Question: Error: installation of package org.Mm.eg.db had non-zero exit status
0
gravatar for zhangdengwei
28 days ago by
zhangdengwei0 wrote:

hi,

I am installing the package, org.Mm.eg.db, using the following command:

BiocManager::install("org.Mm.eg.db")

But I have got the warning and failed to install. My R version is 3.5.1.

Warning message:
In install.packages(...) :
  installation of package ‘org.Mm.eg.db’ had non-zero exit status

Any suggestion is appreciated. Thanks in advance.

orgdb • 104 views
ADD COMMENTlink written 28 days ago by zhangdengwei0

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

> BiocManager::install("org.Mm.eg.db")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 Patched (2019-10-04
  r77256)
Installing package(s) 'org.Mm.eg.db'
trying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/org.Mm.eg.db_3.8.2.tar.gz'
Content type 'application/x-gzip' length 71122045 bytes (67.8 MB)
==================================================
downloaded 67.8 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
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (org.Mm.eg.db)
> 
ADD REPLYlink written 28 days ago by Martin Morgan ♦♦ 24k

Thanks. My path does not contain Chinese characters, and I attached my command as follows:

> getwd()
[1] "C:/Users/zhangdengwei/Documents"
> BiocManager::install("org.Mm.eg.db")
Bioconductor version 3.8 (BiocManager 1.30.8), ?BiocManager::install for help
Bioconductor version '3.8' is out-of-date; the current release version '3.9' is available with R version
  '3.6'; see https://bioconductor.org/install
Bioconductor version 3.8 (BiocManager 1.30.8), R 3.5.1 (2018-07-02)
Installing package(s) 'org.Mm.eg.db'
installing the source package ‘org.Mm.eg.db’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Mm.eg.db_3.7.0.tar.gz'
Content type 'application/x-gzip' length 69822781 bytes (66.6 MB)
downloaded 66.6 MB

* installing *source* package 'org.Mm.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.Mm.eg.db'
* removing 'C:/Users/zhangdengwei/Documents/R/win-library/3.5/org.Mm.eg.db'
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign,
  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, rpart, survival
Old packages: 'digest'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
       binary source needs_compilation
digest 0.6.21 0.6.22              TRUE

  Binaries will be installed
trying URL 'https://cran.csiro.au/bin/windows/contrib/3.5/digest_0.6.21.zip'
Content type 'application/zip' length 237366 bytes (231 KB)
downloaded 231 KB

package ‘digest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages
Warning message:
In install.packages(...) :
  installation of package ‘org.Mm.eg.db’ had non-zero exit status
ADD REPLYlink written 27 days ago by zhangdengwei0

I finally fixed it by installing it from the local file using install.packages(). Thanks very much!

ADD REPLYlink written 27 days ago by zhangdengwei0

For help understanding what the problem is, can you provide the output of the following command?

inst <- installed.packages()
ridx <- inst[, "Package"] %in% c("RSQLite", "AnnotationDbi", "org.Mm.eg.db")
cidx <- c("Package", "LibPath", "Version")
inst[ ridx, cidx ]

Mine is

> inst[ ridx, cidx ]
              Package         LibPath                                 Version
AnnotationDbi "AnnotationDbi" "/Users/ma38727/Library/R/3.6/Bioc/3.9" "1.46.0"
org.Mm.eg.db  "org.Mm.eg.db"  "/Users/ma38727/Library/R/3.6/Bioc/3.9" "3.8.2"
RSQLite       "RSQLite"       "/Users/ma38727/Library/R/3.6/Bioc/3.9" "2.1.1"
ADD REPLYlink written 27 days ago by Martin Morgan ♦♦ 24k

Sure. Mine is

> inst <- installed.packages()
> ridx <- inst[, "Package"] %in% c("RSQLite", "AnnotationDbi", "org.Mm.eg.db")
> cidx <- c("Package", "LibPath", "Version")
> inst[ ridx, cidx ]
              Package         LibPath                                             Version 
AnnotationDbi "AnnotationDbi" "C:/Users/zhangdengwei/Documents/R/win-library/3.5" "1.44.0"
org.Mm.eg.db  "org.Mm.eg.db"  "C:/Users/zhangdengwei/Documents/R/win-library/3.5" "3.7.0" 
RSQLite       "RSQLite"       "C:/Users/zhangdengwei/Documents/R/win-library/3.5" "2.1.2"

Moreover, I found there was a lack of RSQLite when installing. So maybe it was the key point.

ADD REPLYlink written 26 days ago by zhangdengwei0

I finally fixed it by installing it from the local file using install.packages(). Thanks very much!

ADD REPLYlink written 27 days ago by zhangdengwei0

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:

setwd('C:/Users/guruiz/Desktop')
install.packages("C:/Users/guruiz/Desktop/org.Mm.eg.db_3.8.2.tar.gz")
Installing package into ‘\\hest.nas.ethz.ch/green_users_all_homes/guruiz/R3UserLibs’
(as ‘lib’ is unspecified)
inferring 'repos = NULL' from 'pkgs'
* installing *source* package 'org.Mm.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in findpack(package, lib.loc) : 
  there is no package called 'org.Mm.eg.db'
Calls: <Anonymous> -> findpack
Execution halted
ERROR: lazy loading failed for package 'org.Mm.eg.db'
* removing '\\hest.nas.ethz.ch/green_users_all_homes/guruiz/R3UserLibs/org.Mm.eg.db'
* restoring previous '\\hest.nas.ethz.ch/green_users_all_homes/guruiz/R3UserLibs/org.Mm.eg.db'
Warning message:
In install.packages("C:/Users/guruiz/Desktop/org.Mm.eg.db_3.8.2.tar.gz") :
  installation of package ‘C:/Users/guruiz/Desktop/org.Mm.eg.db_3.8.2.tar.gz’ had non-zero exit status

I have and old version of the package but I need the new one

    inst <- installed.packages()
ridx <- inst[, "Package"] %in% c("RSQLite", "AnnotationDbi", "org.Mm.eg.db")
cidx <- c("Package", "LibPath", "Version")
inst[ ridx, cidx ]
              Package         LibPath                                                        Version 
AnnotationDbi "AnnotationDbi" "\\\\hest.nas.ethz.ch/green_users_all_homes/guruiz/R3UserLibs" "1.47.1"
org.Mm.eg.db  "org.Mm.eg.db"  "\\\\hest.nas.ethz.ch/green_users_all_homes/guruiz/R3UserLibs" "2.7.1" 
RSQLite       "RSQLite"       "\\\\hest.nas.ethz.ch/green_users_all_homes/guruiz/R3UserLibs" "2.1.2"

Any help will be appreciated. Thanks.

ADD REPLYlink written 27 days ago by guillermoturiel0

When installing from source, install.packages() should have the repos=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...

ADD REPLYlink written 27 days ago by Martin Morgan ♦♦ 24k

Maybe you can try it again using Rstudio, Tools -> Install Packages, not type in install.packages() though the Console interface.

ADD REPLYlink written 26 days ago by zhangdengwei0
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