Nakamarusan
commented
3 weeks ago Hi, nlmixr2 team! Thanks for providing very useful information about nlmixr2 on AWS.
Following the installation instructions, R and RStudio Server were installed without any issues, but I encountered a few problems while installing the tidyverse package, which I would like to share.
Information of EC2 instance
OS Images: Ubuntu AMI (Ubuntu Server 24.04 LTS (HVM), SSD Volume Type). Instance type: t2.large instance
R and RStudio-server version
R:
sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C
[3] LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8
[5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] babelmixr2_0.1.2 nlmixr2_2.1.2 nlmixr2data_2.0.9
[4] rxode2_2.1.3 lubridate_1.9.3 forcats_1.0.0
[7] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[10] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[13] ggplot2_3.5.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 gridExtra_2.3 gld_2.6.6
[4] nlmixr2plot_2.0.9 readxl_1.4.3 rlang_1.1.4
[7] magrittr_2.0.3 e1071_1.7-14 compiler_4.4.0
[10] png_0.1-8 vctrs_0.6.5 PreciseSums_0.6
[13] pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.2.0
[16] backports_1.5.0 labeling_0.4.3 pander_0.6.5
[19] utf8_1.2.4 rmarkdown_2.27 tzdb_0.4.0
[22] xfun_0.44 rxode2et_2.0.13 cachem_1.1.0
[25] rxode2parse_2.0.19 Deriv_4.1.3 cluster_2.1.6
[28] DescTools_0.99.54 R6_2.5.1 stringi_1.8.4
[31] qs_0.26.3 boot_1.3-30 rpart_4.1.23
[34] cellranger_1.1.0 Rcpp_1.0.12 assertthat_0.2.1
[37] knitr_1.47 base64enc_0.1-3 Matrix_1.7-0
[40] nnet_7.3-19 timechange_0.3.0 tidyselect_1.2.1
[43] rstudioapi_0.16.0 dparser_1.3.1-11 stringfish_0.16.0
[46] minpack.lm_1.2-4 lbfgsb3c_2024-3.4 lattice_0.22-5
[49] rxode2ll_2.0.11 withr_3.0.0 evaluate_0.23
[52] foreign_0.8-86 proxy_0.4-27 RcppParallel_5.1.7
[55] nonmem2rx_0.1.4 pillar_1.9.0 checkmate_2.3.1
[58] rex_1.2.1 generics_0.1.3 RCurl_1.98-1.14
[61] hms_1.1.3 munsell_0.5.1 scales_1.3.0
[64] rootSolve_1.8.2.4 RApiSerialize_0.1.3 n1qn1_6.0.1-11
[67] class_7.3-22 glue_1.7.0 nlmixr2est_2.2.2
[70] symengine_0.2.6 lotri_0.4.3 Hmisc_5.1-3
[73] lmom_3.0 lazyeval_0.2.2 tools_4.4.0
[76] sys_3.4.2 data.table_1.15.4 Exact_3.2
[79] mvtnorm_1.2-5 grid_4.4.0 colorspace_2.1-0
[82] nlme_3.1-164 rxode2random_2.1.1 htmlTable_2.4.2
[85] Formula_1.2-5 cli_3.6.2 fansi_1.0.6
[88] expm_0.999-9 binom_1.1-1.1 gtable_0.3.5
[91] digest_0.6.35 farver_2.1.2 htmlwidgets_1.6.4
[94] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4
[97] httr_1.4.7 xgxr_1.1.2 MASS_7.3-60.0.1 RStudio-server: 2022.12.0+353
Installation of some packages
Installation of tidyverse
Running install.packages("tidyverse") resulted in the following error:
ERROR: dependency ‘ragg’ is not available for package ‘tidyverse’
Attempting to install ragg using install.packages("ragg") led to another error:
ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’
Trying to install systemfonts using install.packages("systemfonts") produced the following error:
ERROR: configuration failed for package ‘systemfonts’"
Finally, by running the following additional commands, I was able to install tidyverse without any issues:
sudo apt-get update
sudo apt-get install libfontconfig1-dev
sudo apt-get install libharfbuzz-dev libfribidi-dev
sudo apt-get install libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev pkg-config
mattfidler
nlmixr2, tidyverse and RStudio on AWS | nlmixr2
nlmixr: open source nonlinear mixed-effects modeling for R.
https://blog.nlmixr2.org/blog/2024-03-05-aws/