Milky way, seen at Kuchinoshima Island, Kagoshima.
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)