Error installing EBImage on Suse 10.1
2
0
Entering edit mode
Mark Dunning ▴ 320
@mark-dunning-1634
Last seen 10.2 years ago
Hi, I am trying to install EBImage on my 64-bit Linux machine, but am running into problems. I am using the command: biocLite("EBImage", type="source") Which seems to get quite far (it finds that I have ImageMagick 6.2.5) but it later fails with the following error: collect2: ld returned 1 exit status make: *** [EBImage.so] Error 1 chmod: cannot access `/home/md392/R/x86_64-unknown-linux-gnu-library/2.5/EBImage/libs/*': No such file or directory ERROR: compilation failed for package 'EBImage' ** Removing '/home/md392/R/x86_64-unknown-linux-gnu- library/2.5/EBImage' Could anyone advise me on what the problem might be? I am always able to build packages in this way without any error. Thanks in advance for any help, Regards, Mark > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base"
EBImage EBImage • 1.3k views
ADD COMMENT
0
Entering edit mode
Mark Dunning ▴ 320
@mark-dunning-1634
Last seen 10.2 years ago
Hi Paolo, Thanks for the reply. Unfortunately, I tried to install as root and my own username and I got the same error message. Regards, Mark On Tue, 2007-06-19 at 16:29 +0200, Paolo Innocenti wrote: > Hi Mark, > are you running the script as a superuser (root)? > It looks like a problem in writing permissions, or maybe the /home is > mounted on a protected partition? Did you change the fstab recently? > > Hope it helps, > best, > Paolo > > Mark Dunning wrote: > > Hi, > > > > I am trying to install EBImage on my 64-bit Linux machine, but am > > running into problems. I am using the command: > > > > biocLite("EBImage", type="source") > > > > Which seems to get quite far (it finds that I have ImageMagick 6.2.5) > > but it later fails with the following error: > > > > > > collect2: ld returned 1 exit status > > make: *** [EBImage.so] Error 1 > > chmod: cannot access > > `/home/md392/R/x86_64-unknown-linux-gnu- library/2.5/EBImage/libs/*': No > > such file or directory > > ERROR: compilation failed for package 'EBImage' > > ** Removing '/home/md392/R/x86_64-unknown-linux-gnu- library/2.5/EBImage' > > > > > > Could anyone advise me on what the problem might be? I am always able to > > build packages in this way without any error. >
ADD COMMENT
0
Entering edit mode
Dear Paolo, generally, it is not a good idea to install R package as a "super- user". Please think of all the security risks and havoc that could be caused (intentionally or unintentionally) by the code that is executed when a package's Makefile are executed. For a global (system-wide) installation, it is recommended to use a special user-id with limited rights except for writing to the directory where the software goes. Best wishes Wolfgang Mark Dunning ha scritto: > Hi Paolo, > > Thanks for the reply. Unfortunately, I tried to install as root and my > own username and I got the same error message. > > Regards, > > Mark > > > On Tue, 2007-06-19 at 16:29 +0200, Paolo Innocenti wrote: >> Hi Mark, >> are you running the script as a superuser (root)? >> It looks like a problem in writing permissions, or maybe the /home is >> mounted on a protected partition? Did you change the fstab recently? >> >> Hope it helps, >> best, >> Paolo >> >> Mark Dunning wrote: >>> Hi, >>> >>> I am trying to install EBImage on my 64-bit Linux machine, but am >>> running into problems. I am using the command: >>> >>> biocLite("EBImage", type="source") >>> >>> Which seems to get quite far (it finds that I have ImageMagick 6.2.5) >>> but it later fails with the following error: >>> >>> >>> collect2: ld returned 1 exit status >>> make: *** [EBImage.so] Error 1 >>> chmod: cannot access >>> `/home/md392/R/x86_64-unknown-linux-gnu- library/2.5/EBImage/libs/*': No >>> such file or directory >>> ERROR: compilation failed for package 'EBImage' >>> ** Removing '/home/md392/R/x86_64-unknown-linux-gnu- library/2.5/EBImage' >>> >>> >>> Could anyone advise me on what the problem might be? I am always able to >>> build packages in this way without any error. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
ADD REPLY
0
Entering edit mode
@wolfgang-huber-3550
Last seen 12 weeks ago
EMBL European Molecular Biology Laborat…
Dear Mark, Oleg is the expert who will probably know the answer, but I could imagine that seeing the full output that you get after biocLite would be helpful for this, esp. your results from 'configure'. Best wishes Wolfgang Dunning ha scritto: > Hi, > > I am trying to install EBImage on my 64-bit Linux machine, but am > running into problems. I am using the command: > > biocLite("EBImage", type="source") > > Which seems to get quite far (it finds that I have ImageMagick 6.2.5) > but it later fails with the following error: > > > collect2: ld returned 1 exit status > make: *** [EBImage.so] Error 1 > chmod: cannot access > `/home/md392/R/x86_64-unknown-linux-gnu-library/2.5/EBImage/libs/*': No > such file or directory > ERROR: compilation failed for package 'EBImage' > ** Removing '/home/md392/R/x86_64-unknown-linux-gnu- library/2.5/EBImage' > > > Could anyone advise me on what the problem might be? I am always able to > build packages in this way without any error. > > Thanks in advance for any help, > > Regards, > > Mark > > >> sessionInfo() > R version 2.5.0 (2007-04-23) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_ GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_G B.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" > "methods" > [7] "base" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
ADD COMMENT

Login before adding your answer.

Traffic: 497 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