Fail to install watermelon with conda install

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I had a trouble to install biconductor-watermelon due to some incompativle conflicting packages, such as zlib. Specifying another version of package to install did not solve this problem.

Found conflicts! Looking for incompatible packages.

This can take several minutes.  Press CTRL-C to abort.

failed                                                                                                                         

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for:

python=3.9 -> libgcc-ng[version='>=7.3.0']

python=3.9 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0']

Package ncurses conflicts for:

python=3.9 -> ncurses[version='>=6.2,<7.0a0']

python=3.9 -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='>=6.1,<7.0a0']

Package xz conflicts for:

bioconductor-watermelon -> r-base[version='>=3.6,<3.7.0a0'] -> xz[version='5.2.*|>=5.2.4,<6.0a0']

python=3.9 -> xz[version='>=5.2.5,<6.0a0']

But it can be solved by adding channels:

conda config --add channels defaults

conda config --add channels bioconda

conda config --add channels conda-forge

conda config --add channels biobakery

Referred here

Then execute install command:

conda install -c bioconda bioconductor-watermelon

Loading wateRmelon package however showed an error message:

library(wateRmelon)

...

Error: package 'FDb.InfiniumMethylation.hg19' required by 'methylumi' could not be found

Try installation

conda install -c bioconda bioconductor-fdb.infiniummethylation.hg19

and it said 

# All requested packages already installed.

I found a possible solution here.

conda install -c bioconda bioconductor-biocinstaller

Launch R and 

library(BiocInstaller)

biocLite("Homo.sapiens")

Installed package is version <4.0, which does not work R 4.0. Instead

conda install -c bioconda bioconductor-ebimage

But does not work properly

Try this

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install(version = "3.12")

and

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("wateRmelon")

Still shows the same error.

Try this

conda install -c bioconda bioconductor-org.hs.eg.db

conda install -c bioconda bioconductor-txdb.hsapiens.ucsc.hg19.knowngene

But it says these packages are already installed.

Launch R again and

library(org.Hs.eg.db)

library(TxDb.Hsapiens.UCSC.hg19.knownGene)

Got errors.

keep on trying...

library(BiocManager)

BiocManager::install("wateRmelon")

Still got errors.

I got really tired. I use source code (BMIQ_1.1.R).

source("BMIQ_1.1.R")

# prepare dummy data

beta.v=runif(max=1,min=0,n=100000)

design.v=c(rep(1,50000),rep(2,50000))

# run BMIQ

bmiqres=BMIQ(beta.v, design.v, nL = 3, doH = TRUE, nfit = 50000, th1.v = c(0.2, 0.75), th2.v = NULL, niter = 5, tol = 0.001, plots = TRUE, sampleID = 1, pri=TRUE)