Knowledge/Tool error correction
[R]ArchR install error.
- -
ArchR
Analyzing single-cell regulatory chromatin in R.
This package is designed to streamline scATAC analyses in R.
www.archrproject.com
-> R package for processing and analyzing single-cell ATAC-seq data.
Error
~~~
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome)
ERROR: dependency ‘DirichletMultinomial’ is not available for package ‘TFBSTools’
* removing ‘/~~~/anaconda3/envs/ATAC_env/lib/R/library/TFBSTools’
ERROR: dependency ‘TFBSTools’ is not available for package ‘chromVAR’
* removing ‘/~~~/anaconda3/envs/ATAC_env/lib/R/library/chromVAR’
ERROR: dependency ‘TFBSTools’ is not available for package ‘motifmatchr’
* removing ‘/~~~/anaconda3/envs/ATAC_env/lib/R/library/motifmatchr’
다운로드한 소스 패키지들은 다음의 위치에 있습니다
‘/tmp/RtmpnFijPc/downloaded_packages’
'.Library'내 HTML 패키지 목록을 업데이트 하고 있습니다
Making 'packages.html' ... 완료
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpnFijPc/remotes3bf442c46bb45/GreenleafLab-ArchR-c61b064/DESCRIPTION’ (632ms)
─ preparing ‘ArchR’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts (369ms)
─ checking for empty or unneeded directories
─ building ‘ArchR_1.0.2.tar.gz’
utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, 에서 경고가 발생했습니다 :
storing paths of more than 100 bytes is not portable:
‘ArchR/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md’
ERROR: dependencies ‘motifmatchr’, ‘chromVAR’ are not available for package ‘ArchR’
* removing ‘/~~~/anaconda3/envs/ATAC_env/lib/R/library/ArchR’
경고메시지(들):
1: i.p(...)에서:
패키지 ‘DirichletMultinomial’의 설치가 0이 아닌 종료상태를 가졌습니다
2: i.p(...)에서:
패키지 ‘TFBSTools’의 설치가 0이 아닌 종료상태를 가졌습니다
3: i.p(...)에서:
패키지 ‘chromVAR’의 설치가 0이 아닌 종료상태를 가졌습니다
4: i.p(...)에서:
패키지 ‘motifmatchr’의 설치가 0이 아닌 종료상태를 가졌습니다
5: i.p(...)에서:
패키지 ‘/tmp/RtmpnFijPc/file3bf44360d793f/ArchR_1.0.2.tar.gz’의 설치가 0이 아닌 종료상태를 가졌습니다
Error Correction
‘motifmatchr’, ‘chromVAR'를 conda environmnet에 따로 설치 후 재설치 해보았음.
https://anaconda.org/bioconda/bioconductor-motifmatchr
Bioconductor Motifmatchr :: Anaconda.org
Description Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.
anaconda.org
https://anaconda.org/bioconda/bioconductor-chromvar
Bioconductor Chromvar :: Anaconda.org
Description Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.
anaconda.org
그 결과 아래와 같이 설치됨.
library(ArchR)
위와 같은 결과.
ArchR::installExtraPackages()
그리고 위와 같이 추가적 설치.
Comment
If you have installed R through Conda, we have had reports of compile errors when installing ArchR that can be fixed by running Sys.setenv(CONDA_BUILD_SYSROOT="/") prior to executing the devtools::install_github() command as outlined in this post.
위와 같은 내용이 있었지만, 따로 설정 안해줘도 해결할 수 있었음.
README에서 알 수 있듯이
https://anaconda.org/anaconda/cairo
https://anaconda.org/bioconda/macs2
설치가 권장된다.
Contents
소중한 공감 감사합니다