failing to install the package clusterProfiler in R (version 3.4.1)
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@fengleiluck-14695
Last seen 3.8 years ago

When I tried to install the package clusterProfiler in R (version 3.4.1), I met some problems which are listed as follows.

Do you have any suggestions?

Thank you.

 

 

###########

 

> library(clusterProfiler)

载入需要的程辑包:DOSE

Error: package or namespace load failed for ‘DOSE’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 不存在叫‘DO.db’这个名字的程辑包

错误: 无法载入程辑包‘DOSE’

 

> biocLite("DOSE")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).

Installing package(s) ‘DOSE’

also installing the dependency ‘DO.db’

 

试开URL’https://bioconductor.org/packages/3.6/bioc/bin/macosx/el-capitan/contrib/3.4/DOSE_3.4.0.tgz'

Content type 'application/x-gzip' length 6546941 bytes (6.2 MB)

==================================================

downloaded 6.2 MB

 

 

The downloaded binary packages are in

/var/folders/vb/rtrqz50s1cq7kc59h061mjl80000gn/T//RtmpTlg2Qs/downloaded_packages

installing the source package ‘DO.db’

 

试开URL’https://bioconductor.org/packages/3.6/data/annotation/src/contrib/DO.db_2.9.tar.gz'

Content type 'application/x-gzip' length 1769978 bytes (1.7 MB)

==================================================

downloaded 1.7 MB

 

* installing *source* package ‘DO.db’ ...

** R

** inst

** preparing package for lazy loading

Error: package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called ‘tibble’

Error : package ‘AnnotationDbi’ could not be loaded

ERROR: lazy loading failed for package ‘DO.db’

* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/DO.db’

 

The downloaded source packages are in

‘/private/var/folders/vb/rtrqz50s1cq7kc59h061mjl80000gn/T/RtmpTlg2Qs/downloaded_packages’

Warning message:

In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘DO.db’ had non-zero exit status

clusterprofiler • 2.6k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 11 months ago
China/Guangzhou/Southern Medical Univer…
 there is no package called ‘tibble’

obviously, this is dependency issue.

You need to install corresponding pkg if any no package message throwed.

For example, here you can try:

biocLite("tibble")

to install tibble, and then try again to install clusterProfiler.

biocLite("clusterProfiler")
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It works. Thank you.

 

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