Question: DESeq2 dependency issues
0
gravatar for Alexistbrown17
23 months ago by
Alexistbrown170 wrote:

Hi I have been working on trying to figure out this R package (DESq2) dependency issue for the past week now and have had little luck it getting everything to work so I can move forward with my analysis. Here is the code below that I have been trying to get working but haven't been successful in remediating the issue to get all packages downloaded to my library path. 

> source("http://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("DESeq2")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.1 (2015-06-18).
Installing package(s) ‘DESeq2’
also installing the dependency ‘genefilter’


  There are binary versions available but the source versions are later:
           binary source needs_compilation
genefilter 1.52.0 1.52.1             FALSE
DESeq2     1.10.0 1.10.1             FALSE

installing the source packages ‘genefilter’, ‘DESeq2’

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 1260k  100 1260k    0     0  4005k      0 --:--:-- --:--:-- --:--:-- 4014k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  6 1226k    6 78648    0     0  1407k      0 --:--:-- --:--:-- --:--:-- 1396k100 1226k  100 1226k    0     0  3629k      0 --:--:-- --:--:-- --:--:-- 3628k
* installing *source* package ‘genefilter’ ...
** libs
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c half_range_mode.cpp -o half_range_mode.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c init.c -o init.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c nd.c -o nd.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c pAUC.c -o pAUC.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c rowPAUCs.c -o rowPAUCs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c rowttests.c -o rowttests.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2  -c ttest.f -o ttest.o
make: gfortran-4.2: No such file or directory
make: *** [ttest.o] Error 1
ERROR: compilation failed for package ‘genefilter’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/genefilter’
ERROR: dependency ‘genefilter’ is not available for package ‘DESeq2’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/DESeq2’

The downloaded source packages are in
    ‘/private/var/folders/j9/f7t6cyg559vcpyc2rr4vmdv00000gn/T/RtmpSY8EwB/downloaded_packages’
Old packages: 'acepack', 'cluster', 'Hmisc', 'Matrix', 'mgcv', 'nlme',
  'RcppArmadillo', 'tibble'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
                   binary      source needs_compilation
acepack           1.3-3.3       1.4.1              TRUE
cluster             2.0.4       2.0.6              TRUE
Hmisc              3.17-4       4.0-2              TRUE
Matrix              1.2-6       1.2-8              TRUE
mgcv               1.8-13      1.8-17              TRUE
nlme              3.1-128     3.1-131              TRUE
RcppArmadillo 0.5.500.2.0 0.7.700.0.0              TRUE
tibble                1.1       1.3.0              TRUE

Do you want to install from sources the packages which need compilation?
y/n: n
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 78998  100 78998    0     0   345k      0 --:--:-- --:--:-- --:--:--  347k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100  484k  100  484k    0     0  1031k      0 --:--:-- --:--:-- --:--:-- 1033k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 1598k  100 1598k    0     0  2947k      0 --:--:-- --:--:-- --:--:-- 2944k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0 64 3457k   64 2240k    0     0  3882k      0 --:--:-- --:--:-- --:--:-- 3883k100 3457k  100 3457k    0     0  4497k      0 --:--:-- --:--:-- --:--:-- 4496k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 2100k  100 2100k    0     0  3696k      0 --:--:-- --:--:-- --:--:-- 3704k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 2090k  100 2090k    0     0  2267k      0 --:--:-- --:--:-- --:--:-- 2266k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0 39 1112k   39  435k    0     0  1649k      0 --:--:-- --:--:-- --:--:-- 1645k100 1112k  100 1112k    0     0  3003k      0 --:--:-- --:--:-- --:--:-- 2999k
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100  165k  100  165k    0     0   505k      0 --:--:-- --:--:-- --:--:--  505k

The downloaded binary packages are in
    /var/folders/j9/f7t6cyg559vcpyc2rr4vmdv00000gn/T//RtmpSY8EwB/downloaded_packages
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

A ran the above code and then based on the output saw that gfortran may be the reason that the DESeq2 and genefilter packages are not installing. I googled how to install gfortran, downloaded the file from this site and save to the root directory(http://r.research.att.com/libs/) and ran this code in terminal:

alexis-browns-macbook-pro:~ alexisbrown$ curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

100 14.7M  100 14.7M    0     0  1102k      0  0:00:13  0:00:13 --:--:-- 1155k

alexis-browns-macbook-pro:~ alexisbrown$ sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /

Password:

tar: Error opening archive: Failed to open 'gmp-4.2.4-darwin8-bin4.tar.gz'

Please help I have been dealing with this DESeq2 dependency issue in order to use this package (and its dependencies) within QIIME to normalize my sequencing data. 

 

 

 

 

 

R • 670 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by Alexistbrown170
Answer: DESeq2 dependency issues
0
gravatar for Steve Lianoglou
23 months ago by
Denali
Steve Lianoglou12k wrote:

I'd first update the version of R (and therefore Bioconductor) you are using ... you are trying to install a two year old version right now

As for your error, it looks like you might simply giving a bad path to your downloaded *tar.gz file?

ADD COMMENTlink written 23 months ago by Steve Lianoglou12k
Answer: DESeq2 dependency issues
0
gravatar for Alexistbrown17
23 months ago by
Alexistbrown170 wrote:

 

Hi Steve,

I initially had the most current version of R however I got the output message that DESeq2 was not available for the R version 3.3.3. Maybe it was something else that I was doing wrong at the time of the attempted install however. I will try the updating of my R package and will repost here if there are issues.

I do have a quick question when you are downloading packages and for example type "DEseq2" rather than "DESeq2" will that cause R to throw the error message that the package is not available?

 

ADD COMMENTlink written 23 months ago by Alexistbrown170

Give it a shot:

R> library(BiocInstaller)
R> biocLite("DEseq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s) 'DEseq2'
Warning messages:
1: package 'DEseq2' is not available (for R version 3.3.3)
2: Perhaps you meant 'DESeq2' ?
ADD REPLYlink written 23 months ago by Steve Lianoglou12k
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