can't find HPO.db, then install HPO.db error

[RockJC]

library(clusterProfiler) 错误: package or namespace load failed for ‘clusterProfiler’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 不存在叫‘HPO.db’这个名字的程辑包

BiocManager::install("HPO.db")

• installing source package 'HPO.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 'HPO.db': .onLoad failed in loadNamespace() for 'HPO.db', details: call: NULL error: database disk image is malformed Error: loading failed Execution halted ERROR: loading failed
• removing 'D:/R-4.3.1/library/HPO.db'

[RockJC]

I‘ve try to add 'force=TRUE', That's not useful.

[huerqiang]

Please use the devel version of Bioconductor to install HPO.db.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HPO.db")

Or install the Github version:

remotes::install_github("YuLab-SMU/HPO.db")

[zxf2046]

library(clusterProfiler) 错误: package or namespace load failed for ‘clusterProfiler’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): 不存在叫‘HPO.db’这个名字的程辑包

BiocManager::install("HPO.db")

• installing source package 'HPO.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 'HPO.db': .onLoad failed in loadNamespace() for 'HPO.db', details: call: NULL error: database disk image is malformed Error: loading failed Execution halted ERROR: loading failed
• removing 'D:/R-4.3.1/library/HPO.db'

Has the problem been solved? I met the same problem now

[xiexielaifang]

Please use the devel version of Bioconductor to install HPO.db.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HPO.db")

Or install the Github version:

remotes::install_github("YuLab-SMU/HPO.db")

I have the same problem and use your method , but it can not solve the problem.

[huerqiang]

Please make sure you are using the devel version of Bioconductor:

BiocManager::install(version='devel')

[pormr]

Clearing the local cache of AnnotationHub may work:

ah <- AnnotationHub::AnnotationHub()
AnnotationHub::removeCache(ah)

[pengouy]

Clearing the local cache of AnnotationHub may work:

ah <- AnnotationHub::AnnotationHub()
AnnotationHub::removeCache(ah)

Finally!!! Thank you so much! I have tried so many times before...

[todaroroad]

l

you saved me, my bro