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satijalab / seurat-data

Dataset distribution for Seurat
GNU General Public License v3.0
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pbmcMultiome seurat data not available #30

Closed bassanio closed 3 years ago

bassanio commented 3 years ago

pbmcMultiome as described in this vignettes :https://satijalab.org/seurat/articles/atacseq_integration_vignette.html for some reason is not available to download. How to fix the issue

InstallData("pbmcMultiome")

Warning: The following datasets are not available: pbmcMultiome Error: No SeuratData datasets provided

AvailableData()

                                   Dataset Version                                                        Summary seurat    species            system ncells
bmcite.SeuratData                   bmcite   0.3.0                                          30k Bone Marrow Cells  3.2.2      human       bone marrow  30672
cbmc.SeuratData                       cbmc   3.1.4                   scRNAseq and 13-antibody sequencing of CBMCs  3.1.4      human CBMC (cord blood)   8617
celegans.embryo.SeuratData celegans.embryo   0.1.0         6k C. elegans embryos from Packer and Zhu et al (2019)   <NA> C. elegans            embryo   6188
hcabm40k.SeuratData               hcabm40k   3.0.0 40,000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset   <NA>      human       bone marrow  40000
ifnb.SeuratData                       ifnb   3.1.0                              IFNB-Stimulated and Control PBMCs   <NA>      human              PBMC  13999
panc8.SeuratData                     panc8   3.0.2               Eight Pancreas Datasets Across Five Technologies   <NA>      human Pancreatic Islets  14892
pbmc3k.SeuratData                   pbmc3k   3.1.4                                     3k PBMCs from 10X Genomics  3.1.4      human              PBMC   2700
pbmcsca.SeuratData                 pbmcsca   3.0.0           Broad Institute PBMC Systematic Comparative Analysis   <NA>      human              PBMC  31021
ssHippo.SeuratData                 ssHippo   3.1.4                      Slide-seq v2 dataset of mouse hippocampus   <NA>      mouse       hippocampus     NA
stxBrain.SeuratData               stxBrain   0.1.1                        10X Genomics Visium Mouse Brain Dataset   <NA>      mouse             brain  12167
stxKidney.SeuratData             stxKidney   0.1.0                       10X Genomics Visium Mouse Kidney Dataset   <NA>      mouse            kidney   1438
thp1.eccite.SeuratData         thp1.eccite   3.1.5                                               ECCITE-seq THP-1   <NA>      human              <NA>     NA
                                                                                      tech default.dataset disk.datasets                               other.datasets
bmcite.SeuratData                                                                     <NA>            <NA>          <NA>                                         <NA>
cbmc.SeuratData                                                                   CITE-seq             raw     processed                                         <NA>
celegans.embryo.SeuratData                                                            <NA>             raw          <NA>                                         <NA>
hcabm40k.SeuratData                                                                 10x v2             raw          <NA>                                         <NA>
ifnb.SeuratData                                                                     10x v1             raw          <NA>                                    processed
panc8.SeuratData                          SMARTSeq2, Fluidigm C1, CelSeq, CelSeq2, inDrops             raw          <NA>                                         <NA>
pbmc3k.SeuratData                                                                   10x v1             raw          <NA>                                 pbmc3k.final
pbmcsca.SeuratData         10x v2, 10x v3, SMARTSeq2, Seq-Well, inDrops, Drop-seq, CelSeq2             raw          <NA>                                         <NA>
ssHippo.SeuratData                                                             slideseq v2             raw          <NA>                                         <NA>
stxBrain.SeuratData                                                                 visium              NA          <NA> posterior1, posterior2, anterior1, anterior2
stxKidney.SeuratData                                                                visium             raw          <NA>                                         <NA>
thp1.eccite.SeuratData                                                                <NA>            <NA>          <NA>                                         <NA>
                                                                                               notes Installed InstalledVersion
bmcite.SeuratData                                                                               <NA>     FALSE             <NA>
cbmc.SeuratData                                                                                 <NA>     FALSE             <NA>
celegans.embryo.SeuratData                                                                      <NA>     FALSE             <NA>
hcabm40k.SeuratData                                                                             <NA>     FALSE             <NA>
ifnb.SeuratData                                                                                 <NA>     FALSE             <NA>
panc8.SeuratData                                                                                <NA>     FALSE             <NA>
pbmc3k.SeuratData                                                                               <NA>     FALSE             <NA>
pbmcsca.SeuratData                                                                     HCA benchmark     FALSE             <NA>
ssHippo.SeuratData                                                                              <NA>     FALSE             <NA>
stxBrain.SeuratData        One sample split across four datasets as paired anterior/posterior slices     FALSE             <NA>
stxKidney.SeuratData                                                                            <NA>     FALSE             <NA>
thp1.eccite.SeuratData                                                                          <NA>     FALSE             <NA>

sessionInfo

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SeuratData_0.2.1          cowplot_1.1.0             patchwork_1.1.0           ggplot2_3.3.2             EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.12.1          AnnotationFilter_1.12.0  
 [8] GenomicFeatures_1.40.1    AnnotationDbi_1.50.3      Biobase_2.48.0            GenomicRanges_1.40.0      GenomeInfoDb_1.24.2       IRanges_2.22.2            S4Vectors_0.26.1         
[15] BiocGenerics_0.34.0       Seurat_4.0.0              Signac_1.1.0              qqman_0.1.4               data.table_1.13.2        

loaded via a namespace (and not attached):
  [1] reticulate_1.18             tidyselect_1.1.0            RSQLite_2.2.1               htmlwidgets_1.5.2           grid_4.0.3                  BiocParallel_1.22.0        
  [7] Rtsne_0.15                  munsell_0.5.0               codetools_0.2-18            ica_1.0-2                   future_1.20.1               miniUI_0.1.1.1             
 [13] withr_2.3.0                 colorspace_1.4-1            OrganismDbi_1.30.0          knitr_1.30                  rstudioapi_0.12             ROCR_1.0-11                
 [19] tensor_1.5                  listenv_0.8.0               labeling_0.4.2              GenomeInfoDbData_1.2.3      polyclip_1.10-0             bit64_4.0.5                
 [25] farver_2.0.3                parallelly_1.21.0           vctrs_0.3.4                 generics_0.1.0              xfun_0.19                   biovizBase_1.36.0          
 [31] BiocFileCache_1.12.1        lsa_0.73.2                  ggseqlogo_0.1               R6_2.5.0                    rsvd_1.0.3                  hdf5r_1.3.3                
 [37] bitops_1.0-6                spatstat.utils_1.17-0       reshape_0.8.8               DelayedArray_0.14.1         assertthat_0.2.1            promises_1.1.1             
 [43] scales_1.1.1                nnet_7.3-14                 gtable_0.3.0                globals_0.13.1              goftest_1.2-2               ggbio_1.36.0               
 [49] rlang_0.4.8                 calibrate_1.7.7             RcppRoll_0.3.0              splines_4.0.3               rtracklayer_1.48.0          lazyeval_0.2.2             
 [55] dichromat_2.0-0             checkmate_2.0.0             BiocManager_1.30.10         reshape2_1.4.4              abind_1.4-5                 backports_1.2.0            
 [61] httpuv_1.5.4                Hmisc_4.4-1                 RBGL_1.64.0                 tools_4.0.3                 ellipsis_0.3.1              RColorBrewer_1.1-2         
 [67] ggridges_0.5.2              Rcpp_1.0.5                  plyr_1.8.6                  base64enc_0.1-3             progress_1.2.2              zlibbioc_1.34.0            
 [73] purrr_0.3.4                 RCurl_1.98-1.2              prettyunits_1.1.1           rpart_4.1-15                openssl_1.4.3               deldir_0.2-2               
 [79] pbapply_1.4-3               zoo_1.8-8                   SummarizedExperiment_1.18.2 ggrepel_0.8.2               cluster_2.1.0               tinytex_0.27               
 [85] magrittr_1.5                RSpectra_0.16-0             lmtest_0.9-38               RANN_2.6.1                  SnowballC_0.7.0             ProtGenerics_1.20.0        
 [91] fitdistrplus_1.1-1          matrixStats_0.57.0          hms_0.5.3                   mime_0.9                    xtable_1.8-4                XML_3.99-0.5               
 [97] jpeg_0.1-8.1                gridExtra_2.3               compiler_4.0.3              biomaRt_2.44.4              tibble_3.0.4                KernSmooth_2.23-18         
[103] crayon_1.3.4                htmltools_0.5.0             mgcv_1.8-33                 later_1.1.0.1               Formula_1.2-4               tidyr_1.1.2                
[109] DBI_1.1.0                   tweenr_1.0.1                dbplyr_2.0.0                MASS_7.3-53                 rappdirs_0.3.1              Matrix_1.2-18              
[115] cli_2.1.0                   igraph_1.2.6                pkgconfig_2.0.3             GenomicAlignments_1.24.0    foreign_0.8-80              plotly_4.9.2.1             
[121] xml2_1.3.2                  XVector_0.28.0              stringr_1.4.0               VariantAnnotation_1.34.0    digest_0.6.27               sctransform_0.3.2          
[127] RcppAnnoy_0.0.18            graph_1.66.0                spatstat.data_1.4-3         Biostrings_2.56.0           leiden_0.3.5                fastmatch_1.1-0            
[133] htmlTable_2.1.0             uwot_0.1.10                 curl_4.3                    shiny_1.5.0                 Rsamtools_2.4.0             lifecycle_0.2.0            
[139] nlme_3.1-150                jsonlite_1.7.1              fansi_0.4.1                 viridisLite_0.3.0           askpass_1.1                 BSgenome_1.56.0            
[145] pillar_1.4.6                lattice_0.20-41             GGally_2.0.0                fastmap_1.0.1               httr_1.4.2                  survival_3.2-7             
[151] glue_1.4.2                  spatstat_1.64-1             png_0.1-7                   bit_4.0.4                   ggforce_0.3.2               stringi_1.5.3              
[157] blob_1.2.1                  latticeExtra_0.6-29         memoise_1.1.0               dplyr_1.0.2                 irlba_2.3.3                 future.apply_1.6.0
andrewwbutler commented 3 years ago

Hi,

Can you try installing again? It should be available now.

bassanio commented 3 years ago

InstallData("pbmcMultiome")

trying URL 'http://seurat.nygenome.org/src/contrib/pbmcMultiome.SeuratData_0.1.0.tar.gz'
Content type 'application/octet-stream' length 280133643 bytes (267.2 MB)
============
downloaded 64.5 MB

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://seurat.nygenome.org/src/contrib/pbmcMultiome.SeuratData_0.1.0.tar.gz' failed
In addition: There were 38 warnings (use warnings() to see them)
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘pbmcMultiome.SeuratData’ failed
Error in loadNamespace(name) : 
  there is no package called ‘pbmcMultiome.SeuratData’

sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] SeuratData_0.2.1

loaded via a namespace (and not attached):
 [1] BiocManager_1.30.10 compiler_4.0.3      assertthat_0.2.1    cli_2.3.1           tools_4.0.3         glue_1.4.2         
 [7] rappdirs_0.3.3      curl_4.3            crayon_1.4.1        remotes_2.2.0
andrewwbutler commented 3 years ago

It looks like you've started the download (meaning that it is available) but the download took too long so it timed out. Could you try setting the timeout option to a larger number?

options(timeout = 1000)
InstallData("pbmcMultiome")
bassanio commented 3 years ago

@andrewwbutler : Thank you. it worked. but there is 48 warnings and when i ran AvailableData() I could find the data but with warnings . Said that I am closing the ticket

AvailableData()
                                   Dataset Version                                                        Summary seurat    species            system ncells
bmcite.SeuratData                   bmcite   0.3.0                                          30k Bone Marrow Cells  3.2.2      human       bone marrow  30672
cbmc.SeuratData                       cbmc   3.1.4                   scRNAseq and 13-antibody sequencing of CBMCs  3.1.4      human CBMC (cord blood)   8617
celegans.embryo.SeuratData celegans.embryo   0.1.0         6k C. elegans embryos from Packer and Zhu et al (2019)   <NA> C. elegans            embryo   6188
hcabm40k.SeuratData               hcabm40k   3.0.0 40,000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset   <NA>      human       bone marrow  40000
ifnb.SeuratData                       ifnb   3.1.0                              IFNB-Stimulated and Control PBMCs   <NA>      human              PBMC  13999
panc8.SeuratData                     panc8   3.0.2               Eight Pancreas Datasets Across Five Technologies   <NA>      human Pancreatic Islets  14892
pbmc3k.SeuratData                   pbmc3k   3.1.4                                     3k PBMCs from 10X Genomics  3.1.4      human              PBMC   2700
pbmcMultiome.SeuratData       pbmcMultiome   0.1.0                             10X Genomics PBMC Multiome Dataset  4.0.0      human              pbmc  11909
pbmcsca.SeuratData                 pbmcsca   3.0.0           Broad Institute PBMC Systematic Comparative Analysis   <NA>      human              PBMC  31021
ssHippo.SeuratData                 ssHippo   3.1.4                      Slide-seq v2 dataset of mouse hippocampus   <NA>      mouse       hippocampus     NA
stxBrain.SeuratData               stxBrain   0.1.1                        10X Genomics Visium Mouse Brain Dataset   <NA>      mouse             brain  12167
stxKidney.SeuratData             stxKidney   0.1.0                       10X Genomics Visium Mouse Kidney Dataset   <NA>      mouse            kidney   1438
thp1.eccite.SeuratData         thp1.eccite   3.1.5                                               ECCITE-seq THP-1   <NA>      human              <NA>     NA
                                                                                      tech default.dataset disk.datasets                               other.datasets
bmcite.SeuratData                                                                     <NA>            <NA>          <NA>                                         <NA>
cbmc.SeuratData                                                                   CITE-seq             raw     processed                                         <NA>
celegans.embryo.SeuratData                                                            <NA>             raw          <NA>                                         <NA>
hcabm40k.SeuratData                                                                 10x v2             raw          <NA>                                         <NA>
ifnb.SeuratData                                                                     10x v1             raw          <NA>                                    processed
panc8.SeuratData                          SMARTSeq2, Fluidigm C1, CelSeq, CelSeq2, inDrops             raw          <NA>                                         <NA>
pbmc3k.SeuratData                                                                   10x v1             raw          <NA>                                 pbmc3k.final
pbmcMultiome.SeuratData                                                               <NA>              NA          <NA>                          pbmc.rna, pbmc.atac
pbmcsca.SeuratData         10x v2, 10x v3, SMARTSeq2, Seq-Well, inDrops, Drop-seq, CelSeq2             raw          <NA>                                         <NA>
ssHippo.SeuratData                                                             slideseq v2             raw          <NA>                                         <NA>
stxBrain.SeuratData                                                                 visium              NA          <NA> posterior1, posterior2, anterior1, anterior2
stxKidney.SeuratData                                                                visium             raw          <NA>                                         <NA>
thp1.eccite.SeuratData                                                                <NA>            <NA>          <NA>                                         <NA>
                                                                                               notes Installed InstalledVersion
bmcite.SeuratData                                                                               <NA>     FALSE             <NA>
cbmc.SeuratData                                                                                 <NA>     FALSE             <NA>
celegans.embryo.SeuratData                                                                      <NA>     FALSE             <NA>
hcabm40k.SeuratData                                                                             <NA>     FALSE             <NA>
ifnb.SeuratData                                                                                 <NA>     FALSE             <NA>
panc8.SeuratData                                                                                <NA>     FALSE             <NA>
pbmc3k.SeuratData                                                                               <NA>     FALSE             <NA>
pbmcMultiome.SeuratData                                 One sample with two modalities, RNA and ATAC      TRUE            0.1.0
pbmcsca.SeuratData                                                                     HCA benchmark     FALSE             <NA>
ssHippo.SeuratData                                                                              <NA>     FALSE             <NA>
stxBrain.SeuratData        One sample split across four datasets as paired anterior/posterior slices     FALSE             <NA>
stxKidney.SeuratData                                                                            <NA>     FALSE             <NA>
thp1.eccite.SeuratData                                                                          <NA>     FALSE

warnings() 

Warning messages:
1: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
2: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
3: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
4: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
5: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
6: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
7: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
8: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
9: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
10: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
11: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
12: In if (is.na(desc)) { ... :
  the condition has length > 1 and only the first element will be used
KoichiHashikawa commented 3 years ago

Hello I have the similar problem. AvailableData() showed a table that pbmcMultiome.SeuratData is in the list.

But when I ran InstallData("pbmcMultiome") I got an error Error in loadNamespace(name): there is no package called 'pbmcMultiome.SeuratData' Traceback:

  1. InstallData("pbmcMultiome")
  2. attachNamespace(ns = pkg)
  3. asNamespace(ns, base.OK = FALSE)
  4. getNamespace(ns)
  5. loadNamespace(name)
  6. withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  7. withOneRestart(expr, restarts[[1L]])
  8. doWithOneRestart(return(expr), restart)

I can install other data like pbmc3k, pbmcsca etc without any issues.

R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] SeuratObject_4.0.0 Seurat_4.0.1

loaded via a namespace (and not attached): [1] Rtsne_0.15 colorspace_2.0-0 deldir_0.2-10
[4] ellipsis_0.3.1 ggridges_0.5.3 IRdisplay_1.0
[7] base64enc_0.1-3 fs_1.5.0 spatstat.data_2.1-0
[10] leiden_0.3.7 listenv_0.8.0 ggrepel_0.9.1
[13] fansi_0.4.2 codetools_0.2-18 splines_4.0.3
[16] polyclip_1.10-0 IRkernel_1.1.1 jsonlite_1.7.2
[19] ica_1.0-2 cluster_2.1.1 png_0.1-7
[22] uwot_0.1.10 shiny_1.6.0 sctransform_0.3.2
[25] spatstat.sparse_2.0-0 compiler_4.0.3 httr_1.4.2
[28] Matrix_1.3-2 fastmap_1.1.0 lazyeval_0.2.2
[31] cli_2.4.0 later_1.1.0.1 htmltools_0.5.1.1
[34] tools_4.0.3 igraph_1.2.6 gtable_0.3.0
[37] glue_1.4.2 RANN_2.6.1 reshape2_1.4.4
[40] dplyr_1.0.5 Rcpp_1.0.6 scattermore_0.7
[43] vctrs_0.3.7 nlme_3.1-152 lmtest_0.9-38
[46] stringr_1.4.0 globals_0.14.0 mime_0.10
[49] miniUI_0.1.1.1 lifecycle_1.0.0 irlba_2.3.3
[52] goftest_1.2-2 future_1.21.0 MASS_7.3-53.1
[55] zoo_1.8-9 scales_1.1.1 spatstat.core_2.0-0
[58] promises_1.2.0.1 spatstat.utils_2.1-0 parallel_4.0.3
[61] RColorBrewer_1.1-2 reticulate_1.18 pbapply_1.4-3
[64] gridExtra_2.3 ggplot2_3.3.3 rpart_4.1-15
[67] stringi_1.5.3 repr_1.1.3 rlang_0.4.10
[70] pkgconfig_2.0.3 matrixStats_0.58.0 evaluate_0.14
[73] lattice_0.20-41 ROCR_1.0-11 purrr_0.3.4
[76] tensor_1.5 patchwork_1.1.1 htmlwidgets_1.5.3
[79] cowplot_1.1.1 tidyselect_1.1.0 parallelly_1.24.0
[82] RcppAnnoy_0.0.18 plyr_1.8.6 magrittr_2.0.1
[85] R6_2.5.0 generics_0.1.0 pbdZMQ_0.3-5
[88] pillar_1.6.0 mgcv_1.8-34 fitdistrplus_1.1-3
[91] survival_3.2-10 abind_1.4-5 tibble_3.1.0
[94] future.apply_1.7.0 crayon_1.4.1 uuid_0.1-4
[97] KernSmooth_2.23-18 utf8_1.2.1 spatstat.geom_2.1-0
[100] plotly_4.9.3 grid_4.0.3 data.table_1.14.0
[103] digest_0.6.27 xtable_1.8-4 tidyr_1.1.3
[106] httpuv_1.5.5 munsell_0.5.0 viridisLite_0.4.0

shellmik commented 3 years ago

I switched to InstallData("pbmcMultiome.SeuratData") and it worked.

Jiayi-Zheng commented 1 year ago

Combining suggestions from @andrewwbutler and @shellmik and do: options(timeout = 1000) InstallData("pbmcMultiome.SeuratData") works well without warnings and problems.