I can't run ChAMP in R 3.6.3

I change my HD for a SSD, rebooted my PC (x64, i5, 8gb RAM) and installed R 3.6.3, R tools and Rstudio again, such as the packages I use in my project. But now, i can't install ChAMP as usual, by typing:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChAMP")

The console return the

Warning messages:
1: In install.packages(...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘DMRcate’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘shiny’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘FDb.InfiniumMethylation.hg19’ had non-zero exit status

I don't know how to fix this.

r champ

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updated 6.4 years ago by h.mon

• written 6.4 years ago by andrechristianes •

I would start by installing these dependencies manually and then see where the error is. Manual installation should give more precise error messages. Probably a low level dependency / package is missing such as a library or something. Are you on Mac?

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written 6.4 years ago by ATpoint

I installed the first and the last packages via gz archive, manually. But when i tried with DRMcate and shiny, they show this error messages:

INSTALL DRMcate

install.packages("C:/Users/Andre/Downloads/DMRcate_2.0.7 (1).tar.gz", repos = NULL, type = "source") Installing package into ‘C:/Users/Andre/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) * installing source package 'DMRcate' ... * using staged installation * R * inst * byte-compile and prepare package for lazy loading Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'shiny' Calls: <anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execução interrompida ERROR: lazy loading failed for package 'DMRcate' * removing 'C:/Users/Andre/Documents/R/win-library/3.6/DMRcate' Warning in install.packages : installation of package ‘C:/Users/Andre/DOWNLO~1/DMRcate_2.0.7 (1).tar.gz’ had non-zero exit status

INSTALL Shiny

install.packages("C:/Users/Andre/Downloads/DMRcate_2.0.7 (1).tar.gz", repos = NULL, type = "source") Installing package into ‘C:/Users/Andre/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) * installing source package 'DMRcate' ... * using staged installation * R * inst * byte-compile and prepare package for lazy loading Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when loading 'DMRcate' Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'shiny' Calls: <anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Run stopped ERROR: lazy loading failed for package 'DMRcate' * removing 'C:/Users/Andre/Documents/R/win-library/3.6/DMRcate' Warning in install.packages : installation of package ‘C:/Users/Andre/DOWNLO~1/DMRcate_2.0.7 (1).tar.gz’ had non-zero exit status install.packages("C:/Users/Andre/Downloads/shiny_1.4.0.2.tar.gz", repos = NULL, type = "source") Installing package into ‘C:/Users/Andre/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) ERROR: failed to lock directory 'C:/Users/Andre/Documents/R/win-library/3.6' for modifying Try removing 'C:/Users/Andre/Documents/R/win-library/3.6/00LOCK-shiny' Warning in install.packages : installation of package ‘C:/Users/Andre/Downloads/shiny_1.4.0.2.tar.gz’ had non-zero exit status

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written 6.4 years ago by andrechristianes •

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