Question

R 3.2.0 problem with DESeq2 - Hmisc error

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rclaire ▴ 20

@rclaire-7689

Last seen 7.8 years ago

United States

Hi All,

I was having compatibility issues with R and bioconductor, so I upgraded to the latest version of R (3.2.0) and am still having trouble. I am trying to install and use DESeq2. Please see the below output and errors. Any help would be greatly appreciated!

Thanks, Claire

R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

#error upon installing DESeq2

> biocLite('DESeq2')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.1), R version 3.2.0.
Installing package(s) ‘DESeq2’
also installing the dependency ‘Hmisc’

There is a binary version available but the source version is later:
binary source needs_compilation
Hmisc 3.15-0 3.16-0 TRUE

Do you want to install from sources the package which needs compilation?
y/n:

y
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/DESeq2_1.8.0.tgz'
Content type 'application/x-gzip' length 1422008 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

The downloaded binary packages are in
/var/folders/9c/y4x9cqdn5_1c_1mbbldfkr640000gn/T//Rtmpn7NXej/downloaded_packages
installing the source package ‘Hmisc’

trying URL 'http://cran.rstudio.com/src/contrib/Hmisc_3.16-0.tar.gz'
Content type 'application/x-gzip' length 629536 bytes (614 KB)
==================================================
downloaded 614 KB

* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Hmisc.c -o Hmisc.o
gfortran-4.8 -fPIC -g -O2 -c cidxcn.f -o cidxcn.o
make: gfortran-4.8: No such file or directory
make: *** [cidxcn.o] Error 1
ERROR: compilation failed for package ‘Hmisc’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Hmisc’

The downloaded source packages are in
‘/private/var/folders/9c/y4x9cqdn5_1c_1mbbldfkr640000gn/T/Rtmpn7NXej/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘Hmisc’ had non-zero exit status

#error in running DESeq2

> dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design= ~trmt)
Error: could not find function "DESeqDataSetFromMatrix"

deseq2 r software error • 7.0k views

ADD COMMENT • link updated 9.7 years ago by Steve Lianoglou ★ 13k • written 9.7 years ago by rclaire ▴ 20

score 2 · Answer 1 · 2015-05-01

I just followed the instructions from this website to install a "an even more correct" gfortran installer for Mavericks (I can't tell if that's what you're running?). The (slightly corrected) instructions from that article are pasted below for persistence/posterity:

Go to the optional libraries, frameworks and applications for Mac OS X on r.research.att.comand download gfortran-4.8.2-darwin13.tar.bz2. Extract the package in /, which is root. The files should be unpacked into /usr/local/

Alternatively, open terminal and type:

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

score 0 · Answer 2 · 2015-05-01

The simplest solution is to reply "n" when you are prompted whether you want to install Hmisc from source. The more complicated solution is to install gfortran on your system (presumably a Mac) which I can't help you with, but google should be able to. HTH, Peter On Fri, May 1, 2015 at 4:13 PM, rclaire [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User rclaire wrote Question: R 3.2.0 problem with DESeq2 - Hmisc error: > > Hi All, > > I was having compatibility issues with R and bioconductor, so I upgraded to > the latest version of R (3.2.0) and am still having trouble. I am trying to > install and use DESeq2. Please see the below output and errors. Any help > would be greatly appreciated! > > Thanks, Claire > > > > R version 3.2.0 (2015-04-16) -- "Full of Ingredients" > Copyright (C) 2015 The R Foundation for Statistical Computing > Platform: x86_64-apple-darwin13.4.0 (64-bit) > > #error upon installing DESeq2 > >> biocLite('DESeq2') > BioC_mirror: http://bioconductor.org > Using Bioconductor version 3.1 (BiocInstaller 1.18.1), R version 3.2.0. > Installing package(s) ‘DESeq2’ > also installing the dependency ‘Hmisc’ > > > There is a binary version available but the source version is later: > binary source needs_compilation > Hmisc 3.15-0 3.16-0 TRUE > > Do you want to install from sources the package which needs compilation? > y/n: > > y > trying URL > 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/DESeq2_1.8.0.tgz' > Content type 'application/x-gzip' length 1422008 bytes (1.4 MB) > ================================================== > downloaded 1.4 MB > > > The downloaded binary packages are in > > /var/folders/9c/y4x9cqdn5_1c_1mbbldfkr640000gn/T//Rtmpn7NXej/downloaded_packages > installing the source package ‘Hmisc’ > > trying URL 'http://cran.rstudio.com/src/contrib/Hmisc_3.16-0.tar.gz' > Content type 'application/x-gzip' length 629536 bytes (614 KB) > ================================================== > downloaded 614 KB > > * installing *source* package ‘Hmisc’ ... > ** package ‘Hmisc’ successfully unpacked and MD5 sums checked > ** libs > clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include > -fPIC -Wall -mtune=core2 -g -O2 -c Hmisc.c -o Hmisc.o > gfortran-4.8 -fPIC -g -O2 -c cidxcn.f -o cidxcn.o > make: gfortran-4.8: No such file or directory > make: *** [cidxcn.o] Error 1 > ERROR: compilation failed for package ‘Hmisc’ > * removing > ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Hmisc’ > > The downloaded source packages are in > > ‘/private/var/folders/9c/y4x9cqdn5_1c_1mbbldfkr640000gn/T/Rtmpn7NXej/downloaded_packages’ > Warning message: > In install.packages(pkgs = doing, lib = lib, ...) : > installation of package ‘Hmisc’ had non-zero exit status > > > > > > #error in running DESeq2 > >> dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, >> design= ~trmt) > Error: could not find function "DESeqDataSetFromMatrix" > > ________________________________ > > You may reply via email or visit R 3.2.0 problem with DESeq2 - Hmisc error