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michal.devir
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@michaldevir-11263
Last seen 8.2 years ago
Hi,
I am trying to install Bioconductor. I tried two different ways, both of them failed:
1. installing via R console:
source('http://bioconductor.org/biocLite.R')
biocLite('BiocGenerics')
As part of the installation, I received a message:
Old packages: 'Rcpp', 'maps', 'mgcv' Update all/some/none? [a/s/n]: a
However, the update failed:
<the download worked, but then...>:
* installing *source* package 'mgcv' ... ** package 'mgcv' successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c coxph.c -o coxph.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c discrete.c -o discrete.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c gdi.c -o gdi.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c init.c -o init.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c magic.c -o magic.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c mat.c -o mat.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c matrix.c -o matrix.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c mgcv.c -o mgcv.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c misc.c -o misc.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c mvn.c -o mvn.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c qp.c -o qp.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c soap.c -o soap.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c sparse-smooth.c -o sparse-smooth.o gcc -std=gnu99 -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/include -DNDEBUG -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -fopenmp -fpic -I/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/include -c tprs.c -o tprs.o gcc -std=gnu99 -shared -L/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/lib -L/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib -lgfortran -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -L/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/lib -lRlapack -L/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/lib -lR installing to /mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/library/mgcv/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/library/mgcv/libs/mgcv.so': /mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/library/mgcv/libs/mgcv.so: undefined symbol: GOMP_parallel Error: loading failed Execution halted ERROR: loading failed * removing '/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/library/mgcv' * restoring previous '/mnt/lustre/hms-01/fs01/iditb/Programs/miniconda3/envs/mutations/lib/R/library/mgcv'
[similar errors are received for the other packeges]
and then...
Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package 'BiocGenerics' had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'Rcpp' had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'maps' had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'mgcv' had non-zero exit status
Session Info:
R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CS HUJI debian 5776 locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.22.3 loaded via a namespace (and not attached): [1] tools_3.3.1
2. the second way was via conda
conda install bioconductor-biobase
and received the following error:
The following specifications were found to be in conflict: - bioconductor-biobase - r-gistr -> r-base 3.3.1*
But I see no conflict between them :-(
Any help will be much appreciated!
Thanks,
Michal.
Thanks a lot for your quick and professional response.
Indeed, BioGenerics failed as well :-(
I tried
install.packages("mgcv", repos=BiocInstaller::biocinstallRepos())and it also failed, as you thought.
So now I understand it is more an R issue than bioconductor. I wasn't responsible for the R installation, but I am afraid that maybe it is was installed in some way, and then was upgraded via coda, or something like that.
Since I do not have root access, is there some way I can fix this mess via conda?
Thanks a lot,
Michal.
I think you should ask the person with system administration responsibilities to straighten things out. This will help you as well as other users they are supporting.
I have no experience with conda.
The alternative is to install R from source; this could be straight-forward if your computer has 'devel' versions of various libraries installed, but if not it would be very challenging and you would likely end up needing the help of the aforementioned system administrator.
Are you trying to install this on a node of a cluster? Often the nodes are provisioned to use packages but not install them, and there is a head or build node with appropriate configuration.
Hi,
I agree with your advise, and will contact the system administrator. Thanks a lot!