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KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
GNU General Public License v2.0
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can not put in more than 1 genes. #219

Closed yaolutian closed 11 months ago

yaolutian commented 1 year ago

Dear Authors,

When I use magic recently, I cannot put in a list of gene names, Error message is "Error in is.null(x = genes) || is.na(x = genes) : 'length = 2' in coercion to 'logical(1)'". I can only put in one gene at a time. I am using R 4.3.1

Thanks! Lutian

SuperSe7enF commented 12 months ago

I had the same problem.

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so; LAPACK version 3.7.1

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

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

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

other attached packages: [1] reticulate_1.30 Rmagic_2.0.3 scales_1.2.1 scRNAtoolVis_0.0.6
[5] harmony_0.1.1 Rcpp_1.0.10 clustree_0.5.0 scCustomize_1.1.1
[9] FlexDotPlot_0.2.2 org.Hs.eg.db_3.17.0 AnnotationDbi_1.62.1 ReactomePA_1.44.0
[13] clusterProfiler_4.8.1 ClusterGVis_0.1.0 monocle_2.28.0 DDRTree_0.1.5
[17] irlba_2.3.5.1 VGAM_1.1-8 Matrix_1.6-0 muscat_1.14.0
[21] SCP_0.4.8 tradeSeq_1.14.0 slingshot_2.8.0 TrajectoryUtils_1.8.0
[25] princurve_2.1.6 philentropy_0.7.0 plyr_1.8.8 pbapply_1.7-0
[29] tidygraph_1.2.3 limma_3.56.2 RColorBrewer_1.1-3 lubridate_1.9.2
[33] forcats_1.0.0 purrr_1.0.1 tibble_3.2.1 tidyverse_2.0.0
[37] scuttle_1.10.1 ComplexHeatmap_2.16.0 SCopeLoomR_0.13.0 doParallel_1.0.17
[41] iterators_1.0.14 foreach_1.5.2 ggraph_2.1.0 AUCell_1.22.0
[45] RcisTarget_1.20.0 SCENIC_1.3.1 arrow_12.0.1 ggsci_3.0.0
[49] shiny_1.7.4 tidyselect_1.2.0 monocle3_1.3.1 SingleCellExperiment_1.22.0 [53] SummarizedExperiment_1.30.2 GenomicRanges_1.52.0 GenomeInfoDb_1.36.0 IRanges_2.34.0
[57] S4Vectors_0.38.1 MatrixGenerics_1.12.2 matrixStats_1.0.0 Biobase_2.60.0
[61] BiocGenerics_0.46.0 ggpubr_0.6.0 reshape2_1.4.4 tidyr_1.3.0
[65] dplyr_1.1.2 COSG_0.9.0 paletteer_1.5.0 Nebulosa_1.10.0
[69] patchwork_1.1.3.9000 stringr_1.5.0 ggplot2_3.4.2 cowplot_1.1.1
[73] SeuratObject_4.1.3 Seurat_4.3.0 qs_0.25.5 data.table_1.14.8
[77] readr_2.1.4

loaded via a namespace (and not attached): [1] igraph_1.5.0 graph_1.78.0 ica_1.0-3 plotly_4.10.2
[5] Formula_1.2-5 scater_1.28.0 rematch2_2.1.2 zlibbioc_1.46.0
[9] bit_4.0.5 clue_0.3-64 lattice_0.21-8 rjson_0.2.21
[13] blob_1.2.4 S4Arrays_1.0.4 pbkrtest_0.5.2 png_0.1-8
[17] cli_3.6.1 ggplotify_0.1.0 goftest_1.2-3 variancePartition_1.30.2 [21] org.Mm.eg.db_3.17.0 BiocNeighbors_1.18.0 Signac_1.10.0 uwot_0.1.14
[25] dendextend_1.17.1 shadowtext_0.1.2 curl_5.0.1 mime_0.12
[29] evaluate_0.21 tidytree_0.4.2 leiden_0.4.3 stringi_1.7.12
[33] backports_1.4.1 lmerTest_3.1-3 parallelDist_0.2.6 XML_3.99-0.14
[37] httpuv_1.6.11 magrittr_2.0.3 leaps_3.1 rappdirs_0.3.3
[41] RcppRoll_0.3.0 mclust_6.0.0 RApiSerialize_0.1.2 jpeg_0.1-10
[45] DT_0.28 ggbeeswarm_0.7.2 sctransform_0.3.5 sessioninfo_1.2.2
[49] DBI_1.1.3 terra_1.7-39 jquerylib_0.1.4 reactome.db_1.84.0
[53] withr_2.5.0 rprojroot_2.0.3 enrichplot_1.20.0 lmtest_0.9-40
[57] ggnewscale_0.4.9 GSEABase_1.62.0 FactoMineR_2.8 colourpicker_1.2.0
[61] BiocManager_1.30.21 htmlwidgets_1.6.2 biomaRt_2.56.1 ggrepel_0.9.3
[65] DESeq2_1.40.2 flashClust_1.01-2 sparsesvd_0.2-2 annotate_1.78.0
[69] zoo_1.8-12 XVector_0.40.0 knitr_1.43 docopt_0.7.1
[73] RhpcBLASctl_0.23-42 timechange_0.2.0 fansi_1.0.4 caTools_1.18.2
[77] ggtree_3.8.0 R.oo_1.25.0 ggrastr_1.0.2 gridGraphics_0.5-1
[81] ellipsis_0.3.2 lazyeval_0.2.2 survival_3.5-5 scattermore_1.2
[85] crayon_1.5.2 RcppAnnoy_0.0.20 progressr_0.13.0 tweenr_2.0.2
[89] later_1.3.1 ggridges_0.5.4 codetools_0.2-19 base64enc_0.1-3
[93] GlobalOptions_0.1.2 HSMMSingleCell_1.20.0 aod_1.3.2 KEGGREST_1.40.0
[97] Rtsne_0.16 shape_1.4.6 fastICA_1.2-3 estimability_1.4.1
[101] bsplus_0.1.4 Rsamtools_2.16.0 filelock_1.0.2 foreign_0.8-82
[105] pkgconfig_2.0.3 xml2_1.3.4 TMB_1.9.6 EnvStats_2.8.0
[109] scatterplot3d_0.3-44 aplot_0.1.10 spatstat.sparse_3.0-1 ape_5.7-1
[113] viridisLite_0.4.2 xtable_1.8-4 grImport2_0.2-0 car_3.1-2
[117] httr_1.4.6 rbibutils_2.2.13 tools_4.3.1 globals_0.16.2
[121] beeswarm_0.4.0 htmlTable_2.4.1 broom_1.0.5 checkmate_2.2.0
[125] nlme_3.1-162 HDO.db_0.99.1 dbplyr_2.3.2 hdf5r_1.3.8
[129] assertthat_0.2.1 lme4_1.1-33 digest_0.6.31 numDeriv_2016.8-1.1
[133] remaCor_0.0.16 farver_2.1.1 tzdb_0.4.0 ks_1.14.0
[137] yulab.utils_0.0.6 viridis_0.6.3 rpart_4.1.19 glue_1.6.2
[141] cachem_1.0.8 BiocFileCache_2.8.0 polyclip_1.10-4 Hmisc_5.1-0
[145] generics_0.1.3 Biostrings_2.68.1 mvtnorm_1.2-2 ggheatmap_2.11
[149] parallelly_1.36.0 here_1.0.1 R.cache_0.16.0 ScaledMatrix_1.8.1
[153] carData_3.0-5 minqa_1.2.5 gson_0.1.0 utf8_1.2.3
[157] gtools_3.9.4 graphlayouts_1.0.0 SeuratWrappers_0.3.1 sisal_0.48
[161] ggsignif_0.6.4 gridExtra_2.3 GenomeInfoDbData_1.2.10 glmmTMB_1.1.7
[165] R.utils_2.12.2 RCurl_1.98-1.12 memoise_2.0.1 rmarkdown_2.22
[169] pheatmap_1.0.12 downloader_0.4 R.methodsS3_1.8.2 future_1.32.0
[173] RANN_2.6.1 stringfish_0.15.8 spatstat.data_3.0-1 rstudioapi_0.14
[177] janitor_2.2.0 cluster_2.1.4 spatstat.utils_3.0-3 hms_1.1.3
[181] fitdistrplus_1.1-11 munsell_0.5.0 colorspace_2.1-0 ggdendro_0.1.23
[185] rlang_1.1.1 shinyWidgets_0.7.6 DelayedMatrixStats_1.22.1 sparseMatrixStats_1.12.0 [189] shinydashboard_0.7.2 ggforce_0.4.1 circlize_0.4.15 mgcv_1.9-0
[193] xfun_0.39 multcompView_0.1-9 TH.data_1.1-2 coda_0.19-4
[197] R.matlab_3.7.0 remotes_2.4.2 emmeans_1.8.6 abind_1.4-5
[201] GOSemSim_2.26.0 treeio_1.24.1 Rdpack_2.4 bitops_1.0-7
[205] promises_1.2.0.1 leidenbase_0.1.25 scatterpie_0.2.1 RSQLite_2.3.1
[209] qvalue_2.32.0 qlcMatrix_0.9.7 sandwich_3.0-2 fgsea_1.26.0
[213] DelayedArray_0.26.3 GO.db_3.17.0 compiler_4.3.1 prettyunits_1.1.1
[217] boot_1.3-28 beachmat_2.16.0 graphite_1.46.0 listenv_0.9.0
[221] BiocSingular_1.16.0 edgeR_3.42.4 tensor_1.5 MASS_7.3-60
[225] progress_1.2.2 BiocParallel_1.34.2 spatstat.random_3.1-5 R6_2.5.1
[229] multcomp_1.4-25 fastmap_1.1.1 fastmatch_1.1-3 rstatix_0.7.2
[233] vipor_0.4.5 ROCR_1.0-11 rsvd_1.0.5 nnet_7.3-19
[237] gtable_0.3.3 KernSmooth_2.23-22 miniUI_0.1.1.1 deldir_1.0-9
[241] htmltools_0.5.5 RcppParallel_5.1.7 bit64_4.0.5 ggprism_1.0.4
[245] spatstat.explore_3.2-1 lifecycle_1.0.3 blme_1.0-5 nloptr_2.0.3
[249] sass_0.4.6 vctrs_0.6.3 snakecase_0.11.0 slam_0.1-50
[253] spatstat.geom_3.2-1 DOSE_3.26.1 ggfun_0.1.0 sp_1.6-1
[257] future.apply_1.11.0 pracma_2.4.2 bslib_0.5.0 pillar_1.9.0
[261] gplots_3.1.3 combinat_0.0-8 locfit_1.5-9.8 jsonlite_1.8.5
[265] GetoptLong_1.0.5

ZheyouCai commented 11 months ago

Dear Authors,

When I use magic recently, I cannot put in a list of gene names, Error message is "Error in is.null(x = genes) || is.na(x = genes) : 'length = 2' in coercion to 'logical(1)'". I can only put in one gene at a time. I am using R 4.3.1

Thanks! Lutian

Hi. After updating the software package to version 3.0.0, I was able to resolve the aforementioned issues.

yaolutian commented 11 months ago

Dear Authors, When I use magic recently, I cannot put in a list of gene names, Error message is "Error in is.null(x = genes) || is.na(x = genes) : 'length = 2' in coercion to 'logical(1)'". I can only put in one gene at a time. I am using R 4.3.1 Thanks! Lutian

Hi. After updating the software package to version 3.0.0, I was able to resolve the aforementioned issues.

Thank you, but 3.0 cannot be installed, any ideas?

Warning in install.packages : package ‘/Users/ltyao/Desktop/MAGIC-3.0.0.tar’ is not available for this version of R

Lutian

yaolutian commented 11 months ago

Dear Authors, When I use magic recently, I cannot put in a list of gene names, Error message is "Error in is.null(x = genes) || is.na(x = genes) : 'length = 2' in coercion to 'logical(1)'". I can only put in one gene at a time. I am using R 4.3.1 Thanks! Lutian

Hi. After updating the software package to version 3.0.0, I was able to resolve the aforementioned issues.

It seems a little tricky to install the 3.0.0, I have managed to make it work, it shows version 2.0.3.999 now. At least, I can magic more than 1 gene now.

Thank you very much

Lutian

shihsama commented 6 months ago

Dear Authors, When I use magic recently, I cannot put in a list of gene names, Error message is "Error in is.null(x = genes) || is.na(x = genes) : 'length = 2' in coercion to 'logical(1)'". I can only put in one gene at a time. I am using R 4.3.1 Thanks! Lutian

Hi. After updating the software package to version 3.0.0, I was able to resolve the aforementioned issues.

It seems a little tricky to install the 3.0.0, I have managed to make it work, it shows version 2.0.3.999 now. At least, I can magic more than 1 gene now.

Thank you very much

Lutian

There's only 2.0.3 ver for R, the latest version, and 3.0.0 is for Python (v3.6.0 at most). It seems no more release after 2.0.3. (制作方跑路了???)