Question: Issues while downloading supraHex package in Linux
0
gravatar for agneet257
22 months ago by
agneet2570
agneet2570 wrote:

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help

A new version of Bioconductor is available after installing the most recent

  version of R; see http://bioconductor.org/install

> biocLite("supraHex")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).

Installing package(s) ‘supraHex’

also installing the dependencies ‘nlme’, ‘hexbin’, ‘ape’

 

trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-131.tar.gz'

Content type 'application/x-gzip' length 780607 bytes (762 KB)

==================================================

downloaded 762 KB

 

trying URL 'https://cran.rstudio.com/src/contrib/hexbin_1.27.1.tar.gz'

Content type 'application/x-gzip' length 550360 bytes (537 KB)

==================================================

downloaded 537 KB

 

trying URL 'https://cran.rstudio.com/src/contrib/ape_4.1.tar.gz'

Content type 'application/x-gzip' length 771308 bytes (753 KB)

==================================================

downloaded 753 KB

 

trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/supraHex_1.8.0.tar.gz'

Content type 'application/x-gzip' length 6053261 bytes (5.8 MB)

==================================================

downloaded 5.8 MB

 

* installing *source* package ‘nlme’ ...

** package ‘nlme’ successfully unpacked and MD5 sums checked

** libs

gfortran   -fpic  -g -O2 -fstack-protector-strong  -c chol.f -o chol.o

/bin/bash: gfortran: command not found

/usr/lib/R/etc/Makeconf:157: recipe for target 'chol.o' failed

make: *** [chol.o] Error 127

ERROR: compilation failed for package ‘nlme’

* removing ‘/home/agneet42/R/x86_64-pc-linux-gnu-library/3.2/nlme’

* installing *source* package ‘hexbin’ ...

** package ‘hexbin’ successfully unpacked and MD5 sums checked

** libs

gfortran   -fpic  -g -O2 -fstack-protector-strong  -c hbin.f -o hbin.o

/bin/bash: gfortran: command not found

/usr/lib/R/etc/Makeconf:157: recipe for target 'hbin.o' failed

make: *** [hbin.o] Error 127

ERROR: compilation failed for package ‘hexbin’

* removing ‘/home/agneet42/R/x86_64-pc-linux-gnu-library/3.2/hexbin’

ERROR: dependency ‘nlme’ is not available for package ‘ape’

* removing ‘/home/agneet42/R/x86_64-pc-linux-gnu-library/3.2/ape’

ERROR: dependencies ‘hexbin’, ‘ape’ are not available for package ‘supraHex’

* removing ‘/home/agneet42/R/x86_64-pc-linux-gnu-library/3.2/supraHex’

 

The downloaded source packages are in

‘/tmp/RtmpCs4obw/downloaded_packages’

Old packages: 'backports', 'BH', 'boot', 'checkmate', 'crayon', 'curl', 'DBI',

  'devtools', 'doParallel', 'dplyr', 'evaluate', 'foreign', 'Formula', 'gdata',

  'git2r', 'gmm', 'gridExtra', 'HSAUR2', 'htmlwidgets', 'httpuv', 'httr',

  'jsonlite', 'knitr', 'Lahman', 'openssl', 'purrr', 'R6', 'Rcpp', 'rlang',

  'rmarkdown', 'RSQLite', 'rstudioapi', 'Rvmmin', 'sandwich', 'scales',

  'shiny', 'shinyjs', 'tibble', 'tidyr', 'withr', 'igraph', 'lattice', 'Matrix'

Update all/some/none? [a/s/n]: n

Warning messages:

1: In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘nlme’ had non-zero exit status

2: In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘hexbin’ had non-zero exit status

3: In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘ape’ had non-zero exit status

4: In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘supraHex’ had non-zero exit status

hexbin ape nlme suprahex • 315 views
ADD COMMENTlink modified 22 months ago by Martin Morgan ♦♦ 23k • written 22 months ago by agneet2570
Answer: Issues while downloading supraHex package in Linux
0
gravatar for Martin Morgan
22 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

The first error is

/bin/bash: gfortran: command not found

so you'll have to install that on your Linux system.

 

ADD COMMENTlink modified 22 months ago • written 22 months ago by Martin Morgan ♦♦ 23k
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