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YuLab-SMU / createKEGGdb

Create KEGG.db Package
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Failed to install 'createKEGGdb' from GitHub #5

Open brightbio opened 4 years ago

brightbio commented 4 years ago

Hi,
I want to try the method to get the latest information about zea mays. But when I type "remotes::install_github("YuLab-SMU/createKEGGdb") " on RStudio, the program reported an error: Downloading GitHub repo YuLab-SMU/createKEGGdb@master Skipping 1 packages not available: clusterProfiler 错误: Failed to install 'createKEGGdb' from GitHub: setup stdio (system error 2, 系统找不到指定的文件。) @win/processx.c:970 I wonder the reason and how to solve it. Thank you!

GuangchuangYu commented 4 years ago

Skipping 1 packages not available: clusterProfiler

首先把clusterProfiler装上再说。

brightbio commented 4 years ago

事实上，在运行 remotes::install_github("YuLab-SMU/createKEGGdb") 之前 我已经安装并加载了clusterProfiler，但是依然报错，并且还发现运行 devtools :: install_github("YuLab-SMU/clusterProfiler")，同样报错，安装其他R包，亦是报错。 之后，我将R 和R Studio卸载，重新安装后同样报错：

library(clusterProfiler)

clusterProfiler v3.10.1 For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite: Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287. Warning message: 程辑包‘clusterProfiler’是用R版本3.5.1 来建造的

devtools::install_github("YuLab-SMU/createKEGGdb")

Error in rethrow_call(c_processx_exec, command, c(command, args), stdin, : setup stdio (system error 2, 系统找不到指定的文件。) @win/processx.c:970

remotes::install_github("YuLab-SMU/createKEGGdb")

Downloading GitHub repo YuLab-SMU/createKEGGdb@master Skipping 1 packages not available: clusterProfiler 错误: Failed to install 'createKEGGdb' from GitHub: setup stdio (system error 2, 系统找不到指定的文件。) @win/processx.c:970

library(clusterProfiler)

此时，加载成功

devtools::install_github("YuLab-SMU/clusterProfiler")

Error in rethrow_call(c_processx_exec, command, c(command, args), stdin, : setup stdio (system error 2, 系统找不到指定的文件。) @win/processx.c:970 Y叔，这该怎么办呢？

sessionInfo()

R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 16299)

Matrix products: default locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] clusterProfiler_3.10.1 processx_3.4.1 callr_3.4.0

loaded via a namespace (and not attached): [1] fs_1.3.1 usethis_1.5.1 enrichplot_1.2.0 devtools_2.2.1
[5] bit64_0.9-7 progress_1.2.2 httr_1.4.1 RColorBrewer_1.1-2
[9] UpSetR_1.4.0 rprojroot_1.3-2 tools_3.5.0 backports_1.1.5
[13] R6_2.4.1 DBI_1.1.0 lazyeval_0.2.2 BiocGenerics_0.28.0 [17] colorspace_1.4-1 withr_2.1.2 tidyselect_0.2.5 gridExtra_2.3
[21] prettyunits_1.0.2 curl_4.3 bit_1.1-14 compiler_3.5.0
[25] cli_2.0.0 Biobase_2.42.0 xml2_1.2.2 desc_1.2.0
[29] triebeard_0.3.0 scales_1.1.0 ggridges_0.5.1 stringr_1.4.0
[33] digest_0.6.23 DOSE_3.8.2 pkgconfig_2.0.3 sessioninfo_1.1.1
[37] rlang_0.4.2 rstudioapi_0.10 RSQLite_2.1.5 gridGraphics_0.4-1
[41] farver_2.0.1 jsonlite_1.6 BiocParallel_1.16.6 GOSemSim_2.8.0
[45] dplyr_0.8.3 magrittr_1.5 ggplotify_0.0.4 GO.db_3.7.0
[49] Matrix_1.2-18 Rcpp_1.0.3 munsell_0.5.0 S4Vectors_0.20.1
[53] fansi_0.4.0 viridis_0.5.1 lifecycle_0.1.0 stringi_1.4.3
[57] ggraph_2.0.0 MASS_7.3-51.5 pkgbuild_1.0.6 plyr_1.8.5
[61] qvalue_2.14.1 grid_3.5.0 blob_1.2.0 parallel_3.5.0
[65] ggrepel_0.8.1 DO.db_2.9 crayon_1.3.4 lattice_0.20-38
[69] cowplot_1.0.0 graphlayouts_0.5.0 splines_3.5.0 hms_0.5.2
[73] zeallot_0.1.0 ps_1.3.0 pillar_1.4.3 fgsea_1.8.0
[77] igraph_1.2.4.2 reshape2_1.4.3 stats4_3.5.0 pkgload_1.0.2
[81] fastmatch_1.1-0 glue_1.3.1 BiocManager_1.30.10 data.table_1.12.8
[85] remotes_2.1.0 urltools_1.7.3 vctrs_0.2.1 tweenr_1.0.1
[89] testthat_2.3.1 gtable_0.3.0 purrr_0.3.3 polyclip_1.10-0
[93] tidyr_1.0.0 assertthat_0.2.1 ggplot2_3.2.1 ggforce_0.3.1
[97] europepmc_0.3 tidygraph_1.1.2 viridisLite_0.3.0 tibble_2.1.3
[101] rvcheck_0.1.7 AnnotationDbi_1.44.0 memoise_1.1.0 IRanges_2.16.0
[105] ellipsis_0.3.0

brightbio commented 4 years ago

此外，我本地安装也没装好

install.packages("C:/Users/Administrator/Downloads/createKEGGdb-master.zip", repos = NULL, type = "win.binary") library(createKEGGdb-master)

Error in library(createKEGGdb-master) : 不存在叫‘createKEGGdb-master’这个名字的程辑包

library(createKEGGdb)

Error in library(createKEGGdb) : 不存在叫‘createKEGGdb’这个名字的程辑包

install.packages("C:/Users/Administrator/Downloads/biobabble-master.zip", repos = NULL, type = "win.binary") library(biobabble-master)

Error in library(biobabble-master) : 不存在叫‘biobabble-master’这个名字的程辑包

GuangchuangYu commented 4 years ago

setup stdio (system error 2, 系统找不到指定的文件。) @win/processx.c:970

首先你要看看你是不是安装所有包都会有这个问题，看上去好像是这样子的。

如果是，那么你的R本身就有问题。

brightbio commented 4 years ago

Many thanks for your timely reply. Y叔，我将R重装或升级（R3.5 升级到R3.5.1）后，问题依然如故：不能从github安装开发版R包，在线和本地安装均不行。只能从Repository ( CRAN 或 bioconductor) 安装 R pakages.