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GuipengLi avatar GuipengLi commented on August 21, 2024

I tested it with R 3.6.3 and it works in my case. Are there more than one version of R installed ?

~$ R

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

install.packages("VGAM")
Installing package into ‘/home/lee/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/VGAM_1.1-5.tar.gz'
Content type 'application/octet-stream' length 1580498 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

  • installing source package ‘VGAM’ ...
    ** package ‘VGAM’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c VGAM_init.c -o VGAM_init.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c caqo3.c -o caqo3.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c ei.f -o ei.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c fgam.f -o fgam.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gautr.c -o gautr.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lerchphi.c -o lerchphi.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c lms.f -o lms.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c muxr3.c -o muxr3.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c rgam.f -o rgam.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgam3.c -o rgam3.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c specfun3.c -o specfun3.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c tyeepolygamma.f -o tyeepolygamma.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tyeepolygamma3.c -o tyeepolygamma3.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c vdigami.f -o vdigami.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c veigen.f -o veigen.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c vgam.f -o vgam.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vgam3.c -o vgam3.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c vlinpack1.f -o vlinpack1.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c vlinpack2.f -o vlinpack2.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c vlinpack3.f -o vlinpack3.o
    gfortran -fpic -g -O2 -fstack-protector-strong -c vmux.f -o vmux.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vmux3.c -o vmux3.o
    gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zeta3.c -o zeta3.o
    gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o VGAM.so VGAM_init.o caqo3.o ei.o fgam.o gautr.o lerchphi.o lms.o muxr3.o rgam.o rgam3.o specfun3.o tyeepolygamma.o tyeepolygamma3.o vdigami.o veigen.o vgam.o vgam3.o vlinpack1.o vlinpack2.o vlinpack3.o vmux.o vmux3.o zeta3.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
    installing to /home/lee/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-VGAM/00new/VGAM/libs
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** demo
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** checking absolute paths in shared objects and dynamic libraries
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (VGAM)

The downloaded source packages are in
‘/tmp/RtmphzDuKs/downloaded_packages’

library(VGAM)
Loading required package: stats4
Loading required package: splines

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bioinfo89 avatar bioinfo89 commented on August 21, 2024

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GuipengLi avatar GuipengLi commented on August 21, 2024

Please check which Rscript you are using.

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bioinfo89 avatar bioinfo89 commented on August 21, 2024

I checked it is 3.6.3. I am not sure the tool is still not able to find the module.

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