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Question: Problems with installing flowClust
0
gravatar for dorin_mirel
19 months ago by
dorin_mirel0 wrote:

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?

ADD COMMENTlink modified 8 months ago by Jiang, Mike1.1k • written 19 months ago by dorin_mirel0

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 

ADD REPLYlink written 8 months ago by oluwafemi.olusoji0

You should use BiocLite to install the binary from bioconductor directly instead of building it from source.

ADD REPLYlink written 8 months ago by Jiang, Mike1.1k

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

ADD REPLYlink written 8 months ago by oluwafemi.olusoji0
0
gravatar for Jiang, Mike
19 months ago by
Jiang, Mike1.1k
(Private Address)
Jiang, Mike1.1k wrote:

The package failed the unit test due to a platform-dependent issue (i.e. windows specific). I've pushed the fix to flowClust 3.12.1 and hopefully the binary will be built tomorrow.

ADD COMMENTlink written 19 months ago by Jiang, Mike1.1k
0
gravatar for Jiang, Mike
8 months ago by
Jiang, Mike1.1k
(Private Address)
Jiang, Mike1.1k wrote:

Bioc has some issue with windows build on release branch. You can install the devel version instead

http://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/flowClust_3.15.0.zip

ADD COMMENTlink written 8 months ago by Jiang, Mike1.1k

Thank you very much

ADD REPLYlink written 8 months ago by oluwafemi.olusoji0
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