YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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Package installation error of package MPO.db #641

Open zhouyuheng19980624 opened 12 months ago

zhouyuheng19980624 commented 12 months ago

I tried to install package MPO.db but encountered following errors.

> BiocManager::install("MPO.db")
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Installing package(s) 'MPO.db'
trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MPO.db_0.99.7.tar.gz'
Content type 'application/x-gzip' length 29300 bytes (28 KB)
==================================================
downloaded 28 KB

* installing *source* package ‘MPO.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Couldn't set cache size: database disk image is malformed
Use `cache_size` = NULL to turn off this warning.
Warning: Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning.
Error: package or namespace load failed for ‘MPO.db’:
 .onLoad failed in loadNamespace() for 'MPO.db', details:
  call: NULL
  error: database disk image is malformed
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/zhouyuheng/.conda/envs/zhouyuheng1/lib/R/library/MPO.db

The downloaded source packages are in ‘/tmp/RtmpoO0pWd/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done`

Session info

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 8

Matrix products: default
BLAS/LAPACK: /home/zhouyuheng/.conda/envs/zhouyuheng1/lib/libopenblasp-r0.3.21.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Shanghai
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.3.1      tools_4.3.1

Could you please help me further?

ShixiangWang commented 12 months ago

You could clone https://github.com/huerqiang/HPO.db_MPO.db and install the package locally.