Entering edit mode
dorin_mirel
•
0
@dorin_mirel-11866
Last seen 8.1 years ago
Hi,
I have been trying to install flowClust and failed. I tried the classical approch to installing bioconductor packages:
source("https://bioconductor.org/biocLite.R")
biocLite("flowClust")
I also followed instruction from here: https://www.bioconductor.org/packages/release/bioc/vignettes/flowClust/inst/doc/flowClust.pdf
Instead I get this messages:
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\GuguMic\Documents\R\win-library\3.3" C:\Users\GuguMic\AppData\Local\Temp\RtmpgfBhW8/downloaded_packages/flowClust_3.12.0.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘flowClust’ had non-zero exit status
Can anyone please help?
I still get this error despite following all instructions carefully. The error message displayed is given below;
c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-34~1.2/include" -DNDEBUG -I/src/include -I/i386/include -I"d:/Compiler/gcc-4.9.3/local330/include" -O3 -Wall -std=gnu99 -mtune=core2 -c BoxCox.c -o BoxCox.o
In file included from BoxCox.c:1:0:
flowClust.h:1:26: fatal error: gsl/gsl_math.h: No such file or directory.
I already installed GSL, included it in the path variable using the short format and I have bioconductor version 3.5 as well as R version 3.4.2
You should use BiocLite to install the binary from bioconductor directly instead of building it from source.
I have tried that as well but this is the message I get;
BiocInstaller::biocLite("flowClust")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.2 (2017-09-28).
Installing package(s) ‘flowClust’
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘flowClust’
Do you want to attempt to install these from sources?
y/n: n
installation path not writeable, unable to update packages: mgcv