Closed baj12 closed 3 years ago
Hi @baj12
Thanks for trying it out! The package currently requires installing the SparseMeasurements
branch of epivizrData
. Install this either through bioc
or devtools
. we plan to push it to bioc release/devel soon
BiocManager::install("epiviz/epivizrData@SparseMeasurements")
Let me know if you continue to have issues.
SC3 is missing in the description file and necessary for the vignette
Thank you @baj12 for testing it out! I made a couple of more fixes wrt installation.
There's a new vignette walking through some fo the features of the app using the pbmc_3k dataset.
https://hcbravolab.github.io/TreeViz/Explore-PBMC.html
let us know if you have any feedback or suggestions!
Sorry, but I am still running into an installation problem:
> BiocManager::install("HCBravoLab/TreeViz")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing github package(s) 'HCBravoLab/TreeViz'
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo HCBravoLab/TreeViz@HEAD
✓ checking for file ‘/private/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T/RtmpFC58rJ/remotes5d851540dc2/HCBravoLab-TreeViz-d6b33c5/DESCRIPTION’ ...
─ preparing ‘TreeViz’: (347ms)
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘TreeViz/data/PBMC3k_TreeViz.RData’
─ building ‘TreeViz_0.1.0.tar.gz’
* installing *source* package ‘TreeViz’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'SummarizedExperiment::shift' by 'data.table::shift' when loading 'TreeViz'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TreeViz'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TreeViz'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TreeViz'
Warning: replacing previous import 'S4Vectors::merge' by 'git2r::merge' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::head' by 'git2r::head' when loading 'epivizrStandalone'
Warning: replacing previous import 'S4Vectors::as.data.frame' by 'git2r::as.data.frame' when loading 'epivizrStandalone'
Warning: replacing previous import 'dplyr::union' by 'igraph::union' when loading 'TreeViz'
Warning: replacing previous import 'dplyr::as_data_frame' by 'igraph::as_data_frame' when loading 'TreeViz'
Warning: replacing previous import 'dplyr::groups' by 'igraph::groups' when loading 'TreeViz'
Warning: replacing previous import 'igraph::normalize' by 'scater::normalize' when loading 'TreeViz'
Warning: replacing previous import 'igraph::groups' by 'tidygraph::groups' when loading 'TreeViz'
Error: class "SparseEpivizMeasurement" is not exported by 'namespace:epivizrData'
Execution halted
ERROR: lazy loading failed for package ‘TreeViz’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/TreeViz’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/TreeViz’
Error: Failed to install 'TreeViz' from GitHub:
(converted from warning) installation of package '/var/folders/d_/g1jsd9v96mvc9n0ds29v7m8m0000gn/T//RtmpFC58rJ/file5d865536544/TreeViz_0.1.0.tar.gz' had non-zero exit status
>
>
Hi @baj12
We merged the sparseMeasurement
branch of epivizrData with the master branch so
BiocManager::install(c("epiviz/epivizrData", "HCBravoLab/TreeViz"))
can you post your sessionInfo
?
It seems the installation worked, but there is still a problem loading the library:
Loading required package: epivizr
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs,
colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps,
colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds,
colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates,
colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians,
colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs,
rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2,
rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads,
rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for 'TreeViz':
class "SparseEpivizMeasurement" is not exported by 'namespace:epivizrData'
In addition: There were 12 warnings (use warnings() to see them)
> sessionInfo()
R version 4.0.3 (2020-10-10)
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/4.0/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] SummarizedExperiment_1.20.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.1
[4] IRanges_2.24.0 S4Vectors_0.28.0 MatrixGenerics_1.2.0
[7] matrixStats_0.57.0 epivizr_2.20.0 synchronicity_1.3.5
[10] bigmemory_4.5.36 Biobase_2.50.0 BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] shinydashboard_0.7.1 tidyselect_1.1.0 heatmaply_1.1.1
[4] RSQLite_2.2.1 AnnotationDbi_1.52.0 htmlwidgets_1.5.2
[7] grid_4.0.3 TSP_1.1-10 BiocParallel_1.24.1
[10] Rtsne_0.15 munsell_0.5.0 codetools_0.2-18
[13] statmod_1.4.35 scran_1.18.1 DT_0.16
[16] withr_2.3.0 colorspace_2.0-0 Category_2.56.0
[19] OrganismDbi_1.32.0 pcaExplorer_2.16.0 knitr_1.30
[22] uuid_0.1-4 rstudioapi_0.13 SingleCellExperiment_1.12.0
[25] NMF_0.23.0 git2r_0.27.1 GenomeInfoDbData_1.2.4
[28] polyclip_1.10-0 topGO_2.42.0 farver_2.0.3
[31] bit64_4.0.5 pheatmap_1.0.12 rprojroot_2.0.2
[34] vctrs_0.3.5 generics_0.1.0 xfun_0.19
[37] BiocFileCache_1.14.0 R6_2.5.0 doParallel_1.0.16
[40] ggbeeswarm_0.6.0 graphlayouts_0.7.1 rsvd_1.0.3
[43] seriation_1.2-9 locfit_1.5-9.4 AnnotationFilter_1.14.0
[46] bitops_1.0-6 shinyAce_0.4.1 DelayedArray_0.16.0
[49] assertthat_0.2.1 promises_1.1.1 scales_1.1.1
[52] ggraph_2.0.4 beeswarm_0.2.3 gtable_0.3.0
[55] beachmat_2.6.2 processx_3.4.5 tidygraph_1.2.0
[58] ensembldb_2.14.0 rlang_0.4.9 genefilter_1.72.0
[61] splines_4.0.3 rtracklayer_1.50.0 lazyeval_0.2.2
[64] epivizrData_1.18.0 shinyjqui_0.3.3 shinyBS_0.61
[67] BiocManager_1.30.10 yaml_2.2.1 reshape2_1.4.4
[70] GenomicFeatures_1.42.1 threejs_0.3.3 crosstalk_1.1.0.1
[73] httpuv_1.5.4 RBGL_1.66.0 tools_4.0.3
[76] gridBase_0.4-7 ggplot2_3.3.2 ellipsis_0.3.1
[79] gplots_3.1.1 RColorBrewer_1.1-2 clustree_0.4.3
[82] Rcpp_1.0.5 plyr_1.8.6 sparseMatrixStats_1.2.0
[85] base64enc_0.1-3 progress_1.2.2 zlibbioc_1.36.0
[88] purrr_0.3.4 RCurl_1.98-1.2 ps_1.4.0
[91] prettyunits_1.1.1 openssl_1.4.3 viridis_0.5.1
[94] epivizrStandalone_1.18.0 ggrepel_0.8.2 cluster_2.1.0
[97] magrittr_2.0.1 data.table_1.13.2 SparseM_1.78
[100] ProtGenerics_1.22.0 hms_0.5.3 mime_0.9
[103] evaluate_0.14 xtable_1.8-4 XML_3.99-0.5
[106] gridExtra_2.3 scater_1.18.3 compiler_4.0.3
[109] biomaRt_2.46.0 tibble_3.0.4 KernSmooth_2.23-18
[112] crayon_1.3.4 htmltools_0.5.0 GOstats_2.56.0
[115] later_1.1.0.1 tidyr_1.1.2 geneplotter_1.68.0
[118] DBI_1.1.0 tweenr_1.0.1 dbplyr_2.0.0
[121] MASS_7.3-53 rappdirs_0.3.1 sys_3.4
[124] Matrix_1.2-18 epivizrServer_1.18.0 cli_2.2.0
[127] igraph_1.2.6 pkgconfig_2.0.3 bigmemory.sri_0.1.3
[130] GenomicAlignments_1.26.0 registry_0.5-1 scuttle_1.0.3
[133] plotly_4.9.2.1 xml2_1.3.2 foreach_1.5.1
[136] annotate_1.68.0 vipor_0.4.5 dqrng_0.2.1
[139] rngtools_1.5 pkgmaker_0.32.2 webshot_0.5.2
[142] XVector_0.30.0 AnnotationForge_1.32.0 stringr_1.4.0
[145] callr_3.5.1 digest_0.6.27 graph_1.68.0
[148] Biostrings_2.58.0 rmarkdown_2.5 edgeR_3.32.0
[151] dendextend_1.14.0 DelayedMatrixStats_1.12.1 GSEABase_1.52.0
[154] curl_4.3 shiny_1.5.0 Rsamtools_2.6.0
[157] gtools_3.8.2 rjson_0.2.20 lifecycle_0.2.0
[160] jsonlite_1.7.1 BiocNeighbors_1.8.1 viridisLite_0.3.0
[163] askpass_1.1 limma_3.46.0 fansi_0.4.1
[166] pillar_1.4.7 lattice_0.20-41 fastmap_1.0.1
[169] httr_1.4.2 pkgbuild_1.1.0 survival_3.2-7
[172] GO.db_3.12.1 glue_1.4.2 remotes_2.2.0
[175] UpSetR_1.4.0 iterators_1.0.13 bluster_1.0.0
[178] bit_4.0.4 Rgraphviz_2.34.0 ggforce_0.3.2
[181] stringi_1.5.3 blob_1.2.1 BiocSingular_1.6.0
[184] DESeq2_1.30.0 caTools_1.18.0 memoise_1.1.0
[187] dplyr_1.0.2 irlba_2.3.3
Hi @baj12, I bumped the version on epivizrData
Sorry for the trouble but can you rerun the command again ?
BiocManager::install(c("epiviz/epivizrData", "HCBravoLab/TreeViz"))
After restarting R it loads. Thanks Bernd
PS. Which license are you using?
Hi, found your package via Twitter and was intrigued.
But I cannot test, because I cannot install: