This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to install preprocessCore package in Rstudio?

Hi everyOne, I am new to RNA-seq data anlaysis. Now I stuck with quantile normalization process. I need to know How can i install preprocessCore package in rstudio? I want to do Quantile normalization.

I tried to install the package externally. I have downloaded the package and I tried to install.But am getting this Error.

collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'preprocessCore.so' failed
make: *** [preprocessCore.so] Error 1
ERROR: compilation failed for package ‘preprocessCore’
* removing ‘/home/bif-workstation/R/x86_64-pc-linux-gnu-library/3.2/preprocessCore’
Warning in install.packages :
  installation of package ‘/home/bif-workstation/Downloads/preprocessCore_1.40.0.tar.gz’ had non-zero exit status
r rna-seq sequence
• 6,545 views • link
updated by shaban.hiba8 • shaban.hiba8 • written by k.kathirvel93 k.kathirvel93

I tried to install the package externally. I have downloaded the package and I tried to install.But am getting this Error.

collect2: error: ld returned 1 exit status

/usr/share/R/share/make/shlib.mk:6: recipe for target 'preprocessCore.so' failed

make: * [preprocessCore.so] Error 1

ERROR: compilation failed for package ‘preprocessCore’

  • removing ‘/home/bif-workstation/R/x86_64-pc-linux-gnu-library/3.2/preprocessCore’ Warning in install.packages :

    installation of package ‘/home/bif-workstation/Downloads/preprocessCore_1.40.0.tar.gz’ had non-zero exit status

• 0 views • link
written by k.kathirvel93 k.kathirvel93

1 answer

Try installing it with bioconductor biocLite

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

biocLite("preprocessCore")

• 0 views • link
written by shaban.hiba8 • shaban.hiba8

Log in to answer this question.

More posts like this
  • gfortran for phyloseq in R
    written by mewgia • mewgia
    Hello! I'm trying to install phyloseq. Ubuntu 18.04. R 4.4.2. And see that: /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status /usr/share/R/share/make/shlib.mk:10: …
  • Leafcutter installation issue
    written by jyotik • jyotik
    I have tried to install leafcutter in my conda environment; everything was fine until I got this error: make: *** [/home/jyoti.k/.conda/envs/leafcutter/lib/R/etc/Makeconf:202: stanExports_bb_glm.o] Error 1 ERROR: …
  • Unable to install "DESeq2"(annobin.so : No such file or directory)
    written by nakane_clan • nakane_clan
    I have R(version 4.1.2) installed on Fedora35. When I tried to install "DESeq2", I got the following warning. > 1: .inet_warning(msg) : installation of package …
  • DESeq2 R package - problem with installation
    written by ja4123 • ja4123
    When I am trying install: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DESeq2") I got error an error: * installing *source* package ‘DESeq2’ ... ** using …
  • Installation error - RNAPLEX
    written by kousi31 • kousi31
    I am trying to install RNAplex software. I downloaded the source code from [here][1] There was no error when I typed `./configure` ` make` /home/d/happy_bin/RNAplex-0.2/lib/alicircfold.inc:80: …
  • Problem in installing mclust package R
    written by Raheleh Raheleh
    Hello, I tried to install mclust package R in RStudio using different ways install.packages("mclust") devtools::install_github("cran/mclust") biocLite('mclust') but I get this error: * installing *source* package …
  • Problems installing devtools in R
    written by sgmiriuka • sgmiriuka
    Hi there, I am having many troubles installing devtools in R (Ubuntu 16-04). No problems in OSX, but not sure why I can't get anywhere …
  • Inability to install R package "sybilSBML"
    written by simone.moro.2 • simone.moro.2
    Hello, I can't install package sybilSBML in R, this is the error message that I get: ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/sybilSBML’ Warning in install.packages …
  • Problem installing cummeRbund in Ubuntu
    written by mfahim • mfahim
    Hi There, I am facing the following error while installing cummeRbund in Ubuntu 15 vivid.. Please help me out.. Thanks :) ``` installing to /home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/GenomicAlignments/libs …
  • Error In Installing Deseq
    written by Medhat Medhat
    <p>Hi,</p> <p>I am trying to install DESeq In Rstudio 0.97.555 on ubuntu 12.04 Using this command; </p> <pre><code>source("http://bioconductor.org/biocLite.R") biocLite("DESeq") </code></pre> <p>But It gives me this …