search

l-magnificence / Mime

Machine learning-based integration model with elegant performance
Other
72 stars 14 forks source link

Mine package installation failure #9

Closed PanSX-Dr closed 2 months ago

PanSX-Dr commented 3 months ago

Hello, when I was in Mime the package installation tips I can't to 0 exit status, checked the, others installation may be because the Mime name conflict with devtools depend on the package name, how to solve?

警告信息: In i.p(...) : 安装程序包‘C:/Users/17209/AppData/Local/Temp/RtmpGSiWaO/file25d6821eb17f0/Mime_0.0.0.9000.tar.gz’时退出狀態的值不是0

Downloading GitHub repo l-magnificence/Mime@HEAD Skipping 7 packages ahead of CRAN: BiocParallel, S4Vectors, BiocGenerics, survcomp, mixOmics, IRanges, ComplexHeatmap ── R CMD build ───────────────────────────────────────────── ✔ checking for file 'C:\Users\17209\AppData\Local\Temp\RtmpGSiWaO\remotes25d683efa25a8\l-magnificence-Mime-91f9d78/DESCRIPTION' ... ─ preparing 'Mime': (797ms) ✔ checking DESCRIPTION meta-information ... Warning: C:/Users/17209/AppData/Local/Temp/Rtmpcbq3FU/Rbuild25cb8460b5fd7/Mime/man/cal_unicox_meta_ml_res.Rd:12: unexpected section header '\value' Warning: C:/Users/17209/AppData/Local/Temp/Rtmpcbq3FU/Rbuild25cb8460b5fd7/Mime/man/cal_unicox_meta_ml_res.Rd:15: unexpected section header '\description' Warning: C:/Users/17209/AppData/Local/Temp/Rtmpcbq3FU/Rbuild25cb8460b5fd7/Mime/man/cal_unicox_meta_ml_res.Rd:18: unexpected END_OF_INPUT ' ' ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building 'Mime_0.0.0.9000.tar.gz' * installing *source* package 'Mime' ... ERROR: cannot remove earlier installation, is it in use? * removing 'D:/profiles/R-4.4.0/library/Mime' * restoring previous 'D:/profiles/R-4.4.0/library/Mime' Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) : problem copying D:\profiles\R-4.4.0\library\00LOCK-Mime\Mime\libs\x64\mime.dll to D:\profiles\R-4.4.0\library\Mime\libs\x64\mime.dll: Permission denied 警告信息: In i.p(...) : 安装程序包‘C:/Users/17209/AppData/Local/Temp/RtmpGSiWaO/file25d6821eb17f0/Mime_0.0.0.9000.tar.gz’时退出狀態的值不是0
PanSX-Dr commented 3 months ago

auc.other.pre <- cal_auc_previous_sig(list_train_vali_Data = list_train_vali_Data,seed = 5201314, train_data = list_train_vali_Data$training, cores_for_parallel = 32) 我再运行相关函数的时候出现了新的问题， Data processing1.1 IFNG.Sig1.2 T.cell.inflamed.Sig1.3 PDL1.Sig1.4 LRRC15.CAF.Sig1.5 NLRP3.Sig错误于gsva(expr, gmt, method = "ssgsea", parallel.sz = 1): Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva'). 请问是什么情况？GSVA我更新到了最新的包

l-magnificence commented 3 months ago

Hello, when I was in Mime the package installation tips I can't to 0 exit status, checked the, others installation may be because the Mime name conflict with devtools depend on the package name, how to solve?

警告信息: In i.p(...) : 安装程序包‘C:/Users/17209/AppData/Local/Temp/RtmpGSiWaO/file25d6821eb17f0/Mime_0.0.0.9000.tar.gz’时退出狀態的值不是0

Downloading GitHub repo l-magnificence/Mime@HEAD Skipping 7 packages ahead of CRAN: BiocParallel, S4Vectors, BiocGenerics, survcomp, mixOmics, IRanges, ComplexHeatmap ── R CMD build ───────────────────────────────────────────── ✔ checking for file 'C:\Users\17209\AppData\Local\Temp\RtmpGSiWaO\remotes25d683efa25a8\l-magnificence-Mime-91f9d78/DESCRIPTION' ... ─ preparing 'Mime': (797ms) ✔ checking DESCRIPTION meta-information ... Warning: C:/Users/17209/AppData/Local/Temp/Rtmpcbq3FU/Rbuild25cb8460b5fd7/Mime/man/cal_unicox_meta_ml_res.Rd:12: unexpected section header '\value' Warning: C:/Users/17209/AppData/Local/Temp/Rtmpcbq3FU/Rbuild25cb8460b5fd7/Mime/man/cal_unicox_meta_ml_res.Rd:15: unexpected section header '\description' Warning: C:/Users/17209/AppData/Local/Temp/Rtmpcbq3FU/Rbuild25cb8460b5fd7/Mime/man/cal_unicox_meta_ml_res.Rd:18: unexpected END_OF_INPUT ' ' ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building 'Mime_0.0.0.9000.tar.gz' installing source package 'Mime' ... ERROR: cannot remove earlier installation, is it in use? removing 'D:/profiles/R-4.4.0/library/Mime' * restoring previous 'D:/profiles/R-4.4.0/library/Mime' Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) : problem copying D:\profiles\R-4.4.0\library\00LOCK-Mime\Mime\libs\x64\mime.dll to D:\profiles\R-4.4.0\library\Mime\libs\x64\mime.dll: Permission denied 警告信息: In i.p(...) : 安装程序包‘C:/Users/17209/AppData/Local/Temp/RtmpGSiWaO/file25d6821eb17f0/Mime_0.0.0.9000.tar.gz’时退出狀態的值不是0

It is not because that the Mime name is conflict with other package name. Mime and other package name ”mime“ coexist on my system and run well. Have you already installed the dependency package from bioconductor. Then install Mime. After installing the dependency package from bioconductor, you can also try download package from github and install local

devtools::install_local("./Mime-main.zip")
PanSX-Dr commented 3 months ago

OK thank you for you help , but I face a new question. when I run the ML.Dev.Pred.Category.Sig function with the own-data, the error showed like this: res.ici <- ML.Dev.Pred.Category.Sig(train_data = list_train_vali_Data$training, list_train_vali_Data = list_train_vali_Data, candidate_genes = genelist, methods = c('nb','svmRadialWeights','rf','kknn','adaboost','LogitBoost','cancerclass'), seed = 5201314, cores_for_parallel = 60 )

---loading the function--- 错误于if (identical(colnames(train_data)[1:2], c("ID", "Var")) & identical(common_feature[1:2], : the condition has length > 1 sessionInfo() R version 4.4.1 (2024-06-14 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 [2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai tzcode source: internal

attached base packages: [1] parallel grid stats graphics grDevices [6] utils datasets methods base

other attached packages: [1] cancerclass_1.48.0 binom_1.1-1.1
[3] Biobase_2.64.0 BiocGenerics_0.50.0
[5] doParallel_1.0.17 iterators_1.0.14
[7] foreach_1.5.2 caret_6.0-94
[9] lattice_0.22-6 ROCit_2.1.2
[11] pROC_1.18.5 e1071_1.7-14
[13] sva_3.52.0 BiocParallel_1.38.0
[15] genefilter_1.86.0 mgcv_1.9-1
[17] nlme_3.1-165 future_1.33.2
[19] gridExtra_2.3 GSVA_1.52.3
[21] paletteer_1.6.0 lubridate_1.9.3
[23] forcats_1.0.0 stringr_1.5.1
[25] dplyr_1.1.4 purrr_1.0.2
[27] readr_2.1.5 tidyr_1.3.1
[29] tibble_3.2.1 tidyverse_2.0.0
[31] ggplot2_3.5.1 ComplexHeatmap_2.20.0 [33] Mime_0.0.0.9000

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3
[2] rstudioapi_0.16.0
[3] jsonlite_1.8.8
[4] shape_1.4.6.1
[5] magrittr_2.0.3
[6] magick_2.8.3
[7] GlobalOptions_0.1.2
[8] fs_1.6.4
[9] zlibbioc_1.50.0
[10] vctrs_0.6.5
[11] memoise_2.0.1
[12] S4Arrays_1.4.1
[13] Rhdf5lib_1.26.0
[14] SparseArray_1.4.8
[15] rhdf5_2.48.0
[16] gridGraphics_0.5-1
[17] parallelly_1.37.1
[18] plyr_1.8.9
[19] cachem_1.1.0
[20] lifecycle_1.0.4
[21] pkgconfig_2.0.3
[22] rsvd_1.0.5
[23] Matrix_1.7-0
[24] R6_2.5.1
[25] fastmap_1.2.0
[26] GenomeInfoDbData_1.2.12
[27] MatrixGenerics_1.16.0
[28] clue_0.3-65
[29] digest_0.6.36
[30] aplot_0.2.3
[31] colorspace_2.1-0
[32] rematch2_2.1.2
[33] patchwork_1.2.0
[34] AnnotationDbi_1.66.0
[35] S4Vectors_0.42.0
[36] irlba_2.3.5.1
[37] GenomicRanges_1.56.1
[38] RSQLite_2.3.7
[39] beachmat_2.20.0
[40] fansi_1.0.6
[41] timechange_0.3.0
[42] httr_1.4.7
[43] abind_1.4-5
[44] compiler_4.4.1
[45] proxy_0.4-27
[46] bit64_4.0.5
[47] withr_3.0.0
[48] DBI_1.2.3
[49] HDF5Array_1.32.0
[50] lava_1.8.0
[51] MASS_7.3-61
[52] DelayedArray_0.30.1
[53] rjson_0.2.21
[54] ModelMetrics_1.2.2.2
[55] tools_4.4.1
[56] future.apply_1.11.2
[57] nnet_7.3-19
[58] glue_1.7.0
[59] rhdf5filters_1.16.0
[60] reshape2_1.4.4
[61] cluster_2.1.6
[62] recipes_1.0.10
[63] generics_0.1.3
[64] gtable_0.3.5
[65] tzdb_0.4.0
[66] class_7.3-22
[67] data.table_1.15.4
[68] hms_1.1.3
[69] BiocSingular_1.20.0
[70] ScaledMatrix_1.12.0
[71] utf8_1.2.4
[72] XVector_0.44.0
[73] pillar_1.9.0
[74] limma_3.60.3
[75] yulab.utils_0.1.4
[76] circlize_0.4.16
[77] splines_4.4.1
[78] survival_3.7-0
[79] bit_4.0.5
[80] annotate_1.82.0
[81] tidyselect_1.2.1
[82] locfit_1.5-9.10
[83] SingleCellExperiment_1.26.0 [84] Biostrings_2.72.1
[85] IRanges_2.38.0
[86] edgeR_4.2.0
[87] SummarizedExperiment_1.34.0 [88] stats4_4.4.1
[89] hardhat_1.4.0
[90] statmod_1.5.0
[91] timeDate_4032.109
[92] matrixStats_1.3.0
[93] stringi_1.8.4
[94] UCSC.utils_1.0.0
[95] ggfun_0.1.5
[96] codetools_0.2-20
[97] graph_1.82.0
[98] ggplotify_0.1.2
[99] cli_3.6.3
[100] rpart_4.1.23
[101] xtable_1.8-4
[102] munsell_0.5.1
[103] Rcpp_1.0.12
[104] GenomeInfoDb_1.40.1
[105] globals_0.16.3
[106] png_0.1-8
[107] XML_3.99-0.17
[108] gower_1.0.1
[109] blob_1.2.4
[110] sparseMatrixStats_1.16.0
[111] listenv_0.9.1
[112] SpatialExperiment_1.14.0
[113] GSEABase_1.66.0
[114] ipred_0.9-14
[115] prodlim_2024.06.25
[116] scales_1.3.0
[117] crayon_1.5.3
[118] GetoptLong_1.0.5
[119] rlang_1.1.4
[120] KEGGREST_1.44.1

l-magnificence commented 3 months ago

OK thank you for you help , but I face a new question. when I run the ML.Dev.Pred.Category.Sig function with the own-data, the error showed like this: res.ici <- ML.Dev.Pred.Category.Sig(train_data = list_train_vali_Data$training, list_train_vali_Data = list_train_vali_Data, candidate_genes = genelist, methods = c('nb','svmRadialWeights','rf','kknn','adaboost','LogitBoost','cancerclass'), seed = 5201314, cores_for_parallel = 60 )

---loading the function--- 错误于if (identical(colnames(train_data)[1:2], c("ID", "Var")) & identical(common_feature[1:2], : the condition has length > 1 sessionInfo() R version 4.4.1 (2024-06-14 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 [2] LC_CTYPE=Chinese (Simplified)_China.utf8 [3] LC_MONETARY=Chinese (Simplified)_China.utf8 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai tzcode source: internal

attached base packages: [1] parallel grid stats graphics grDevices [6] utils datasets methods base

other attached packages: [1] cancerclass_1.48.0 binom_1.1-1.1 [3] Biobase_2.64.0 BiocGenerics_0.50.0 [5] doParallel_1.0.17 iterators_1.0.14 [7] foreach_1.5.2 caret_6.0-94 [9] lattice_0.22-6 ROCit_2.1.2 [11] pROC_1.18.5 e1071_1.7-14 [13] sva_3.52.0 BiocParallel_1.38.0 [15] genefilter_1.86.0 mgcv_1.9-1 [17] nlme_3.1-165 future_1.33.2 [19] gridExtra_2.3 GSVA_1.52.3 [21] paletteer_1.6.0 lubridate_1.9.3 [23] forcats_1.0.0 stringr_1.5.1 [25] dplyr_1.1.4 purrr_1.0.2 [27] readr_2.1.5 tidyr_1.3.1 [29] tibble_3.2.1 tidyverse_2.0.0 [31] ggplot2_3.5.1 ComplexHeatmap_2.20.0 [33] Mime_0.0.0.9000

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 [2] rstudioapi_0.16.0 [3] jsonlite_1.8.8 [4] shape_1.4.6.1 [5] magrittr_2.0.3 [6] magick_2.8.3 [7] GlobalOptions_0.1.2 [8] fs_1.6.4 [9] zlibbioc_1.50.0 [10] vctrs_0.6.5 [11] memoise_2.0.1 [12] S4Arrays_1.4.1 [13] Rhdf5lib_1.26.0 [14] SparseArray_1.4.8 [15] rhdf5_2.48.0 [16] gridGraphics_0.5-1 [17] parallelly_1.37.1 [18] plyr_1.8.9 [19] cachem_1.1.0 [20] lifecycle_1.0.4 [21] pkgconfig_2.0.3 [22] rsvd_1.0.5 [23] Matrix_1.7-0 [24] R6_2.5.1 [25] fastmap_1.2.0 [26] GenomeInfoDbData_1.2.12 [27] MatrixGenerics_1.16.0 [28] clue_0.3-65 [29] digest_0.6.36 [30] aplot_0.2.3 [31] colorspace_2.1-0 [32] rematch2_2.1.2 [33] patchwork_1.2.0 [34] AnnotationDbi_1.66.0 [35] S4Vectors_0.42.0 [36] irlba_2.3.5.1 [37] GenomicRanges_1.56.1 [38] RSQLite_2.3.7 [39] beachmat_2.20.0 [40] fansi_1.0.6 [41] timechange_0.3.0 [42] httr_1.4.7 [43] abind_1.4-5 [44] compiler_4.4.1 [45] proxy_0.4-27 [46] bit64_4.0.5 [47] withr_3.0.0 [48] DBI_1.2.3 [49] HDF5Array_1.32.0 [50] lava_1.8.0 [51] MASS_7.3-61 [52] DelayedArray_0.30.1 [53] rjson_0.2.21 [54] ModelMetrics_1.2.2.2 [55] tools_4.4.1 [56] future.apply_1.11.2 [57] nnet_7.3-19 [58] glue_1.7.0 [59] rhdf5filters_1.16.0 [60] reshape2_1.4.4 [61] cluster_2.1.6 [62] recipes_1.0.10 [63] generics_0.1.3 [64] gtable_0.3.5 [65] tzdb_0.4.0 [66] class_7.3-22 [67] data.table_1.15.4 [68] hms_1.1.3 [69] BiocSingular_1.20.0 [70] ScaledMatrix_1.12.0 [71] utf8_1.2.4 [72] XVector_0.44.0 [73] pillar_1.9.0 [74] limma_3.60.3 [75] yulab.utils_0.1.4 [76] circlize_0.4.16 [77] splines_4.4.1 [78] survival_3.7-0 [79] bit_4.0.5 [80] annotate_1.82.0 [81] tidyselect_1.2.1 [82] locfit_1.5-9.10 [83] SingleCellExperiment_1.26.0 [84] Biostrings_2.72.1 [85] IRanges_2.38.0 [86] edgeR_4.2.0 [87] SummarizedExperiment_1.34.0 [88] stats4_4.4.1 [89] hardhat_1.4.0 [90] statmod_1.5.0 [91] timeDate_4032.109 [92] matrixStats_1.3.0 [93] stringi_1.8.4 [94] UCSC.utils_1.0.0 [95] ggfun_0.1.5 [96] codetools_0.2-20 [97] graph_1.82.0 [98] ggplotify_0.1.2 [99] cli_3.6.3 [100] rpart_4.1.23 [101] xtable_1.8-4 [102] munsell_0.5.1 [103] Rcpp_1.0.12 [104] GenomeInfoDb_1.40.1 [105] globals_0.16.3 [106] png_0.1-8 [107] XML_3.99-0.17 [108] gower_1.0.1 [109] blob_1.2.4 [110] sparseMatrixStats_1.16.0 [111] listenv_0.9.1 [112] SpatialExperiment_1.14.0 [113] GSEABase_1.66.0 [114] ipred_0.9-14 [115] prodlim_2024.06.25 [116] scales_1.3.0 [117] crayon_1.5.3 [118] GetoptLong_1.0.5 [119] rlang_1.1.4 [120] KEGGREST_1.44.1

It have solved, reinstall package and try.

PanSX-Dr commented 3 months ago

您好，之前的问题好像是解决了，但是又出现了新问题当我运行 res.ici <- ML.Dev.Pred.Category.Sig(train_data = list_train_vali_Data$training, list_train_vali_Data = list_train_vali_Data, candidate_genes = genelist, methods = c('nb','svmRadialWeights','rf','kknn','adaboost','LogitBoost','cancerclass'), seed = 5201314, cores_for_parallel = 60 ) 提示错误: package klaR is required。 但是当我安装klaR包之后，再次运行又提示我 错误: package or namespace load failed for ‘klaR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 不存在叫‘mime’这个名称的程序包。 请问这是什么情况

l-magnificence commented 3 months ago

Have you run successfully in the example data not your own data?

PanSX-Dr commented 3 months ago

I used the example data , and it showed the error as above. klaR package always showed error

PanSX-Dr commented 3 months ago

res.ici <- ML.Dev.Pred.Category.Sig(train_data = list_train_vali_Data$training, list_train_vali_Data = list_train_vali_Data, candidate_genes = genelist, methods = c('nb','svmRadialWeights','rf','kknn','adaboost','LogitBoost','cancerclass'), seed = 5201314, cores_for_parallel = 60 )#报错。 error like: ---loading the function--- [1] "There existing 42 genes in candidate genes" [1] "Intersetion of the candidate genes and the colnames of the provided data" [1] "There existing 42 genes in candidate genes, colnames of training data, colnames of validation data" 错误: package klaR is required

PanSX-Dr commented 3 months ago

library(klaR) 载入需要的程序包：MASS

载入程序包：‘MASS’

The following object is masked from ‘package:dplyr’:

select

The following object is masked from ‘package:genefilter’:

area

错误: package or namespace load failed for ‘klaR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 不存在叫‘mime’这个名称的程序包

PanSX-Dr commented 3 months ago

The name of this package can be duplicated with the name of the single-cell dependent package mime. Once Mime is installed, it overrides the mime package. However, if you reinstall Mime, it will overwrite the mime packet and cause an error

res.ici <- ML.Dev.Pred.Category.Sig(train_data = list_train_vali_Data$training, list_train_vali_Data = list_train_vali_Data, candidate_genes = genelist, methods = c('nb','svmRadialWeights','rf','kknn','adaboost','LogitBoost','cancerclass'), seed = 5201314, cores_for_parallel = 60 )#报错。

---loading the function--- [1] "There existing 42 genes in candidate genes" [1] "Intersetion of the candidate genes and the colnames of the provided data" [1] "There existing 42 genes in candidate genes, colnames of training data, colnames of validation data" 错误: package klaR is required

library(klaR) 载入需要的程序包：MASS

载入程序包：‘MASS’

The following object is masked from ‘package:dplyr’:

select

The following object is masked from ‘package:genefilter’:

area

错误: package or namespace load failed for ‘klaR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 不存在叫‘mime’这个名称的程序包

sessionInfo() R version 4.4.1 (2024-06-14 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 [2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai tzcode source: internal

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

other attached packages: [1] SeuratObject_5.0.2 sp_2.1-4
[3] MASS_7.3-61 dplyr_1.1.4
[5] cancerclass_1.48.0 binom_1.1-1.1
[7] Biobase_2.64.0 BiocGenerics_0.50.0 [9] doParallel_1.0.17 iterators_1.0.14
[11] foreach_1.5.2 caret_6.0-94
[13] lattice_0.22-6 ggplot2_3.5.1
[15] ROCit_2.1.2 pROC_1.18.5
[17] e1071_1.7-14 sva_3.52.0
[19] BiocParallel_1.38.0 genefilter_1.86.0
[21] mgcv_1.9-1 nlme_3.1-165
[23] future_1.33.2 gridExtra_2.3
[25] stringr_1.5.1 mime_0.12

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0
[3] jsonlite_1.8.8 magrittr_2.0.3
[5] fs_1.6.4 zlibbioc_1.50.0
[7] vctrs_0.6.5 ROCR_1.0-11
[9] memoise_2.0.1 htmltools_0.5.8.1
[11] gridGraphics_0.5-1 parallelly_1.37.1
[13] KernSmooth_2.23-24 ica_1.0-3
[15] plyr_1.8.9 zoo_1.8-12
[17] lubridate_1.9.3 cachem_1.1.0
[19] igraph_2.0.3 lifecycle_1.0.4
[21] pkgconfig_2.0.3 Matrix_1.7-0
[23] R6_2.5.1 fastmap_1.2.0
[25] fitdistrplus_1.1-11 GenomeInfoDbData_1.2.12 [27] MatrixGenerics_1.16.0 digest_0.6.36
[29] aplot_0.2.3 colorspace_2.1-0
[31] patchwork_1.2.0 AnnotationDbi_1.66.0
[33] S4Vectors_0.42.0 irlba_2.3.5.1
[35] RSpectra_0.16-1 RSQLite_2.3.7
[37] progressr_0.14.0 fansi_1.0.6
[39] timechange_0.3.0 httr_1.4.7
[41] compiler_4.4.1 proxy_0.4-27
[43] remotes_2.5.0 bit64_4.0.5
[45] withr_3.0.0 DBI_1.2.3
[47] fastDummies_1.7.3 lava_1.8.0
[49] ModelMetrics_1.2.2.2 tools_4.4.1
[51] lmtest_0.9-40 httpuv_1.6.15
[53] future.apply_1.11.2 nnet_7.3-19
[55] glue_1.7.0 promises_1.3.0
[57] grid_4.4.1 Rtsne_0.17
[59] cluster_2.1.6 reshape2_1.4.4
[61] generics_0.1.3 recipes_1.0.10
[63] gtable_0.3.5 class_7.3-22
[65] data.table_1.15.4 utf8_1.2.4
[67] XVector_0.44.0 RcppAnnoy_0.0.22
[69] ggrepel_0.9.5 RANN_2.6.1
[71] pillar_1.9.0 RcppHNSW_0.6.0
[73] spam_2.10-0 yulab.utils_0.1.4
[75] limma_3.60.3 later_1.3.2
[77] splines_4.4.1 survival_3.7-0
[79] bit_4.0.5 annotate_1.82.0
[81] tidyselect_1.2.1 locfit_1.5-9.10
[83] Biostrings_2.72.1 IRanges_2.38.0
[85] edgeR_4.2.0 stats4_4.4.1
[87] statmod_1.5.0 hardhat_1.4.0
[89] timeDate_4032.109 matrixStats_1.3.0
[91] stringi_1.8.4 UCSC.utils_1.0.0
[93] ggfun_0.1.5 codetools_0.2-20
[95] tibble_3.2.1 ggplotify_0.1.2
[97] cli_3.6.3 rpart_4.1.23
[99] reticulate_1.38.0 xtable_1.8-4
[101] munsell_0.5.1 Rcpp_1.0.12
[103] GenomeInfoDb_1.40.1 globals_0.16.3
[105] png_0.1-8 XML_3.99-0.17
[107] gower_1.0.1 blob_1.2.4
[109] dotCall64_1.1-1 listenv_0.9.1
[111] ipred_0.9-14 ggridges_0.5.6
[113] scales_1.3.0 prodlim_2024.06.25
[115] leiden_0.4.3.1 purrr_1.0.2
[117] crayon_1.5.3 combinat_0.0-8
[119] rlang_1.1.4 cowplot_1.1.3
[121] KEGGREST_1.44.1

zzchr1s commented 3 months ago

Hi sir, appreciate your excellent work! However, I encountered exactly the same problem as stated in this issue:

checking for LF line-endings in source and make files and shell scripts (612ms)

And I pretty sure all dependencies has been downloaded, and loaded. Besides, I also have "mime" package in my library. I also tried install Mime from the local zip file, and the same problem appearred. Totally don't know how to solve it, need your gentle help!! Thanks!!

update: I delete the "mime" folder from my library, then:

devtools::install_github("l-magnificence/Mime") 错误于loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): 不存在叫‘mime’这个名称的程序包 收捲时出错: 'length = 4' in coercion to 'logical(1)' Error: no more error handlers available (recursive errors?); invoking 'abort' restart

l-magnificence commented 3 months ago

We have changed the package name to Mime1, please reinstall using 

devtools::install_github("l-magnificence/Mime")
zzchr1s commented 3 months ago

We have changed the package name to Mime1, please reinstall using

devtools::install_github("l-magnificence/Mime")

Successfully install your package, thanks very much!!

zifeng17 commented 2 months ago

当我运行load("./Example.cohort.Rdata") list_train_vali_Data[["Dataset1"]][1:5,1:5] load("./Example.ici.Rdata") list_train_vali_Data[["training"]][1:5,1:5] load("./genelist.Rdata") library(Mime1) load("./Example.cohort.Rdata") load("./genelist.Rdata") res <- ML.Dev.Prog.Sig(train_data = list_train_vali_Data$Dataset1, list_train_vali_Data = list_train_vali_Data, unicox.filter.for.candi = T, unicox_p_cutoff = 0.05, candidate_genes = genelist, mode = 'all',nodesize =5,seed = 5201314 )

--- 10.Lasso + superPC --- Error: infinite argument in coxph.wtest