Question:Error installing BiocManager::install("org.Hs.eg.db") package.
1
0
Entering edit mode
2211738718 • 0
@2211738718-23773
Last seen 3.7 years 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’

试开URL’https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Hs.eg.db_3.7.0.tar.gz'
Content type 'application/x-gzip' length 77962833 bytes (74.4 MB)
downloaded 74.4 MB

* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** byte-compile and prepare package for lazy loading
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
ERROR: lazy loading failed for package 'org.Hs.eg.db'
* removing 'd:/Documents/R/win-library/3.5/org.Hs.eg.db'
In R CMD INSTALL

The downloaded source packages are in
        ‘C:\Users\Administrator\AppData\Local\Temp\RtmpmObljz\downloaded_packages’
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

Would you please help me what is the problem for? and how can I solve it?

Thank you very much

software error • 1.2k views
ADD COMMENT
0
Entering edit mode
@miguelcosenza-14267
Last seen 3.3 years 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

ADD COMMENT
0
Entering edit mode

Thanks ,Miguel.I removed it.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 704 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6