做富集分析这里报错:
In bitr(DEG_list, fromType = opt$idtype, toType = opt$totype, OrgDb = opt$ann.db) :
26.02% of input gene IDs are fail to map...
--> No gene can be mapped....
--> Expected input gene ID:
--> return NULL...
NULL
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘dotplot’ for signature ‘"NULL"’
Calls: dotplot -> <Anonymous>
查了下需要升级R包:clusterProfiler等等
但是升级不成功:说magick安装不上,这里报错:
Error: package or namespace load failed for ‘magick’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/share/work/biosoft/R/R-v4.2.0/lib64/R/library/00LOCK-magick/00new/magick/libs/magick.so':
/share/work/biosoft/R/R-v4.2.0/lib64/R/library/00LOCK-magick/00new/magick/libs/magick.so: undefined symbol: _ZN6Magick5Image5writeEPNS_4BlobERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/share/work/biosoft/R/R-v4.2.0/lib64/R/library/magick’
* restoring previous ‘/share/work/biosoft/R/R-v4.2.0/lib64/R/library/magick’
Warning message:
解决办法手动高版本的ImageMagick,之后手动安装magick包:
PKG_CONFIG_PATH=/share/work/biosoft/ImageMagick/ImageMagick-v7.1.0-62/lib/pkgconfig/ R CMD INSTALL magick_2.8.0.tar.gz
再重新升级:clusterProfiler
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