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.
Give it a shot: