Question: problem loading library in R
0
gravatar for 786
2.4 years ago by
78650
78650 wrote:

I'm installing this package hu6800.db from Bioconductor packages and as a result i get this...

Warning messages:
1: running command '"C:/Program Files/R/R-32~1.3/bin/i386/R" CMD INSTALL -l "C:\Users\\Documents\R\win-library\3.2" C:\Users\~1\AppData\Local\Temp\RtmpYviEP2/downloaded_packages/org.Hs.eg.db_3.2.3.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
3: running command '"C:/Program Files/R/R-32~1.3/bin/i386/R" CMD INSTALL -l "C:\Users\\Documents\R\win-library\3.2" C:\Users\~1\AppData\Local\Temp\RtmpYviEP2/downloaded_packages/hu6800.db_3.2.2.tar.gz' had status 1 
4: In install.packages(pkgs = doing, lib = lib, ...) :
  **installation of package ‘hu6800.db’ had non-zero exit status**

What does mean by the 4th point?I just don't understand. Does it mean that this package isn't installed if yes then please let me know why and what is the error?? And when i load library i get this...

**Error in library(hu6800.db) : there is no package called ‘hu6800.db’**

what is it?? Please help me out from this situation....

genechip bioclite bioconductor R • 1.3k views
ADD COMMENTlink modified 2.4 years ago by Tanvir Ahamed 270 • written 2.4 years ago by 78650
1

Format your question better, add a quote chunk to the code that's outputted. Also, include the results of

sessionInfo()

ADD REPLYlink written 2.4 years ago by andrew.j.skelton735.2k

I really don't understand what did u said please explain it.

ADD REPLYlink written 2.4 years ago by 78650

Type sessionInfo() in your R terminal and provide us with the result of that command.

ADD REPLYlink written 2.4 years ago by WouterDeCoster31k

Please post the commands that you used to try and install these packages - stressing the point where you used 'biocLite'.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by russhh3.7k

source("https://bioconductor.org/biocLite.R")

biocLite()

to install the additional one

biocLite("hu6800.db")

biocLite("hu6800cdf")

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by 78650

try biocLite('org.Hs.eg.db') and when it doesn't work, please post some detailed error messages

ADD REPLYlink written 2.4 years ago by russhh3.7k

okay and thank u so much

ADD REPLYlink written 2.4 years ago by 78650

And what was the output of these commands?

ADD REPLYlink written 2.4 years ago by Sean Davis24k

The problem still exists please help me out when I used **

biocLite('org.Hs.eg.db')

** The results are:

BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10). Installing package(s) ‘org.Hs.eg.db’ installing the source package ‘org.Hs.eg.db’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/org.Hs.eg.db_3.2.3.tar.gz' Content type 'application/x-gzip' length 68856557 bytes (65.7 MB) downloaded 65.7 MB

'C:\Program' is not recognized as an internal or external command, operable program or batch file.

The downloaded source packages are in ‘C:\Users\Nada Mushtaq\AppData\Local\Temp\RtmpSEVNBm\downloaded_packages’ Warning messages: 1: running command '"C:/Program Files/R/R-32~1.3/bin/i386/R" CMD INSTALL -l "C:\Users\Nada Mushtaq\Documents\R\win-library\3.2" C:\Users\NADAMU~1\AppData\Local\Temp\RtmpSEVNBm/downloaded_packages/org.Hs.eg.db_3.2.3.tar.gz' had status 1 2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘org.Hs.eg.db’ had non-zero exit status

It shows that the package is still not installed now what should I do???

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by 78650

Have you googled the error message: 'C:\Program' is not recognized as an internal or external command, operable program or batch file.

Could you find the value of R_HOME in your enviroment variables, and, if so check if the path is in quotes or not?

ADD REPLYlink written 2.4 years ago by russhh3.7k
1
gravatar for mastal511
2.4 years ago by
mastal5111.9k
mastal5111.9k wrote:

Non-zero exit status means the package was not succesfully installed.

ADD COMMENTlink written 2.4 years ago by mastal5111.9k

to install it successfully what should i do and why it wasn't installed properly??Can u please mention the reasons it'll be very helpful fr me

ADD REPLYlink written 2.4 years ago by 78650
0
gravatar for WouterDeCoster
2.4 years ago by
Belgium
WouterDeCoster31k wrote:

I tested and installation was successful here. Could you elaborate on which version of R and bioconductor you use? If outdated, you might want to try to first update those. I think your R is outdated, since org.Hs.eg.db requires 2.7.0 or higher.

ADD COMMENTlink written 2.4 years ago by WouterDeCoster31k
1

From the trail, you can assume R-3.2.3

ADD REPLYlink written 2.4 years ago by russhh3.7k
0
gravatar for Tanvir Ahamed
2.4 years ago by
Sweden
Tanvir Ahamed 270 wrote:

Try to delete all the packages (org.Hs.eg.db, hu6800.db if exists), that you want to install in the library folder of your R installation Example location of library folder: C:\Program Files\R\R-3.2.3\library

Restart R and try to install all again !!

ADD COMMENTlink written 2.4 years ago by Tanvir Ahamed 270

It may be a little too late but thought of adding a comment for the use of others who may run in to the same issue.

I ran into the same problem and person in-charge of the uni server asked me to run "stringi" in R and it solved my issues with installing packages in R.

code: install.packages("stringi")

Thanks! D

ADD REPLYlink written 21 months ago by Dtriumph20
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