Closed baj12 closed 3 years ago
jkanche
commented
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.
baj12
commented
3 years ago SC3 is missing in the description file and necessary for the vignette
jkanche
commented
3 years ago 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!
baj12
commented
3 years ago 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 ?
baj12
commented
3 years ago 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"))
baj12
commented
3 years ago 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: