelock_1.0.2                affyio_1.68.0                 BiocFileCache_2.6.0          
 [67] modelr_0.1.10                 AnnotationHub_3.6.0           dichromat_2.0-0.1            
 [70] cellranger_1.1.0              rngtools_1.5.2                base64_2.0.1                 
 [73] Matrix_1.5-3                  Rhdf5lib_1.20.0               reprex_2.0.2                 
 [76] base64enc_0.1-3               googlesheets4_1.0.1           png_0.1-8                    
 [79] rjson_0.2.21                  bitops_1.0-7                  KernSmooth_2.23-20           
 [82] rhdf5filters_1.10.0           blob_1.2.3                    DelayedMatrixStats_1.20.0    
 [85] doRNG_1.8.2                   nor1mix_1.3-0                 jpeg_0.1-10                  
 [88] memoise_2.0.1                 magrittr_2.0.3                zlibbioc_1.44.0              
 [91] compiler_4.2.2                BiocIO_1.8.0                  Rsamtools_2.14.0             
 [94] cli_3.4.1                     affy_1.76.0                   htmlTable_2.4.1              
 [97] Formula_1.2-4                 mgcv_1.8-41                   tidyselect_1.2.0             
[100] stringi_1.7.8                 textshaping_0.3.6             yaml_2.3.6                   
[103] askpass_1.1                   latticeExtra_0.6-30           VariantAnnotation_1.44.0     
[106] timechange_0.1.1              tools_4.2.2                   rstudioapi_0.14              
[109] foreign_0.8-83                farver_2.1.1                  digest_0.6.30                
[112] BiocManager_1.30.19           shiny_1.7.3                   quadprog_1.5-8               
[115] Rcpp_1.0.9                    siggenes_1.72.0               broom_1.0.1                  
[118] later_1.3.0                   BiocVersion_3.16.0            httr_1.4.4                   
[121] biovizBase_1.46.0             colorspace_2.0-3              rvest_1.0.3                  
[124] XML_3.99-0.12                 fs_1.5.2                      splines_4.2.2                
[127] xlsxjars_0.6.1                multtest_2.54.0               systemfonts_1.0.4            
[130] xtable_1.8-4                  jsonlite_1.8.3                R6_2.5.1                     
[133] Hmisc_4.7-2                   mime_0.12                     pillar_1.8.1                 
[136] htmltools_0.5.3               glue_1.6.2                    fastmap_1.1.0                
[139] BiocParallel_1.32.5           interactiveDisplayBase_1.36.0 beanplot_1.3.1               
[142] codetools_0.2-18              maps_3.4.1                    utf8_1.2.2                   
[145] lattice_0.20-45               curl_4.3.3                    gtools_3.9.4                 
[148] openssl_2.0.4                 interp_1.1-3                  survival_3.4-0               
[151] rmarkdown_2.18                munsell_0.5.0                 rhdf5_2.42.0                 
[154] GenomeInfoDbData_1.2.9        HDF5Array_1.26.0              haven_2.5.1                  
[157] gtable_0.3.1
rcavalcante commented 1 year ago

Hi,

Apologies for the delay in response. I think this error might be transient? I just did

wget http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Enhancers/mouse_permissive_enhancers_phase_1_and_2.bed.gz

And was able to retrieve the resource. I also ran your code above without issue. This is on an R install that is basically the same as in your sessionInfo() (thanks for that by the way).

Perhaps you can try it again and let me know if it is, indeed, transient?

Thanks, Raymond

jffpviana commented 1 year ago

Yes, I no longer have this issue. Thank you!

K-chae0 commented 1 year ago

@jffpviana The same problem occurs for me too. This error is not transient.

If you access FANTOM below, you will get 403 Forbidden(You don't have permission to access this resource). https://fantom.gsc.riken.jp/5/datafiles

Code:

library(annotatr)
annots = c('hg38_cpgs','hg38_basicgenes','hg38_genes_intergenic',
           'hg38_genes_intronexonboundaries','hg38_enhancers_fantom','hg38_lncrna_gencode')
annotations = build_annotations(genome = 'hg38', annotations = annots)

Error:

Building enhancers...
snapshotDate(): 2022-10-31
loading from cache
Error in url(x, open = "rb") : 
  cannot open the connection to 'http://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Enhancers/human_permissive_enhancers_phase_1_and_2.bed.gz'
sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=Korean_Korea.utf8  LC_CTYPE=Korean_Korea.utf8    LC_MONETARY=Korean_Korea.utf8 LC_NUMERIC=C                 
[5] LC_TIME=Korean_Korea.utf8    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocManager_1.30.20  rtracklayer_1.58.0   GenomicRanges_1.50.2 GenomeInfoDb_1.34.9  IRanges_2.32.0       S4Vectors_0.36.2    
 [7] BiocGenerics_0.44.0  dplyr_1.1.0          xlsx_0.6.5           annotatr_1.24.0     

loaded via a namespace (and not attached):
 [1] bitops_1.0-7                  matrixStats_0.63.0            bit64_4.0.5                   filelock_1.0.2               
 [5] progress_1.2.2                httr_1.4.5                    tools_4.2.2                   utf8_1.2.3                   
 [9] R6_2.5.1                      DBI_1.1.3                     colorspace_2.1-0              withr_2.5.0                  
[13] tidyselect_1.2.0              prettyunits_1.1.1             bit_4.0.5                     curl_5.0.0                   
[17] compiler_4.2.2                cli_3.6.0                     Biobase_2.58.0                xml2_1.3.3                   
[21] DelayedArray_0.24.0           scales_1.2.1                  readr_2.1.4                   rappdirs_0.3.3               
[25] stringr_1.5.0                 digest_0.6.31                 Rsamtools_2.14.0              rmarkdown_2.20               
[29] XVector_0.38.0                pkgconfig_2.0.3               htmltools_0.5.4               MatrixGenerics_1.10.0        
[33] dbplyr_2.3.1                  fastmap_1.1.1                 BSgenome_1.66.3               regioneR_1.30.0              
[37] rlang_1.1.0                   rstudioapi_0.14               RSQLite_2.3.0                 shiny_1.7.4                  
[41] BiocIO_1.8.0                  generics_0.1.3                BiocParallel_1.32.5           RCurl_1.98-1.10              
[45] magrittr_2.0.3                GenomeInfoDbData_1.2.9        Matrix_1.5-1                  Rcpp_1.0.10                  
[49] munsell_0.5.0                 fansi_1.0.4                   lifecycle_1.0.3               stringi_1.7.12               
[53] yaml_2.3.7                    SummarizedExperiment_1.28.0   zlibbioc_1.44.0               plyr_1.8.8                   
[57] BiocFileCache_2.6.1           AnnotationHub_3.6.0           grid_4.2.2                    blob_1.2.4                   
[61] parallel_4.2.2                promises_1.2.0.1              crayon_1.5.2                  lattice_0.20-45              
[65] Biostrings_2.66.0             xlsxjars_0.6.1                GenomicFeatures_1.50.4        hms_1.1.2                    
[69] KEGGREST_1.38.0               knitr_1.42                    pillar_1.8.1                  rjson_0.2.21                 
[73] reshape2_1.4.4                codetools_0.2-18              biomaRt_2.54.0                XML_3.99-0.14                
[77] glue_1.6.2                    BiocVersion_3.16.0            evaluate_0.20                 png_0.1-8                    
[81] vctrs_0.6.0                   tzdb_0.3.0                    httpuv_1.6.9                  purrr_1.0.1                  
[85] gtable_0.3.2                  cachem_1.0.7                  ggplot2_3.4.1                 xfun_0.37                    
[89] mime_0.12                     xtable_1.8-4                  restfulr_0.0.15               later_1.3.0                  
[93] tibble_3.2.0                  rJava_1.0-6                   GenomicAlignments_1.34.1      AnnotationDbi_1.60.2         
[97] memoise_2.0.1                 ellipsis_0.3.2                interactiveDisplayBase_1.36.0
rcavalcante commented 1 year ago

Interesting, yes, both seem to be failing now. I'll have a look into this and figure out what the right URLs are now.

jffpviana commented 1 year ago

FYI I believe this is the new path prefix: https://dbarchive.biosciencedbc.jp/data/fantom5/datafiles/LATEST/extra/Enhancers/