Hi，

When I change the source file of ChAMP for some reason, I counld not built the ChAMP file again with "Rcmd built ChAMP". The error message is as follows,

C:\Users\Lab\Desktop\R temp\ChAMP_2.16.1.tar>Rcmd build ChAMP
* checking for file 'ChAMP/DESCRIPTION' ... OK
* preparing 'ChAMP':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
Warning: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/Rcmd.exe" INSTALL -l "C:\Users\Lab\AppData\Local\Temp\RtmpIhXtDG\Rinst1121506f78616f" --no-multiarch
      -----------------------------------
ERROR: dependencies 'ChAMPdata', 'FEM', 'DMRcate', 'Illumina450ProbeVariants.db', 'DT', 'prettydoc', 'globaltest', 'sva', 'RPMM', 'DNAcopy', 'impute', 'marray','plotly', 'dendextend' are not available for package 'ChAMP'

* removing 'C:/Users/Lab/AppData/Local/Temp/RtmpIhXtDG/Rinst1121506f78616f/ChAMP'
      -----------------------------------
ERROR: package installation failed

best,

Lei

Install the dependencies

pkgs = c(
    'ChAMPdata', 'FEM', 'DMRcate', 'Illumina450ProbeVariants.db', 'DT', 'prettydoc', 'globaltest',
     'sva', 'RPMM', 'DNAcopy', 'impute', 'marray','plotly', 'dendextend
)
BiocManager::install(pkgs)

If there are still problems, make sure that the interactive R session is using the same R and .libPaths()

.libPaths()
````
as the command line

R -e ".libPaths()"

or install the package from within R

install.packages("path_to/ChAMP", repos = NULL, type = "source") ```