"/home/wubin/05.tests/DECoN"
Error in if (result$source == "unknown" && fallback.ok) { :
missing value where TRUE/FALSE needed
Calls: ... getPackageRecords -> getPackageRecordsExternalSource -> lapply -> FUN
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
my command is as follows:
export PATH='/home/wubin/01.Program/02.software/R-3.1.2/bin':$PATH
export R_LIBS_USER='/mnt/lustre/user/wubin/01.Program/Scripts/02.software/DECoN/Linux/packrat/lib/x86_64-unknown-linux-gnu/3.1.2' export R_LIBS_USER=$R_LIBS_USER:'/mnt/lustre/user/wubin/01.Program/Scripts/02.software/DECoN/Linux/packrat/lib-ext' export R_LIBS_USER=$R_LIBS_USER:'/home/wubin/01.Program/02.software/R-3.1.2/library'
cd /mnt/lustre/user/wubin/01.Program/Scripts/02.software/DECoN/Linux
Rscript /mnt/lustre/user/wubin/01.Program/Scripts/02.software/DECoN/Linux/ReadInBams.R --bams /home/wubin/05.tests/DECoN/bams/bamList.txt --bed /mnt/lustre/user/wubin/01.Program/Scripts/01.script/GeneLab/Config/bed/BGI171.CNV_Analysis.bed --fasta /mnt/lustre/user/wubin/01.Program/Scripts/02.software/GATK/fasta_index/hg19.fa --out /home/wubin/05.tests/DECoN/bams/test_result/DECoNtest
and the error is:
Initializing packrat project in directory:
"/home/wubin/05.tests/DECoN" Error in if (result$source == "unknown" && fallback.ok) { : missing value where TRUE/FALSE needed Calls: ... getPackageRecords -> getPackageRecordsExternalSource -> lapply -> FUN
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
I don't know what the real problem is