Error installing EBImage on Suse 10.1
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Mark Dunning ▴ 320
@mark-dunning-1634
Last seen 9.6 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 • 1.1k views
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Mark Dunning ▴ 320
@mark-dunning-1634
Last seen 9.6 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. >
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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
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@wolfgang-huber-3550
Last seen 15 days 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
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