avallonking / lrtq Goto Github PK

Hi there,

I am trying to install the LRTq package but get the following error:

install_github("avallonking/LRTq")
Loading required package: usethis
Downloading GitHub repo avallonking/LRTq@HEAD
✔ checking for file ‘/tmp/RtmpRcTxrm/remotesb4e522376a4/avallonking-LRTq-d9f8424/DESCRIPTION’ (415ms)
─ preparing ‘LRTq’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘LRTq_1.0.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘LRTq/analysis_scripts/gtex/association_tests/faster.gtex_power_test.modified.fixed.more_perm.speed_up.other_tissues.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘LRTq/analysis_scripts/gtex/association_tests/faster.gtex_power_test.modified.fixed.more_perm.speed_up.other_tissues.maf01.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘LRTq/analysis_scripts/gtex/association_tests/faster.gtex_power_test.modified.fixed.more_perm.speed_up.other_tissues.regress_out_common_eqtls.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘LRTq/analysis_scripts/gtex/statistical_analysis/all_tissues.egene.outliers.log2.standardized.corrected_tpm.only.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘LRTq/analysis_scripts/gtex/statistical_analysis/all_tissues.non_egene.outliers.log2.standardized.corrected_tpm.only.R’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘LRTq/analysis_scripts/gtex/statistical_analysis/all_tissues.tissue_sharing.prop.num_shared_egenes.all.cv.rv.egenes.R’

• installing source package ‘LRTq’ ...
  ** using staged installation
  ** libs
  x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/lib/R/include" -DNDEBUG -I'/share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/include -I/share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/include -Wl,-rpath-link,/share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/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 /share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1639563404388/work=/usr/local/src/conda/r-base-4.1.2 -fdebug-prefix-map=/share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook=/usr/local/src/conda-prefix -c LRTq.cpp -o LRTq.o
  LRTq.cpp: In function 'double LRTq(Rcpp::NumericVector, Rcpp::IntegerMatrix, Rcpp::NumericVector, int)':
  LRTq.cpp:55:50: error: 'PI' was not declared in this scope
  55 | ln_a = log(1 - causal_ratio) - N / 2 * log(2 * PI * sigma) - N / 2;
  | ^~
  make: *** [/share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/lib/R/etc/Makeconf:177: LRTq.o] Error 1
  ERROR: compilation failed for package ‘LRTq’
• removing ‘/share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/lib/R/library/LRTq’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpRcTxrm/fileb4e5183bf283/LRTq_1.0.tar.gz’ had non-zero exit status

see my sessionInfo() output below:

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/r_notebook/lib/libopenblasp-r0.3.17.so

locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] devtools_2.4.3 usethis_2.1.5

loaded via a namespace (and not attached):
[1] magrittr_2.0.2 pkgload_1.2.4 R6_2.5.1 rlang_1.0.2
[5] fastmap_1.1.0 tools_4.1.2 pkgbuild_1.3.1 sessioninfo_1.2.2
[9] cli_3.2.0 withr_2.5.0 ellipsis_0.3.2 remotes_2.4.2
[13] rprojroot_2.0.2 lifecycle_1.0.1 crayon_1.5.0 brio_1.1.3
[17] processx_3.5.2 purrr_0.3.4 callr_3.7.0 fs_1.5.2
[21] ps_1.6.0 curl_4.3.2 testthat_3.1.2 memoise_2.0.1
[25] glue_1.6.2 cachem_1.0.6 compiler_4.1.2 desc_1.4.0
[29] prettyunits_1.1.1

Could you help me figure out what to do to get this to install properly?

Thanks so much!

Hi,
I am installing LRTq as described on the LINUX server, but I always get error in invalid ELF header of LRTq.so. detailed below:

library(devtools)
install_github("avallonking/LRTq")
Downloading GitHub repo avallonking/LRTq@master
from URL https://api.github.com/repos/avallonking/LRTq/zipball/master
Installing LRTq
'/DATA1/user/software/conda/lib/R/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/tmp/RtmpoYmlSa/devtools822f4add2c73/avallonking-LRTq-d9f8424'
--library='/DATA1/user/software/conda/lib/R/library' --install-tests

• installing source package ‘LRTq’ ...
  ** libs
  make: Nothing to be done for 'all'.
  installing to /DATA1/user/software/conda/lib/R/library/LRTq/libs
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  Error: package or namespace load failed for ‘LRTq’ in dyn.load(file, DLLpath = DLLpath, ...):
  unable to load shared object '/DATA1/user/software/conda/lib/R/library/LRTq/libs/LRTq.so':
  /DATA1/user/software/conda/lib/R/library/LRTq/libs/LRTq.so: invalid ELF header
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing ‘/DATA1/user/software/conda/lib/R/library/LRTq’
  Installation failed: Command failed (1)

the R on my LINUX server is in version 3.5.1.
Do you have any idea what I need to do to get it installed ?