Question:Error installing BiocManager::install("org.Hs.eg.db") package.
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2211738718 • 0
@2211738718-23773
Last seen 14 months ago
 BiocManager::install("org.Hs.eg.db")
Bioconductor version 3.8 (BiocManager 1.30.10), R 3.5.2 (2018-12-20)
Installing package(s) 'org.Hs.eg.db'
installing the source package ‘org.Hs.eg.db’

Content type 'application/x-gzip' length 77962833 bytes (74.4 MB)

* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called 'RSQLite'
Error : package 'AnnotationDbi' could not be loaded
* removing 'd:/Documents/R/win-library/3.5/org.Hs.eg.db'
In R CMD INSTALL

Installation path not writeable, unable to update packages: boot, class,
cluster, codetools, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet,
rpart, spatial, survival
Old packages: 'backports', 'dplyr', 'ellipsis', 'ggforce', 'ggraph', 'glue',
'graphlayouts', 'isoband', 'jsonlite', 'openssl', 'pkgload', 'ps',
'RcppArmadillo', 'rlang', 'tidygraph', 'tidyr', 'tidyselect', 'vctrs'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(...) :
installation of package ‘org.Hs.eg.db’ had non-zero exit status


Thank you very much

software error • 316 views
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@miguelcosenza-14267
Last seen 9 months ago
Germany / Freiburg / University Medical…

Hello,

It might be useful if you share on which operating system you are having this error.

Anyway, although I am not completely sure, I could point out a couple things that I notice and others you could try when installing packages that are usually helpful for me.

1. To install your packages, do it from the R GUI (not RStudio) after opening it as admin; close any other instances of R that you have open (I am assuming you are on Windows).

2. It seems you need to install the RSQLite package and or AnnotationDbi before installing org.Hs.eg.db.

3. You have a version of R that is already a bit old, this shouldn't be an issue (org.Hs.eg.db requires version > 2.7) but maybe you could try updating it?

I hope this is helpful in anyway.

Best, Miguel

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Thanks ,Miguel.I removed it.

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The problem is solved? - as per Miguel's second point, it looks like you first need to install the RSQLite package.

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Yeah.I 've solved the problem.thanks,Kevin

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Generally it is not necessary, and highly unadvisable, to install R or its packages as administrator.

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Interesting. I didn't know it was unadvisable, could you explain why is it that way?

That usually helps me when receiving package installation errors.

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Administrator accounts can do much more damage (e.g., deleting other user files; access data that might be restricted from a normal user) than a user account; the general principle is to use minimal permissions required for a task.

Usually what happens is that you start with an administrator installation, and then subsequently only an administrator can update or fix (e.g., remove a package) the installation. If instead you'd started with a regular user installation, then the regular user could update or fix the installation.

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