stack1kg error in dataman2017.Rmd about labs HOT 6 CLOSED

genomicsclass commented on August 23, 2024

stack1kg error in dataman2017.Rmd

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vjcitn commented on August 23, 2024

I have just committed ldblock 1.14.1 in the Bioconductor 3.9 branch. It should rectify this problem. It will probably take a day to get into the general 3.9 distribution. To get it immediately you could use devtools::install_github("vjcitn/ldblock", ref="RELEASE_3_9")

…

On Wed, Aug 14, 2019 at 2:22 PM gillsignals ***@***.***> wrote: The stack1kg function does not run successfully: >library(ldblock) >sta = stack1kg() Error in validObject(.Object) : invalid class “VcfStack” object: all rownames(object) must be in seqlevels(object) The content in the textbook section "1000 Genomes VCF in the cloud" depends on the sta object produced by running this function with no arguments. > sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ldblock_1.14.0 HDF5Array_1.12.2 [3] rhdf5_2.28.0 ArrayExpress_1.44.0 [5] magrittr_1.5 dplyr_0.8.3 [7] bigrquery_1.2.0 VariantTools_1.26.0 [9] VariantAnnotation_1.30.1 RaggedExperiment_1.8.0 [11] MultiAssayExperiment_1.10.4 GenomicAlignments_1.20.1 [13] BiocStyle_2.12.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 [15] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.30.0 [17] bumphunter_1.26.0 locfit_1.5-9.1 [19] iterators_1.0.12 foreach_1.4.7 [21] GSE5859Subset_1.0 airway_1.4.0 [23] ph525x_0.0.48 png_0.1-7 [25] RNAseqData.HNRNPC.bam.chr14_0.22.0 erma_1.0.0 [27] GenomicFiles_1.20.0 rtracklayer_1.44.2 [29] Rsamtools_2.0.0 Biostrings_2.52.0 [31] XVector_0.24.0 SummarizedExperiment_1.14.1 [33] DelayedArray_0.10.0 BiocParallel_1.18.0 [35] matrixStats_0.54.0 Homo.sapiens_1.3.1 [37] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.8.2 [39] GO.db_3.8.2 OrganismDbi_1.26.0 [41] GenomicFeatures_1.36.4 GenomicRanges_1.36.0 [43] GenomeInfoDb_1.20.0 GEOquery_2.52.0 [45] data.table_1.12.2 knitr_1.24 [47] geneplotter_1.62.0 annotate_1.62.0 [49] XML_3.98-1.20 AnnotationDbi_1.46.0 [51] IRanges_2.18.1 S4Vectors_0.22.0 [53] lattice_0.20-38 Biobase_2.44.0 [55] BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] snow_0.4-3 backports_1.1.4 plyr_1.8.4 lazyeval_0.2.2 [5] oligo_1.48.0 splines_3.6.1 ggplot2_3.2.1 digest_0.6.20 [9] htmltools_0.3.6 memoise_1.1.0 BSgenome_1.52.0 limma_3.40.6 [13] readr_1.3.1 askpass_1.1 siggenes_1.58.0 prettyunits_1.0.2 [17] colorspace_1.4-1 blob_1.2.0 xfun_0.8 jsonlite_1.6 [21] crayon_1.3.4 RCurl_1.95-4.12 graph_1.62.0 genefilter_1.66.0 [25] zeallot_0.1.0 survival_2.44-1.1 glue_1.3.1 registry_0.5-1 [29] gtable_0.3.0 zlibbioc_1.30.0 Rhdf5lib_1.6.0 scales_1.0.0 [33] DBI_1.0.0 rngtools_1.4 bibtex_0.4.2 Rcpp_1.0.1 [37] xtable_1.8-4 progress_1.2.2 bit_1.1-14 mclust_5.4.5 [41] preprocessCore_1.46.0 httr_1.4.1 RColorBrewer_1.1-2 ff_2.2-14 [45] pkgconfig_2.0.2 reshape_0.8.8 labeling_0.3 reshape2_1.4.3 [49] tidyselect_0.2.5 rlang_0.4.0 later_0.8.0 munsell_0.5.0 [53] tools_3.6.1 RSQLite_2.1.2 evaluate_0.14 stringr_1.4.0 [57] yaml_2.2.0 bit64_0.9-7 oligoClasses_1.46.0 beanplot_1.2 [61] scrime_1.3.5 purrr_0.3.2 RBGL_1.60.0 nlme_3.1-141 [65] doRNG_1.7.1 mime_0.7 nor1mix_1.3-0 xml2_1.2.2 [69] biomaRt_2.40.3 compiler_3.6.1 rstudioapi_0.10 curl_4.0 [73] affyio_1.54.0 tibble_2.1.3 stringi_1.4.3 Matrix_1.2-17 [77] multtest_2.40.0 vctrs_0.2.0 pillar_1.4.2 BiocManager_1.30.4 [81] snpStats_1.34.0 bitops_1.0-6 httpuv_1.5.1 R6_2.4.0 [85] promises_1.0.1 affxparser_1.56.0 codetools_0.2-16 MASS_7.3-51.4 [89] assertthat_0.2.1 openssl_1.4.1 pkgmaker_0.27 withr_2.1.2 [93] GenomeInfoDbData_1.2.1 hms_0.5.0 quadprog_1.5-7 tidyr_0.8.3 [97] base64_2.0 rmarkdown_1.14 DelayedMatrixStats_1.6.0 illuminaio_0.26.0 [101] shiny_1.3.2 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#73?email_source=notifications&email_token=ABDI5QVIKFMXZXRNHMSFDD3QEREMTA5CNFSM4ILXUCC2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HFIYAEQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABDI5QUGJQ2MPPP45ICNTBLQEREMTANCNFSM4ILXUCCQ> .

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vjcitn commented on August 23, 2024

Please close this issue if it resolves for you @gillsignals
Thanks

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gillsignals commented on August 23, 2024

This change did not correct the error. First, running ldblock::stack1kg generated this error:

Error in Seqinfo(chrs) : could not find function "Seqinfo"

I resolved that by loading the GenomeInfoDb package, which contains the Seqinfo function with capital S. (If that's the function intended for use here, perhaps GenomeInfoDb should be imported as a dependency.)

However, then my original VcfStack error recurred:

Error in validObject(.Object): invalid class “VcfStack” object: all rownames(object) must be in seqlevels(object)

I haven't found the source code for stack1kg yet, but I'm wondering if the Seqinfo function call was supposed to be seqinfo. This is just a guess, but looks like some data is not being correctly assigned to seqlevels of an object.

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] GenomeInfoDb_1.20.0 IRanges_2.18.1      S4Vectors_0.22.0    BiocGenerics_0.30.0 stringr_1.4.0       pdftools_2.2       

loaded via a namespace (and not attached):
 [1] Biobase_2.44.0                          httr_1.4.1                              bit64_0.9-7                            
 [4] splines_3.6.1                           GenomicFiles_1.20.0                     shiny_1.3.2                            
 [7] assertthat_0.2.1                        askpass_1.1                             BiocManager_1.30.4                     
[10] RBGL_1.60.0                             blob_1.2.0                              BSgenome_1.52.0                        
[13] GenomeInfoDbData_1.2.1                  Rsamtools_2.0.0                         progress_1.2.2                         
[16] qpdf_1.1                                Homo.sapiens_1.3.1                      pillar_1.4.2                           
[19] RSQLite_2.1.2                           backports_1.1.4                         lattice_0.20-38                        
[22] glue_1.3.1                              digest_0.6.20                           GenomicRanges_1.36.0                   
[25] promises_1.0.1                          XVector_0.24.0                          colorspace_1.4-1                       
[28] htmltools_0.3.6                         httpuv_1.5.1                            Matrix_1.2-17                          
[31] OrganismDbi_1.26.0                      ldblock_1.14.0                          XML_3.98-1.20                          
[34] pkgconfig_2.0.2                         biomaRt_2.40.4                          zlibbioc_1.30.0                        
[37] purrr_0.3.2                             xtable_1.8-4                            GO.db_3.8.2                            
[40] scales_1.0.0                            erma_1.0.0                              later_0.8.0                            
[43] BiocParallel_1.18.1                     tibble_2.1.3                            ggplot2_3.2.1                          
[46] SummarizedExperiment_1.14.1             GenomicFeatures_1.36.4                  lazyeval_0.2.2                         
[49] survival_2.44-1.1                       magrittr_1.5                            crayon_1.3.4                           
[52] mime_0.7                                memoise_1.1.0                           graph_1.62.0                           
[55] tools_3.6.1                             prettyunits_1.0.2                       org.Hs.eg.db_3.8.2                     
[58] hms_0.5.0                               matrixStats_0.54.0                      munsell_0.5.0                          
[61] DelayedArray_0.10.0                     AnnotationDbi_1.46.1                    snpStats_1.34.0                        
[64] Biostrings_2.52.0                       compiler_3.6.1                          rlang_0.4.0                            
[67] grid_3.6.1                              RCurl_1.95-4.12                         rstudioapi_0.10                        
[70] VariantAnnotation_1.30.1                bitops_1.0-6                            gtable_0.3.0                           
[73] DBI_1.0.0                               R6_2.4.0                                GenomicAlignments_1.20.1               
[76] dplyr_0.8.3                             rtracklayer_1.44.2                      bit_1.1-14                             
[79] zeallot_0.1.0                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 stringi_1.4.3                          
[82] Rcpp_1.0.1                              vctrs_0.2.0                             tidyselect_0.2.5

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vjcitn commented on August 23, 2024

yes i will work on it soon

…

On Thu, Aug 22, 2019 at 4:18 PM gillsignals ***@***.***> wrote: This change did not correct the error. First, running ldblock::stack1kg generated this error: Error in Seqinfo(chrs) : could not find function "Seqinfo" I resolved that by loading the GenomeInfoDb package, which contains the Seqinfo function with capital S. (If that's the function intended for use here, perhaps GenomeInfoDb should be imported as a dependency.) However, then my original VcfStack error recurred: Error in validObject(.Object): invalid class “VcfStack” object: all rownames(object) must be in seqlevels(object) I haven't found the source code for stack1kg yet, but I'm wondering if the Seqinfo function call was supposed to be seqinfo. This is just a guess, but looks like some data is not being correctly assigned to seqlevels of an object. sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomeInfoDb_1.20.0 IRanges_2.18.1 S4Vectors_0.22.0 BiocGenerics_0.30.0 stringr_1.4.0 pdftools_2.2 loaded via a namespace (and not attached): [1] Biobase_2.44.0 httr_1.4.1 bit64_0.9-7 [4] splines_3.6.1 GenomicFiles_1.20.0 shiny_1.3.2 [7] assertthat_0.2.1 askpass_1.1 BiocManager_1.30.4 [10] RBGL_1.60.0 blob_1.2.0 BSgenome_1.52.0 [13] GenomeInfoDbData_1.2.1 Rsamtools_2.0.0 progress_1.2.2 [16] qpdf_1.1 Homo.sapiens_1.3.1 pillar_1.4.2 [19] RSQLite_2.1.2 backports_1.1.4 lattice_0.20-38 [22] glue_1.3.1 digest_0.6.20 GenomicRanges_1.36.0 [25] promises_1.0.1 XVector_0.24.0 colorspace_1.4-1 [28] htmltools_0.3.6 httpuv_1.5.1 Matrix_1.2-17 [31] OrganismDbi_1.26.0 ldblock_1.14.0 XML_3.98-1.20 [34] pkgconfig_2.0.2 biomaRt_2.40.4 zlibbioc_1.30.0 [37] purrr_0.3.2 xtable_1.8-4 GO.db_3.8.2 [40] scales_1.0.0 erma_1.0.0 later_0.8.0 [43] BiocParallel_1.18.1 tibble_2.1.3 ggplot2_3.2.1 [46] SummarizedExperiment_1.14.1 GenomicFeatures_1.36.4 lazyeval_0.2.2 [49] survival_2.44-1.1 magrittr_1.5 crayon_1.3.4 [52] mime_0.7 memoise_1.1.0 graph_1.62.0 [55] tools_3.6.1 prettyunits_1.0.2 org.Hs.eg.db_3.8.2 [58] hms_0.5.0 matrixStats_0.54.0 munsell_0.5.0 [61] DelayedArray_0.10.0 AnnotationDbi_1.46.1 snpStats_1.34.0 [64] Biostrings_2.52.0 compiler_3.6.1 rlang_0.4.0 [67] grid_3.6.1 RCurl_1.95-4.12 rstudioapi_0.10 [70] VariantAnnotation_1.30.1 bitops_1.0-6 gtable_0.3.0 [73] DBI_1.0.0 R6_2.4.0 GenomicAlignments_1.20.1 [76] dplyr_0.8.3 rtracklayer_1.44.2 bit_1.1-14 [79] zeallot_0.1.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 stringi_1.4.3 [82] Rcpp_1.0.1 vctrs_0.2.0 tidyselect_0.2.5 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#73?email_source=notifications&email_token=ABDI5QWJ3P3WMFNUK6HXFHDQF3X7TA5CNFSM4ILXUCC2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD46IS2I#issuecomment-524061033>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABDI5QTAB44XXZKHEVOLYYDQF3X7TANCNFSM4ILXUCCQ> .

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vjcitn commented on August 23, 2024

ldblock 1.14.2 must be used. i just committed it. there was an irrelevant error and it never propagated so you have 1.14.0 in the above sessioninfo On Thu, Aug 22, 2019 at 4:19 PM Vincent Carey <[email protected]> wrote:

…

yes i will work on it soon On Thu, Aug 22, 2019 at 4:18 PM gillsignals ***@***.***> wrote: > This change did not correct the error. First, running ldblock::stack1kg > generated this error: > > Error in Seqinfo(chrs) : could not find function "Seqinfo" > > I resolved that by loading the GenomeInfoDb package, which contains the > Seqinfo function with capital S. (If that's the function intended for > use here, perhaps GenomeInfoDb should be imported as a dependency.) > > However, then my original VcfStack error recurred: > > Error in validObject(.Object): invalid class “VcfStack” object: all > rownames(object) must be in seqlevels(object) > > I haven't found the source code for stack1kg yet, but I'm wondering if > the Seqinfo function call was supposed to be seqinfo. This is just a > guess, but looks like some data is not being correctly assigned to > seqlevels of an object. > > sessionInfo() > > R version 3.6.1 (2019-07-05) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > Running under: Windows 10 x64 (build 17763) > > > > Matrix products: default > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats4 parallel stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] GenomeInfoDb_1.20.0 IRanges_2.18.1 S4Vectors_0.22.0 BiocGenerics_0.30.0 stringr_1.4.0 pdftools_2.2 > > > > loaded via a namespace (and not attached): > > [1] Biobase_2.44.0 httr_1.4.1 bit64_0.9-7 > > [4] splines_3.6.1 GenomicFiles_1.20.0 shiny_1.3.2 > > [7] assertthat_0.2.1 askpass_1.1 BiocManager_1.30.4 > > [10] RBGL_1.60.0 blob_1.2.0 BSgenome_1.52.0 > > [13] GenomeInfoDbData_1.2.1 Rsamtools_2.0.0 progress_1.2.2 > > [16] qpdf_1.1 Homo.sapiens_1.3.1 pillar_1.4.2 > > [19] RSQLite_2.1.2 backports_1.1.4 lattice_0.20-38 > > [22] glue_1.3.1 digest_0.6.20 GenomicRanges_1.36.0 > > [25] promises_1.0.1 XVector_0.24.0 colorspace_1.4-1 > > [28] htmltools_0.3.6 httpuv_1.5.1 Matrix_1.2-17 > > [31] OrganismDbi_1.26.0 ldblock_1.14.0 XML_3.98-1.20 > > [34] pkgconfig_2.0.2 biomaRt_2.40.4 zlibbioc_1.30.0 > > [37] purrr_0.3.2 xtable_1.8-4 GO.db_3.8.2 > > [40] scales_1.0.0 erma_1.0.0 later_0.8.0 > > [43] BiocParallel_1.18.1 tibble_2.1.3 ggplot2_3.2.1 > > [46] SummarizedExperiment_1.14.1 GenomicFeatures_1.36.4 lazyeval_0.2.2 > > [49] survival_2.44-1.1 magrittr_1.5 crayon_1.3.4 > > [52] mime_0.7 memoise_1.1.0 graph_1.62.0 > > [55] tools_3.6.1 prettyunits_1.0.2 org.Hs.eg.db_3.8.2 > > [58] hms_0.5.0 matrixStats_0.54.0 munsell_0.5.0 > > [61] DelayedArray_0.10.0 AnnotationDbi_1.46.1 snpStats_1.34.0 > > [64] Biostrings_2.52.0 compiler_3.6.1 rlang_0.4.0 > > [67] grid_3.6.1 RCurl_1.95-4.12 rstudioapi_0.10 > > [70] VariantAnnotation_1.30.1 bitops_1.0-6 gtable_0.3.0 > > [73] DBI_1.0.0 R6_2.4.0 GenomicAlignments_1.20.1 > > [76] dplyr_0.8.3 rtracklayer_1.44.2 bit_1.1-14 > > [79] zeallot_0.1.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 stringi_1.4.3 > > [82] Rcpp_1.0.1 vctrs_0.2.0 tidyselect_0.2.5 > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#73?email_source=notifications&email_token=ABDI5QWJ3P3WMFNUK6HXFHDQF3X7TA5CNFSM4ILXUCC2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD46IS2I#issuecomment-524061033>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ABDI5QTAB44XXZKHEVOLYYDQF3X7TANCNFSM4ILXUCCQ> > . >

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gillsignals commented on August 23, 2024

This fixed the issue - thanks!

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stack1kg error in dataman2017.Rmd about labs HOT 6 CLOSED

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