hey，
when I used the example code to run the flow, first, the code genomeFile <- "BSgenome.Hsapiens.UCSC.hg19" ,how get it?
The above reference genome BSgenome. Hsapiens. UCSC. Hg19.fa . Is it need manual download to my work path?At the beginning, there was no download, the operation error, I can run after manual download. But the following second error occurs when comparing.I again, error : Failed to install the index package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie'. How can I solved it, thank you！
clObj=cl, alignmentsDir = working_dir)
alignment files missing - need to:
create alignment index for the genome
create 1 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
将程序包安装入'C:/Users/yangskyfucker/Documents/R/win-library/4.1'
(因为'lib'没有被指定)
installing source package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie' ...
using staged installation
inst
Warning in file.append(to[okay], from[okay]) : 文件追加时书写出错
Warning in file.append(to[okay], from[okay]) : 文件追加时书写出错
help
* installing help indices
Warning in FUN(X[[i]], ...) : internal error -3 in R_decompress1
Warning in close.connection(outcon) :
Problem closing connection: No space left on device
converting help for package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie'
finding HTML links ... done
Warning in FUN(X[[i]], ...) : internal error -3 in R_decompress1
package html
Rd warning: Problem closing connection: No space left on device
building package indices
Warning in FUN(X[[i]], ...) : internal error -3 in R_decompress1
* testing if installed package can be loaded from temporary location
arch - i386
Warning: 程辑包'GenomicRanges'是用R版本4.1.2 来建造的
* arch - x64
Warning: 程辑包'GenomicRanges'是用R版本4.1.2 来建造的
* testing if installed package can be loaded from final location
arch - i386
Warning: 程辑包'GenomicRanges'是用R版本4.1.2 来建造的
Warning in base::file("C:\Users\YANGSK~1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2", :
无法打开文件'C:\Users\YANGSK~1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2': No space left on device
Error in base::file("C:\Users\YANGSK~1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2", :
无法打开链结
停止执行
*** arch - x64
Warning: 程辑包'GenomicRanges'是用R版本4.1.2 来建造的
Warning in base::file("C:\Users\YANGSK~1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2", :
无法打开文件'C:\Users\YANGSK~1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2': No space left on device
Error in base::file("C:\Users\YANGSK~1\AppData\Local\Temp\Rtmp6B8TRI\file757c41fe54b2", :
无法打开链结
停止执行
ERROR: loading failed for 'i386', 'x64'
removing 'C:/Users/yangskyfucker/Documents/R/win-library/4.1/BSgenome.Hsapiens.UCSC.hg19.Rbowtie'
Error in buildIndexPackage(proj@genome, proj@aligner, proj@alnModeID, :
Failed to install the index package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie'
In addition: Warning messages:
1: In object@elementType :
closing unused connection 5 (<-apps.corel.com:11244)
2: In object@elementType :
closing unused connection 4 (<-apps.corel.com:11244)
3: In object@elementType :
closing unused connection 3 (<-apps.corel.com:11244)
4: In utils::install.packages(file.path(cacheDir, indexPackageName), :
installation of package 'C:/Users/YANGSK~1/AppData/Local/Temp/RtmpMxfTDu/BSgenome.Hsapiens.UCSC.hg19.Rbowtie' had non-zero exit status
hey， when I used the example code to run the flow, first, the code genomeFile <- "BSgenome.Hsapiens.UCSC.hg19" ,how get it? The above reference genome BSgenome. Hsapiens. UCSC. Hg19.fa . Is it need manual download to my work path?At the beginning, there was no download, the operation error, I can run after manual download. But the following second error occurs when comparing.I again, error : Failed to install the index package 'BSgenome.Hsapiens.UCSC.hg19.Rbowtie'. How can I solved it, thank you！