can not install iDEA

[tishida-github]

Hello, Thank you for developing the nice tool. I am interested in using this and trying to install following the instructions. But I am having the error in installing iDEA. I got below errors.

library(devtools) devtools::install_github('xzhoulab/iDEA') Downloading GitHub repo xzhoulab/iDEA@HEAD Error: Failed to install 'iDEA' from GitHub: Could not find tools necessary to compile a package Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem. pkgbuild::check_build_tools(debug = TRUE) Error: Could not find tools necessary to compile a package Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

I would appreciate if you could give me an advice. Thank you in advance.

session info R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.16

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] splines stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] scales_1.1.1 sf_0.9-6 leidenbase_0.1.2 ggpubr_0.4.0
[5] ggsci_2.9 mygene_1.22.0 GenomicFeatures_1.38.2 AnnotationDbi_1.48.0
[9] garnett_0.2.16 ggplot2_3.3.2.9000 magrittr_1.5 dplyr_1.0.2
[13] pheatmap_1.0.12 reticulate_1.18 tibble_3.0.4 stringr_1.4.0
[17] Seurat_3.2.2 viridis_0.5.1 viridisLite_0.3.0 VGAM_1.1-4
[21] doSNOW_1.0.19 snow_0.4-3 doParallel_1.0.16 iterators_1.0.13
[25] foreach_1.5.1 RcppArmadillo_0.10.1.2.0 Rcpp_1.0.5 pkgconfig_2.0.3
[29] devtools_2.3.2 usethis_1.6.3 pkgbuild_1.2.0 monocle3_0.2.3.0
[33] SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.1 DelayedArray_0.12.3 BiocParallel_1.20.1
[37] matrixStats_0.57.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 IRanges_2.20.2
[41] S4Vectors_0.24.4 Biobase_2.46.0 BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] proto_1.0.0 tidyselect_1.1.0 RSQLite_2.2.1 htmlwidgets_1.5.2 grid_3.6.3
[6] Rtsne_0.15 munsell_0.5.0 units_0.6-7 codetools_0.2-18 ica_1.0-2
[11] chron_2.3-56 future_1.20.1 miniUI_0.1.1.1 withr_2.3.0 colorspace_1.4-1
[16] knitr_1.30 rstudioapi_0.11 ROCR_1.0-11 ggsignif_0.6.0 tensor_1.5
[21] listenv_0.8.0 GenomeInfoDbData_1.2.2 polyclip_1.10-0 bit64_4.0.5 rprojroot_1.3-2
[26] parallelly_1.21.0 vctrs_0.3.4 generics_0.1.0 xfun_0.19 BiocFileCache_1.10.2
[31] R6_2.5.0 rsvd_1.0.3 bitops_1.0-6 spatstat.utils_1.17-0 assertthat_0.2.1
[36] promises_1.1.1 nnet_7.3-14 gtable_0.3.0 globals_0.13.1 processx_3.4.4
[41] goftest_1.2-2 rlang_0.4.8 rstatix_0.6.0 rtracklayer_1.46.0 lazyeval_0.2.2
[46] broom_0.7.2 checkmate_2.0.0 reshape2_1.4.4 abind_1.4-5 backports_1.2.0
[51] httpuv_1.5.4 Hmisc_4.4-1 tools_3.6.3 ellipsis_0.3.1 RColorBrewer_1.1-2
[56] sessioninfo_1.1.1 ggridges_0.5.2 gsubfn_0.7 plyr_1.8.6 base64enc_0.1-3
[61] progress_1.2.2 zlibbioc_1.32.0 classInt_0.4-3 purrr_0.3.4 RCurl_1.98-1.2
[66] ps_1.4.0 prettyunits_1.1.1 sqldf_0.4-11 rpart_4.1-15 openssl_1.4.3
[71] deldir_0.2-3 pbapply_1.4-3 cowplot_1.1.0 zoo_1.8-8 haven_2.3.1
[76] ggrepel_0.8.2 cluster_2.1.0 fs_1.5.0 data.table_1.13.2 openxlsx_4.2.3
[81] lmtest_0.9-38 RANN_2.6.1 fitdistrplus_1.1-1 pkgload_1.1.0 hms_0.5.3
[86] patchwork_1.1.0 mime_0.9 xtable_1.8-4 XML_3.99-0.3 rio_0.5.16
[91] jpeg_0.1-8.1 readxl_1.3.1 gridExtra_2.3 testthat_3.0.0 compiler_3.6.3
[96] biomaRt_2.42.1 KernSmooth_2.23-18 crayon_1.3.4 htmltools_0.5.0 mgcv_1.8-33
[101] later_1.1.0.1 Formula_1.2-4 tidyr_1.1.2 DBI_1.1.0 dbplyr_2.0.0
[106] MASS_7.3-53 rappdirs_0.3.1 car_3.0-10 Matrix_1.2-18 cli_2.1.0
[111] igraph_1.2.6 forcats_0.5.0 GenomicAlignments_1.22.1 foreign_0.8-75 plotly_4.9.2.1
[116] XVector_0.26.0 callr_3.5.1 digest_0.6.27 sctransform_0.3.1 RcppAnnoy_0.0.16
[121] spatstat.data_1.4-3 Biostrings_2.54.0 cellranger_1.1.0 leiden_0.3.5 htmlTable_2.1.0
[126] uwot_0.1.8 curl_4.3 shiny_1.5.0 Rsamtools_2.2.3 lifecycle_0.2.0
[131] nlme_3.1-150 jsonlite_1.7.1 carData_3.0-4 desc_1.2.0 askpass_1.1
[136] fansi_0.4.1 pillar_1.4.6 lattice_0.20-41 fastmap_1.0.1 httr_1.4.2
[141] survival_3.2-7 glue_1.4.2 remotes_2.2.0 zip_2.1.1 spatstat_1.64-1
[146] png_0.1-7 bit_4.0.4 class_7.3-17 stringi_1.5.3 blob_1.2.1
[151] latticeExtra_0.6-29 memoise_1.1.0 e1071_1.7-4 irlba_2.3.3 future.apply_1.6.0

[YingMa0107]

Hi @tishida-github, Thank you for providing the details. This is probably an issue with the available compilers. Could you please type pkgbuild::check_build_tools(debug = TRUE) in the R to see if there are some errors? Also, could you please check if you have a compiler like gcc installed? You can type gcc --version in the terminal to check it. If there is no gcc compiler installed, please install it.

[tishida-github]

Hello YingMa1993,

Thank you for your reply. Here is what I did based on your comments. I appreciate it.

pkgbuild::check_build_tools(debug = TRUE) Error: Could not find tools necessary to compile a package Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

gcc --version gcc (Homebrew GCC 10.2.0_2) 10.2.0 Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[YingMa0107]

Hi @tishida-github,

Sorry about the late reply. Have you tried to re-install the devtools? Or here is a link which might be helpful to solve the issue.

[tishida-github]

Hi YingMa0107, No worries. I have now installed iDEA somehow. Thank you for your comment!