install error #106
Description
Hi, when i install cellassign with devtools::install_github("Irrationone/cellassign") , i encountered this error. I tried to install beachmat and it is ok. I don't know how to fix it. Can u give me some guidance?
Installing 2 packages: scuttle, scran
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/scuttle_1.0.4.tar.gz'
Content type 'application/octet-stream' length 387528 bytes (378 KB)
==================================================
downloaded 378 KB
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/scran_1.18.7.tar.gz'
Content type 'application/octet-stream' length 1818902 bytes (1.7 MB)
downloaded 1.7 MB
- installing source package 'scuttle' ...
** using staged installation
** libs
x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/public/home/lixinjie/.conda/envs/R_env/lib/R/include" -DNDEBUG -I../inst/include/ -I'/public/home/lixinjie/.conda/envs/R_env/lib/R/library/Rcpp/include' -I'/public/home/lixinjie/.conda/envs/R_env/lib/R/library/beachmat/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /public/home/lixinjie/.conda/envs/R_env/include -I/public/home/lixinjie/.conda/envs/R_env/include -Wl,-rpath-link,/public/home/lixinjie/.conda/envs/R_env/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /public/home/lixinjie/.conda/envs/R_env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/public/home/lixinjie/.conda/envs/R_env=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o
x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/public/home/lixinjie/.conda/envs/R_env/lib/R/include" -DNDEBUG -I../inst/include/ -I'/public/home/lixinjie/.conda/envs/R_env/lib/R/library/Rcpp/include' -I'/public/home/lixinjie/.conda/envs/R_env/lib/R/library/beachmat/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /public/home/lixinjie/.conda/envs/R_env/include -I/public/home/lixinjie/.conda/envs/R_env/include -Wl,-rpath-link,/public/home/lixinjie/.conda/envs/R_env/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /public/home/lixinjie/.conda/envs/R_env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1595316670215/work=/usr/local/src/conda/r-base-4.0.2 -fdebug-prefix-map=/public/home/lixinjie/.conda/envs/R_env=/usr/local/src/conda-prefix -c cumulative_prop.cpp -o cumulative_prop.o
cumulative_prop.cpp:2:10: fatal error: beachmat3/beachmat.h: No such file or directory
#include "beachmat3/beachmat.h"
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/public/home/lixinjie/.conda/envs/R_env/lib/R/etc/Makeconf:175: cumulative_prop.o] Error 1
ERROR: compilation failed for package 'scuttle' - removing '/public/home/lixinjie/.conda/envs/R_env/lib/R/library/scuttle'
ERROR: dependency 'scuttle' is not available for package 'scran' - removing '/public/home/lixinjie/.conda/envs/R_env/lib/R/library/scran'
The downloaded source packages are in
'/tmp/RtmpVkBvcY/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
v checking for file '/tmp/RtmpVkBvcY/remotes75fa4c039188/Irrationone-cellassign-be66325/DESCRIPTION' (1.5s)
- preparing 'cellassign':
v checking DESCRIPTION meta-information ... - checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'cellassign_0.99.21.tar.gz'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
'cellassign/docs/articles/constructing-markers-from-purified-data_files/figure-html/unnamed-chunk-17-1.png'
ERROR: dependency 'scran' is not available for package 'cellassign'
- removing '/public/home/lixinjie/.conda/envs/R_env/lib/R/library/cellassign'
Warning messages:
1: In i.p(...) :
installation of package 'scuttle' had non-zero exit status
2: In i.p(...) : installation of package 'scran' had non-zero exit status
3: In i.p(...) :
installation of package '/tmp/RtmpVkBvcY/file75fa198a640e/cellassign_0.99.21.tar.gz' had non-zero exit status
My sessionInfo:
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /public/home/lixinjie/.conda/envs/R_env/lib/libopenblasp-r0.3.10.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] ps_1.3.4 prettyunits_1.1.1 rprojroot_2.0.3 assertthat_0.2.1
[5] crayon_1.3.4 withr_2.5.0 R6_2.4.1 magrittr_2.0.1
[9] rlang_1.1.0 cachem_1.0.6 cli_3.6.1 curl_4.3
[13] fs_1.5.0 remotes_2.4.2.1 testthat_2.3.2 callr_3.4.4
[17] ellipsis_0.3.1 devtools_2.3.2 desc_1.2.0 tools_4.0.2
[21] glue_1.4.2 pkgload_1.1.0 fastmap_1.1.0 compiler_4.0.2
[25] processx_3.7.0 pkgbuild_1.1.0 sessioninfo_1.1.1 memoise_2.0.1
[29] usethis_1.6.3
library(Seurat)
Attaching SeuratObject
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /public/home/lixinjie/.conda/envs/R_env/lib/libopenblasp-r0.3.10.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeuratObject_4.1.4 Seurat_4.0.5
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_1.4-1 deldir_1.0-6
[4] ellipsis_0.3.1 ggridges_0.5.2 rprojroot_2.0.3
[7] fs_1.5.0 spatstat.data_3.0-1 leiden_0.3.6
[10] listenv_0.8.0 remotes_2.4.2.1 ggrepel_0.8.2
[13] fansi_1.0.6 codetools_0.2-16 splines_4.0.2
[16] cachem_1.0.6 polyclip_1.10-0 pkgload_1.1.0
[19] jsonlite_1.7.1 ica_1.0-2 cluster_2.1.0
[22] png_0.1-7 uwot_0.1.10 shiny_1.5.0
[25] sctransform_0.4.1 spatstat.sparse_3.0-1 compiler_4.0.2
[28] httr_1.4.2 assertthat_0.2.1 Matrix_1.6-4
[31] fastmap_1.1.0 lazyeval_0.2.2 cli_3.6.1
[34] later_1.1.0.1 htmltools_0.5.5 prettyunits_1.1.1
[37] tools_4.0.2 igraph_1.2.5 gtable_0.3.0
[40] glue_1.4.2 RANN_2.6.1 reshape2_1.4.4
[43] dplyr_1.0.2 Rcpp_1.0.12 scattermore_1.2
[46] vctrs_0.6.1 nlme_3.1-149 progressr_0.9.0
[49] lmtest_0.9-38 stringr_1.4.0 globals_0.14.0
[52] ps_1.3.4 testthat_2.3.2 mime_0.9
[55] miniUI_0.1.1.1 lifecycle_1.0.3 irlba_2.3.3
[58] devtools_2.3.2 goftest_1.2-2 future_1.21.0
[61] MASS_7.3-53 zoo_1.8-8 scales_1.2.1
[64] spatstat.core_2.3-1 promises_1.1.1 spatstat.utils_3.0-2
[67] parallel_4.0.2 RColorBrewer_1.1-2 curl_4.3
[70] memoise_2.0.1 reticulate_1.35.0 pbapply_1.4-3
[73] gridExtra_2.3 ggplot2_3.4.1 rpart_4.1-15
[76] stringi_1.5.3 desc_1.2.0 pkgbuild_1.1.0
[79] rlang_1.1.0 pkgconfig_2.0.3 matrixStats_1.2.0
[82] lattice_0.20-41 tensor_1.5 ROCR_1.0-11
[85] purrr_0.3.4 patchwork_1.1.1 htmlwidgets_1.5.1
[88] cowplot_1.1.0 processx_3.7.0 tidyselect_1.1.0
[91] parallelly_1.22.0 RcppAnnoy_0.0.22 plyr_1.8.6
[94] magrittr_2.0.1 R6_2.4.1 generics_0.1.3
[97] mgcv_1.8-33 pillar_1.9.0 withr_2.5.0
[100] fitdistrplus_1.1-3 abind_1.4-5 survival_3.2-3
[103] sp_2.1-2 tibble_3.2.1 future.apply_1.6.0
[106] crayon_1.3.4 KernSmooth_2.23-17 utf8_1.1.4
[109] spatstat.geom_3.1-0 plotly_4.9.2.1 usethis_1.6.3
[112] grid_4.0.2 data.table_1.13.0 callr_3.4.4
[115] digest_0.6.25 xtable_1.8-4 tidyr_1.1.2
[118] httpuv_1.5.4 munsell_0.5.0 viridisLite_0.3.0