Closed SalimMegat closed 9 months ago
Hi @SalimMegat,
Rather cryptic message..
Can you share the exact sessionInfo()
output from the R environment?
Also, how are you trying to install the package? Through CRAN or github? You may want to try the complementary method
Also, does your machine have Intel or Apple silicon?
Also please post full command output of the installation
Hi,
Sorry I just saw that a lot of info was missing :) My machine has an intel and I installed it via CRAN and github (same error) see below :
devtools::install_github("immunogenomics/harmony", build_vignettes=TRUE)
ERROR: package installation failed Error: Failed to install 'harmony' from GitHub: ! System command 'R' failed
SessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.6.8
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding
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] stats graphics grDevices utils datasets methods base
other attached packages: [1] devtools_2.4.5 usethis_2.1.6 presto_1.0.0 data.table_1.14.2 sf_1.0-14 Rcpp_1.0.9
loaded via a namespace (and not attached):
[1] pkgload_1.3.0 tidyr_1.3.0 splines_4.2.1 shiny_1.7.2 assertthat_0.2.1 remotes_2.4.2.1 sessioninfo_1.2.2 globals_0.16.1 Rttf2pt1_1.3.12 pillar_1.8.1
[11] backports_1.4.1 lattice_0.20-45 glue_1.6.2.9000 extrafontdb_1.0 digest_0.6.29 promises_1.2.0.1 colorspace_2.0-3 htmltools_0.5.3 httpuv_1.6.6 Matrix_1.6-1.1
[21] plyr_1.8.9 pkgconfig_2.0.3 broom_1.0.4 listenv_0.8.0 purrr_1.0.2 xtable_1.8-4 scales_1.2.1 processx_3.7.0 later_1.3.0 proxy_0.4-27
[31] tibble_3.2.1 generics_0.1.3 ggplot2_3.4.3 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0 lazyeval_0.2.2 cli_3.6.1 survival_3.4-0 magrittr_2.0.3
[41] crayon_1.5.1 mime_0.12 memoise_2.0.1 ps_1.7.1 fs_1.5.2 future_1.33.0 fansi_1.0.3 parallelly_1.36.0 class_7.3-20 pkgbuild_1.3.1
[51] profvis_0.3.7 tools_4.2.1 prettyunits_1.1.1 lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 callr_3.7.2 e1071_1.7-13 compiler_4.2.1 rlang_1.1.1
[61] units_0.8-1 classInt_0.4-8 grid_4.2.1 rstudioapi_0.14 htmlwidgets_1.5.4 igraph_1.5.0.1 miniUI_0.1.1.1 gtable_0.3.1 codetools_0.2-18 DBI_1.1.3
[71] curl_4.3.2 ggforestplot_0.1.0 reshape2_1.4.4 R6_2.5.1 dplyr_1.0.10 fastmap_1.1.0 future.apply_1.9.1 extrafont_0.19 utf8_1.2.2 rprojroot_2.0.3
[81] KernSmooth_2.23-20 stringi_1.7.8 parallel_4.2.1 vctrs_0.6.3 tidyselect_1.2.0 urlchecker_1.0.1
Thanks for the complete output. Still unable to understand the problem. One thing that is not there is BLAS so it may be causing problems.
Do you get the same error when installing from CRAN with install.packages('harmony')
?
Hi,
Yes I do have the same problem when installing with install.packages('harmony').
Here is the error :
install.packages('harmony')
There is a binary version available but the source version is later: binary source needs_compilation harmony 0.1.1 1.0.3 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes installing the source package ‘harmony’
downloaded 5.0 MB
The downloaded source packages are in ‘/private/var/folders/9m/x38vkwtx06d2lyn8b8l0tr0c0000gn/T/RtmpCbahT0/downloaded_packages’
The error message looks unfamiliar. I am not sure how specific this is to harmony or if you are having trouble installing this with other R packages.
Also, OSX Darwin 17 goes all the way back to 2017 according to Wikipedia. Is this system up to date/still supported?
One thing I would recommend trying out is a fresh and recent R environment, perhaps through conda? This comes bundled with new compilers and all the toolchains needed for harmony.
Feel free to re-open if this is still an issue
Hi,
I am trying to install harmony on MacOS Monterey. Getting this error
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-harmony-master/00new/harmony/libs R data moving datasets to lazyload DB byte-compile and prepare package for lazy loading help installing help indices * copying figures building package indices installing vignettes testing if installed package can be loaded from temporary location sh: line 1: 81021 Abort trap: 6 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/9m/x38vkwtx06d2lyn8b8l0tr0c0000gn/T//RtmpxTEPhU/file13c4c1e59e8b' ERROR: loading failed
I can compile other packages (ggrepel, glue, presto) without any issue. Here is my session Info.
setting value version R version 4.2.1 (2022-06-23) os macOS Monterey 12.6.8 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/Paris date 2023-10-13 rstudio 2022.07.2+576 Spotted Wakerobin (desktop) pandoc NA
I have tried many things as reinstalling gfortran but did not solve the issue.