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🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
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Error for sesameDataGet with sesame 1.17.11 and sesameData 1.17.8 #99

Open yang050036 opened 1 year ago

yang050036 commented 1 year ago

Hi, I could not get the information of EPICv2 from ExperimentHub(localHub=TRUE). I don't undartand where is wrong for me. Any help!

packageVersion("sesame") [1] ‘1.17.11’ packageVersion("sesameData") [1] ‘1.17.8’

eh <- query(ExperimentHub(localHub=TRUE), 'sesameData') ExperimentHub with 78 records # snapshotDate(): 2023-04-13 # $dataprovider: ZhouLab, Wanding Zhou zhouwanding@gmail.com, Illumina Inc... # $species: Homo sapiens, Mus musculus # $rdataclass: list, SummarizedExperiment, data.frame, SigDF, matrix, random... # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH3662"]]'

EH3662 | HM450.10.TCGA.PAAD.normal EH3663 | HM450.10.TCGA.BLCA.normal EH3664 | HM450.76.TCGA.matched EH3676 | EPIC.probeInfo EH3677 | HM450.probeInfo ... ... EH7351 | KYCG.HM450.HMconsensus.20211013 EH7352 | KYCG.HM450.probeType.20211013 EH7353 | KYCG.HM450.seqContext.20211013 EH7354 | KYCG.HM450.TFBSconsensus.20211013 EH7355 | KYCG.HM450.tissueSignature.20211013

ah = ExperimentHub(localHub = TRUE) ExperimentHub with 91 records # snapshotDate(): 2023-04-13 # $dataprovider: ZhouLab, Wanding Zhou zhouwanding@gmail.com, Illumina Inc... # $species: Homo sapiens, Mus musculus # $rdataclass: list, SummarizedExperiment, data.frame, SigDF, matrix, random... # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH3662"]]'

EH3662 | HM450.10.TCGA.PAAD.normal EH3663 | HM450.10.TCGA.BLCA.normal EH3664 | HM450.76.TCGA.matched EH3676 | EPIC.probeInfo EH3677 | HM450.probeInfo ... ... EH8074 | KYCG.EPICv2.MetagenePC.20220911 EH8075 | KYCG.EPICv2.CTCFbind.20220911 EH8076 | idatSignature EH8077 | probeIDSignature EH8078 | EPICv2.address

sessionInfo() R Under development (unstable) (2023-04-19 r84287) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /mnt/beegfs/Clinical/users/wenyanhua/soft/R/R-devel/lib64/R/lib/libRblas.so LAPACK: /mnt/beegfs/Clinical/users/wenyanhua/soft/R/R-devel/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Shanghai tzcode source: system (glibc)

attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] ggplot2_3.4.2 dplyr_1.1.2 sesame_1.17.11 [4] sesameData_1.17.8 ExperimentHub_2.7.1 AnnotationHub_3.7.4 [7] BiocFileCache_2.7.2 dbplyr_2.3.2 BiocGenerics_0.45.3

loaded via a namespace (and not attached): [1] tidyselect_1.2.0 blob_1.2.4 [3] filelock_1.0.2 Biostrings_2.67.2 [5] bitops_1.0-7 fastmap_1.1.1 [7] RCurl_1.98-1.12 promises_1.2.0.1 [9] digest_0.6.31 mime_0.12 [11] lifecycle_1.0.3 ellipsis_0.3.2 [13] KEGGREST_1.39.0 interactiveDisplayBase_1.37.0 [15] RSQLite_2.3.1 magrittr_2.0.3 [17] compiler_4.4.0 rlang_1.1.0 [19] tools_4.4.0 utf8_1.2.3 [21] yaml_2.3.7 bit_4.0.5 [23] curl_5.0.0 DelayedArray_0.25.0 [25] plyr_1.8.8 RColorBrewer_1.1-3 [27] BiocParallel_1.33.12 purrr_1.0.1 [29] withr_2.5.0 grid_4.4.0 [31] stats4_4.4.0 preprocessCore_1.61.0 [33] fansi_1.0.4 wheatmap_0.2.0 [35] xtable_1.8-4 colorspace_2.1-0 [37] scales_1.2.1 SummarizedExperiment_1.29.1 [39] cli_3.6.1 crayon_1.5.2 [41] generics_0.1.3 reshape2_1.4.4 [43] httr_1.4.5 tzdb_0.3.0 [45] DBI_1.1.3 cachem_1.0.7 [47] stringr_1.5.0 zlibbioc_1.45.0 [49] AnnotationDbi_1.61.2 BiocManager_1.30.20 [51] XVector_0.39.0 matrixStats_0.63.0 [53] vctrs_0.6.2 Matrix_1.5-4 [55] IRanges_2.33.1 hms_1.1.3 [57] S4Vectors_0.37.7 bit64_4.0.5 [59] glue_1.6.2 codetools_0.2-19 [61] stringi_1.7.12 gtable_0.3.3 [63] BiocVersion_3.17.1 later_1.3.0 [65] GenomeInfoDb_1.35.17 GenomicRanges_1.51.4 [67] munsell_0.5.0 tibble_3.2.1 [69] pillar_1.9.0 rappdirs_0.3.3 [71] htmltools_0.5.5 GenomeInfoDbData_1.2.10 [73] R6_2.5.1 shiny_1.7.4 [75] Biobase_2.59.0 lattice_0.21-8 [77] readr_2.1.4 png_0.1-8 [79] memoise_2.0.1 httpuv_1.6.9 [81] Rcpp_1.0.10 MatrixGenerics_1.11.1 [83] pkgconfig_2.0.3

zwdzwd commented 1 year ago

Hi I believe EPICv2 is in your result, e.g., EH8078 | EPICv2.address. Can you be more specific about your question perhaps?

yang050036 commented 1 year ago

Yes. I get an error when I use sesameDataGet() to get EPICv2.address

a <- sesameDataGet("EPICv2.address") Error in stopAndCache(title) : | File EPICv2.address needs to be cached to be used in sesame. | Please make sure you have updated ExperimentHub and try | > sesameDataCache() | to retrieve and cache needed sesame data.

zwdzwd commented 1 year ago

Did you run sesameDataCache as suggested? just in case

yang050036 commented 1 year ago

Yes, I ran sesameDataCache. I check the source for function of .sesameDataGet, and found that I count not get any information of EPICv2 in the cache

eh <- query(ExperimentHub(localHub=TRUE), 'sesameData') eh ExperimentHub with 78 records # snapshotDate(): 2023-04-13 # $dataprovider: ZhouLab, Wanding Zhou zhouwanding@gmail.com, Illumina Inc... # $species: Homo sapiens, Mus musculus # $rdataclass: list, SummarizedExperiment, data.frame, SigDF, matrix, random... # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH3662"]]'

EH3662 | HM450.10.TCGA.PAAD.normal EH3663 | HM450.10.TCGA.BLCA.normal EH3664 | HM450.76.TCGA.matched EH3676 | EPIC.probeInfo EH3677 | HM450.probeInfo ... ... EH7351 | KYCG.HM450.HMconsensus.20211013 EH7352 | KYCG.HM450.probeType.20211013 EH7353 | KYCG.HM450.seqContext.20211013 EH7354 | KYCG.HM450.TFBSconsensus.20211013 EH7355 | KYCG.HM450.tissueSignature.20211013

ExperimentHub(localHub=TRUE) Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2023-04-13 ExperimentHub with 91 records # snapshotDate(): 2023-04-13 # $dataprovider: ZhouLab, Wanding Zhou zhouwanding@gmail.com, Illumina Inc... # $species: Homo sapiens, Mus musculus # $rdataclass: list, SummarizedExperiment, data.frame, SigDF, matrix, random... # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH3662"]]'

EH3662 | HM450.10.TCGA.PAAD.normal EH3663 | HM450.10.TCGA.BLCA.normal EH3664 | HM450.76.TCGA.matched EH3676 | EPIC.probeInfo EH3677 | HM450.probeInfo ... ... EH8074 | KYCG.EPICv2.MetagenePC.20220911 EH8075 | KYCG.EPICv2.CTCFbind.20220911 EH8076 | idatSignature EH8077 | probeIDSignature EH8078 | EPICv2.address

yang050036 commented 1 year ago

I redownload the cache database. It work well. Thanks for you reply.

rtrelator commented 1 year ago

Hello, I am having a similar issue when running readIDATpair due to sesameDataGet('idatSignature') in the inferPlatformFromTango function. After some investigation, I found that some of the data are not in the updated ExperimentHub. Please see details below:

> eh
ExperimentHub with 6306 records
# snapshotDate(): 2022-04-26
# $dataprovider: Eli and Edythe L. Broad Institute of Harvard and MIT, NCBI, Jonathan Griffiths, NA, GEO, The Tabula Muris Consortium, The National Center for Biotechnology Information, Broad Institute, BCLL@las, D...
# $species: Homo sapiens, Mus musculus, Saccharomyces cerevisiae, human gut metagenome, Rattus norvegicus, Saccharomyces cerevisiae S288C, groundwater metagenome, Papio cynocephalus, Mus musculus (E18 mice), Drosop...
# $rdataclass: SummarizedExperiment, ExpressionSet, matrix, character, list, DFrame, RaggedExperiment, data.frame, SummarizedBenchmark, dgCMatrix
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["EH1"]]' 

           title                                                                               
  EH1    | RNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlas
  EH166  | ERR188297                                                                           
  EH167  | ERR188088                                                                           
  EH168  | ERR188204                                                                           
  EH169  | ERR188317                                                                           
  ...      ...                                                                                 
  EH7538 | Visium_humanDLPFC                                                                   
  EH7539 | Visium_mouseCoronal                                                                 
  EH7540 | seqFISH_mouseEmbryo                                                                 
  EH7541 | ST_mouseOB                                                                          
  EH7542 | SlideSeqV2_mouseHPC 
> as.data.frame(robj2[!robj2$EHID %in% eh$ah_id,])
   Comments Example   EHID VERSION IN_USE                              Title                                                                    Description BiocVersion Genome SourceType
1      <NA>       0 EH8066  1.17.1   TRUE             EPIC.imputationDefault                                               Imputation default of EPIC array        3.17     NA        RDA
2      <NA>       0 EH8067  1.17.1   TRUE            HM450.imputationDefault                                              Imputation default of HM450 array        3.17     NA        RDA
3      <NA>       0 EH8068  1.17.1   TRUE          KYCG.EPICv2.TFBS.20220921           KYCG categorical database holding transcription factor binding sites        3.17     NA        RDA
4      <NA>       0 EH8069  1.17.1   TRUE            KYCG.EPICv2.HM.20221013                        KYCG categorical database holding histone modifications        3.17     NA        RDA
5      <NA>       0 EH8070  1.17.1   TRUE          KYCG.EPICv2.Mask.20230314                              KYCG categorical database holding technical masks        3.17     NA        RDA
6      <NA>       0 EH8071  1.17.1   TRUE KYCG.EPICv2.ABCompartment.20220911                              KYCG categorical database holding AB compartments        3.17     NA        RDA
7      <NA>       0 EH8072  1.17.1   TRUE KYCG.EPICv2.ImprintingDMR.20220818 KYCG categorical database holding imprinting differentially methylated regions        3.17     NA        RDA
8      <NA>       0 EH8073  1.17.1   TRUE      KYCG.EPICv2.ChromHMM.20220303                    KYCG categorical database holding consensus ChromHMM states        3.17     NA        RDA
9      <NA>       0 EH8074  1.17.1   TRUE    KYCG.EPICv2.MetagenePC.20220911                     KYCG categorical database holding protein coding metagenes        3.17     NA        RDA
10     <NA>       0 EH8075  1.17.1   TRUE      KYCG.EPICv2.CTCFbind.20220911                           KYCG categorical database holding CTCF binding sites        3.17     NA        RDA
11     <NA>       0 EH8076  1.17.1   TRUE                      idatSignature                              idat tango address to discriminate array platform        3.17     NA        RDA
12     <NA>       0 EH8077  1.17.1   TRUE                   probeIDSignature                                        probe ID to discriminate array platform        3.17     NA        RDA
13     <NA>       0 EH8078  1.17.1   TRUE                     EPICv2.address                EPICv2 array probe addresses, $ordering and $controls and $hg38        3.17     NA        RDA
                                    SourceUrl SourceVersion      Species TaxonomyId Coordinate_1_based DataProvider                           Maintainer RDataClass DispatchClass
1  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
2  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
3  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
4  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
5  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
6  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
7  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
8  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
9  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
10 http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
11 http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
12 http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
13 http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
                                                   RDataPath Tags Notes
1              sesameData/v1.17.1/EPIC.imputationDefault.rda   NA    NA
2             sesameData/v1.17.1/HM450.imputationDefault.rda   NA    NA
3           sesameData/v1.17.1/KYCG.EPICv2.TFBS.20220921.rda   NA    NA
4             sesameData/v1.17.1/KYCG.EPICv2.HM.20221013.rda   NA    NA
5           sesameData/v1.17.1/KYCG.EPICv2.Mask.20230314.rda   NA    NA
6  sesameData/v1.17.1/KYCG.EPICv2.ABCompartment.20220911.rda   NA    NA
7  sesameData/v1.17.1/KYCG.EPICv2.ImprintingDMR.20220818.rda   NA    NA
8       sesameData/v1.17.1/KYCG.EPICv2.ChromHMM.20220303.rda   NA    NA
9     sesameData/v1.17.1/KYCG.EPICv2.MetagenePC.20220911.rda   NA    NA
10      sesameData/v1.17.1/KYCG.EPICv2.CTCFbind.20220911.rda   NA    NA
11                      sesameData/v1.17.1/idatSignature.rda   NA    NA
12                   sesameData/v1.17.1/probeIDSignature.rda   NA    NA
13                     sesameData/v1.17.1/EPICv2.address.rda   NA    NA
> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

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

other attached packages:
[1] sesame_1.18.4       sesameData_1.18.0   ExperimentHub_2.8.0 AnnotationHub_3.4.0 BiocFileCache_2.4.0 dbplyr_2.3.2        BiocGenerics_0.42.0

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.8.1          Biobase_2.56.0                httr_1.4.6                    bit64_4.0.5                   shiny_1.7.4                   interactiveDisplayBase_1.34.0 BiocManager_1.30.20          
 [8] stats4_4.2.1                  blob_1.2.4                    GenomeInfoDbData_1.2.8        yaml_2.3.7                    BiocVersion_3.15.2            lattice_0.21-8                pillar_1.9.0                 
[15] RSQLite_2.3.1                 glue_1.6.2                    digest_0.6.31                 GenomicRanges_1.48.0          RColorBrewer_1.1-3            promises_1.2.0.1              XVector_0.36.0               
[22] colorspace_2.1-0              plyr_1.8.8                    preprocessCore_1.58.0         Matrix_1.5-4                  htmltools_0.5.5               httpuv_1.6.10                 pkgconfig_2.0.3              
[29] zlibbioc_1.42.0               purrr_1.0.1                   xtable_1.8-4                  scales_1.2.1                  later_1.3.1                   tzdb_0.3.0                    BiocParallel_1.30.4          
[36] tibble_3.2.1                  KEGGREST_1.36.3               generics_0.1.3                IRanges_2.30.1                ggplot2_3.4.2                 ellipsis_0.3.2                cachem_1.0.8                 
[43] withr_2.5.0                   SummarizedExperiment_1.26.1   wheatmap_0.2.0                cli_3.6.1                     magrittr_2.0.3                crayon_1.5.2                  mime_0.12                    
[50] memoise_2.0.1                 fansi_1.0.4                   tools_4.2.1                   hms_1.1.3                     matrixStats_0.63.0            lifecycle_1.0.3               stringr_1.5.0                
[57] S4Vectors_0.34.0              munsell_0.5.0                 DelayedArray_0.22.0           AnnotationDbi_1.58.0          Biostrings_2.64.1             compiler_4.2.1                GenomeInfoDb_1.32.4          
[64] rlang_1.1.1                   grid_4.2.1                    RCurl_1.98-1.12               rstudioapi_0.14               rappdirs_0.3.3                bitops_1.0-7                  gtable_0.3.3                 
[71] codetools_0.2-19              DBI_1.1.3                     curl_5.0.0                    reshape2_1.4.4                R6_2.5.1                      dplyr_1.1.2                   fastmap_1.1.1                
[78] bit_4.0.5                     utf8_1.2.3                    filelock_1.0.2                readr_2.1.4                   stringi_1.7.12                parallel_4.2.1                Rcpp_1.0.10                  
[85] vctrs_0.6.2                   png_0.1-8                     tidyselect_1.2.0

The robj2 is the df_master in the sysdata.rda file from the sesameData package. I'd appreciate any thoughts on how to get around this issue. Thank you!

yang050036 commented 1 year ago

Hello, I am having a similar issue when running readIDATpair due to sesameDataGet('idatSignature') in the inferPlatformFromTango function. After some investigation, I found that some of the data are not in the updated ExperimentHub. Please see details below:

> eh
ExperimentHub with 6306 records
# snapshotDate(): 2022-04-26
# $dataprovider: Eli and Edythe L. Broad Institute of Harvard and MIT, NCBI, Jonathan Griffiths, NA, GEO, The Tabula Muris Consortium, The National Center for Biotechnology Information, Broad Institute, BCLL@las, D...
# $species: Homo sapiens, Mus musculus, Saccharomyces cerevisiae, human gut metagenome, Rattus norvegicus, Saccharomyces cerevisiae S288C, groundwater metagenome, Papio cynocephalus, Mus musculus (E18 mice), Drosop...
# $rdataclass: SummarizedExperiment, ExpressionSet, matrix, character, list, DFrame, RaggedExperiment, data.frame, SummarizedBenchmark, dgCMatrix
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["EH1"]]' 

           title                                                                               
  EH1    | RNA-Sequencing and clinical data for 7706 tumor samples from The Cancer Genome Atlas
  EH166  | ERR188297                                                                           
  EH167  | ERR188088                                                                           
  EH168  | ERR188204                                                                           
  EH169  | ERR188317                                                                           
  ...      ...                                                                                 
  EH7538 | Visium_humanDLPFC                                                                   
  EH7539 | Visium_mouseCoronal                                                                 
  EH7540 | seqFISH_mouseEmbryo                                                                 
  EH7541 | ST_mouseOB                                                                          
  EH7542 | SlideSeqV2_mouseHPC 
> as.data.frame(robj2[!robj2$EHID %in% eh$ah_id,])
   Comments Example   EHID VERSION IN_USE                              Title                                                                    Description BiocVersion Genome SourceType
1      <NA>       0 EH8066  1.17.1   TRUE             EPIC.imputationDefault                                               Imputation default of EPIC array        3.17     NA        RDA
2      <NA>       0 EH8067  1.17.1   TRUE            HM450.imputationDefault                                              Imputation default of HM450 array        3.17     NA        RDA
3      <NA>       0 EH8068  1.17.1   TRUE          KYCG.EPICv2.TFBS.20220921           KYCG categorical database holding transcription factor binding sites        3.17     NA        RDA
4      <NA>       0 EH8069  1.17.1   TRUE            KYCG.EPICv2.HM.20221013                        KYCG categorical database holding histone modifications        3.17     NA        RDA
5      <NA>       0 EH8070  1.17.1   TRUE          KYCG.EPICv2.Mask.20230314                              KYCG categorical database holding technical masks        3.17     NA        RDA
6      <NA>       0 EH8071  1.17.1   TRUE KYCG.EPICv2.ABCompartment.20220911                              KYCG categorical database holding AB compartments        3.17     NA        RDA
7      <NA>       0 EH8072  1.17.1   TRUE KYCG.EPICv2.ImprintingDMR.20220818 KYCG categorical database holding imprinting differentially methylated regions        3.17     NA        RDA
8      <NA>       0 EH8073  1.17.1   TRUE      KYCG.EPICv2.ChromHMM.20220303                    KYCG categorical database holding consensus ChromHMM states        3.17     NA        RDA
9      <NA>       0 EH8074  1.17.1   TRUE    KYCG.EPICv2.MetagenePC.20220911                     KYCG categorical database holding protein coding metagenes        3.17     NA        RDA
10     <NA>       0 EH8075  1.17.1   TRUE      KYCG.EPICv2.CTCFbind.20220911                           KYCG categorical database holding CTCF binding sites        3.17     NA        RDA
11     <NA>       0 EH8076  1.17.1   TRUE                      idatSignature                              idat tango address to discriminate array platform        3.17     NA        RDA
12     <NA>       0 EH8077  1.17.1   TRUE                   probeIDSignature                                        probe ID to discriminate array platform        3.17     NA        RDA
13     <NA>       0 EH8078  1.17.1   TRUE                     EPICv2.address                EPICv2 array probe addresses, $ordering and $controls and $hg38        3.17     NA        RDA
                                    SourceUrl SourceVersion      Species TaxonomyId Coordinate_1_based DataProvider                           Maintainer RDataClass DispatchClass
1  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
2  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
3  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
4  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
5  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
6  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
7  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
8  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
9  http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
10 http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
11 http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
12 http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
13 http://zwdzwd.github.io/InfiniumAnnotation    2022-11-13 Homo sapiens       9606               TRUE      ZhouLab Wanding Zhou <zhouwanding@gmail.com>       list           Rda
                                                   RDataPath Tags Notes
1              sesameData/v1.17.1/EPIC.imputationDefault.rda   NA    NA
2             sesameData/v1.17.1/HM450.imputationDefault.rda   NA    NA
3           sesameData/v1.17.1/KYCG.EPICv2.TFBS.20220921.rda   NA    NA
4             sesameData/v1.17.1/KYCG.EPICv2.HM.20221013.rda   NA    NA
5           sesameData/v1.17.1/KYCG.EPICv2.Mask.20230314.rda   NA    NA
6  sesameData/v1.17.1/KYCG.EPICv2.ABCompartment.20220911.rda   NA    NA
7  sesameData/v1.17.1/KYCG.EPICv2.ImprintingDMR.20220818.rda   NA    NA
8       sesameData/v1.17.1/KYCG.EPICv2.ChromHMM.20220303.rda   NA    NA
9     sesameData/v1.17.1/KYCG.EPICv2.MetagenePC.20220911.rda   NA    NA
10      sesameData/v1.17.1/KYCG.EPICv2.CTCFbind.20220911.rda   NA    NA
11                      sesameData/v1.17.1/idatSignature.rda   NA    NA
12                   sesameData/v1.17.1/probeIDSignature.rda   NA    NA
13                     sesameData/v1.17.1/EPICv2.address.rda   NA    NA
> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

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

other attached packages:
[1] sesame_1.18.4       sesameData_1.18.0   ExperimentHub_2.8.0 AnnotationHub_3.4.0 BiocFileCache_2.4.0 dbplyr_2.3.2        BiocGenerics_0.42.0

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.8.1          Biobase_2.56.0                httr_1.4.6                    bit64_4.0.5                   shiny_1.7.4                   interactiveDisplayBase_1.34.0 BiocManager_1.30.20          
 [8] stats4_4.2.1                  blob_1.2.4                    GenomeInfoDbData_1.2.8        yaml_2.3.7                    BiocVersion_3.15.2            lattice_0.21-8                pillar_1.9.0                 
[15] RSQLite_2.3.1                 glue_1.6.2                    digest_0.6.31                 GenomicRanges_1.48.0          RColorBrewer_1.1-3            promises_1.2.0.1              XVector_0.36.0               
[22] colorspace_2.1-0              plyr_1.8.8                    preprocessCore_1.58.0         Matrix_1.5-4                  htmltools_0.5.5               httpuv_1.6.10                 pkgconfig_2.0.3              
[29] zlibbioc_1.42.0               purrr_1.0.1                   xtable_1.8-4                  scales_1.2.1                  later_1.3.1                   tzdb_0.3.0                    BiocParallel_1.30.4          
[36] tibble_3.2.1                  KEGGREST_1.36.3               generics_0.1.3                IRanges_2.30.1                ggplot2_3.4.2                 ellipsis_0.3.2                cachem_1.0.8                 
[43] withr_2.5.0                   SummarizedExperiment_1.26.1   wheatmap_0.2.0                cli_3.6.1                     magrittr_2.0.3                crayon_1.5.2                  mime_0.12                    
[50] memoise_2.0.1                 fansi_1.0.4                   tools_4.2.1                   hms_1.1.3                     matrixStats_0.63.0            lifecycle_1.0.3               stringr_1.5.0                
[57] S4Vectors_0.34.0              munsell_0.5.0                 DelayedArray_0.22.0           AnnotationDbi_1.58.0          Biostrings_2.64.1             compiler_4.2.1                GenomeInfoDb_1.32.4          
[64] rlang_1.1.1                   grid_4.2.1                    RCurl_1.98-1.12               rstudioapi_0.14               rappdirs_0.3.3                bitops_1.0-7                  gtable_0.3.3                 
[71] codetools_0.2-19              DBI_1.1.3                     curl_5.0.0                    reshape2_1.4.4                R6_2.5.1                      dplyr_1.1.2                   fastmap_1.1.1                
[78] bit_4.0.5                     utf8_1.2.3                    filelock_1.0.2                readr_2.1.4                   stringi_1.7.12                parallel_4.2.1                Rcpp_1.0.10                  
[85] vctrs_0.6.2                   png_0.1-8                     tidyselect_1.2.0

The robj2 is the df_master in the sysdata.rda file from the sesameData package. I'd appreciate any thoughts on how to get around this issue. Thank you!

Hi, I think you could update the R4.2 to R4.3 to sovled the error. Becuase many new database is uploaded to bioconductor 3.17, but bioconductor 3.17 is base on R4.3.

rtrelator commented 1 year ago

Thank you for the advice. Updating R and Bioconductor resolved the issue.