Hi,
I have the same warning (non-zero exit status) when I try to install the package org.Mm.eg.db.
My R version is 3.6.3 and I'm using RStudio. My OS is windows 10. And I'm a R beginner.
The full command is :
> BiocManager::install("org.Mm.eg.db")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'org.Mm.eg.db'
installing the source package ‘org.Mm.eg.db’
trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/org.Mm.eg.db_3.10.0.tar.gz'
Content type 'application/x-gzip' length 72221575 bytes (68.9 MB)
downloaded 68.9 MB
* installing *source* package 'org.Mm.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'org.Mm.eg.db'
finding HTML links ... done
org.Mm.egACCNUM html
org.Mm.egALIAS2EG html
org.Mm.egBASE html
org.Mm.egCHR html
org.Mm.egCHRLENGTHS html
org.Mm.egCHRLOC html
org.Mm.egENSEMBL html
org.Mm.egENSEMBLPROT html
org.Mm.egENSEMBLTRANS html
org.Mm.egENZYME html
org.Mm.egGENENAME html
org.Mm.egGO html
org.Mm.egMAPCOUNTS html
org.Mm.egMGI html
org.Mm.egORGANISM html
org.Mm.egPATH html
org.Mm.egPFAM html
org.Mm.egPMID html
org.Mm.egPROSITE html
org.Mm.egREFSEQ html
org.Mm.egSYMBOL html
org.Mm.egUNIGENE html
org.Mm.egUNIPROT html
org.Mm.eg_dbconn html
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error: package or namespace load failed for 'org.Mm.eg.db':
.onLoad failed in loadNamespace() for 'org.Mm.eg.db', details:
call: NULL
error: Failed to load extension: Le module spécifié est introuvable.
Error: loading failed
Execution halted
*** arch - x64
Error: package or namespace load failed for 'org.Mm.eg.db':
.onLoad failed in loadNamespace() for 'org.Mm.eg.db', details:
call: NULL
error: Failed to load extension: Le module spécifié est introuvable.
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Program Files/R/R-3.6.3/library/org.Mm.eg.db'
The downloaded source packages are in
‘C:\Users\Propriétaire\AppData\Local\Temp\RtmpQT03YD\downloaded_packages’
Old packages: 'nlme', 'survival'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
nlme 3.1-145 3.1-147 TRUE
survival 3.1-11 3.1-12 TRUE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/nlme_3.1-145.zip'
Content type 'application/zip' length 2374770 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/survival_3.1-11.zip'
Content type 'application/zip' length 7774086 bytes (7.4 MB)
downloaded 7.4 MB
package ‘nlme’ successfully unpacked and MD5 sums checked
Error in unpackPkgZip(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib, libs_only, :
ERROR: failed to lock directory ‘C:\Program Files\R\R-3.6.3\library’ for modifying
Try removing ‘C:\Program Files\R\R-3.6.3\library/00LOCK’
In addition: Warning message:
In install.packages(...) :
installation of package ‘org.Mm.eg.db’ had non-zero exit status
(I'm sorry, even if I changed language to english, there are still some part in french "Le module spécifié est introuvable" means that R can't find the module)
When I delete C:\Program Files\R\R-3.6.3\library/00LOCK
, it still doesn't work.
As discussed in messages above, I tried to install the package using the RStudio tool (Tools , Install packages).
I have the same error (see the next message, this one is too long, I can't past the entire R code)
Please show the full command. Make sure your temporary directory path does not contain Chinese characters by setting the environment variable TEMPDIR (see
?tempdir()
for more help).I have
Thanks. My path does not contain Chinese characters, and I attached my command as follows:
I finally fixed it by installing it from the local file using
install.packages()
. Thanks very much!For help understanding what the problem is, can you provide the output of the following command?
Mine is
Sure. Mine is
Moreover, I found there was a lack of
RSQLite
when installing. So maybe it was the key point.I finally fixed it by installing it from the local file using
install.packages()
. Thanks very much!Hi I'm having the same problem but it's still not working for me when I try to install with install.packages(). I got this:
I have and old version of the package but I need the new one
Any help will be appreciated. Thanks.
When installing from source,
install.packages()
should have therepos=NULL
argument provided explicitly.I think this is a problem with the network drive
\\\h...
and that the work-around (I think this is addressed in R-devel...) is to use Windows to 'map network drive' (via google) and use the mapped drive to set.libPaths()
. Hope that's enough of a hint...Maybe you can try it again using Rstudio,
Tools -> Install Packages
, not type ininstall.packages()
though the Console interface.