User: daniel.gaffney

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Posts by daniel.gaffney

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Comment: C: Difference between biomart R and biomart website GO query
... Thanks very much Mike, this solved my problem! Dan ...
written 11 months ago by daniel.gaffney20
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Difference between biomart R and biomart website GO query
... Hi, I'm searching for all ENSEMBL gene IDs associated with a particular GO ID (GO:0065005), which - using biomaRt - returns a single gene. I do: library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") out <- getBM(attributes=c('ensembl_gene_id', 'go_id'),filters = 'go', v ...
go biomart getbm ensemblbiomart written 12 months ago by daniel.gaffney20 • updated 12 months ago by Mike Smith3.3k
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Answer: A: Beachmat install / compile issue
... This problem was caused by using an old version of gcc and is solved by updating to a newer version of the compiler. First, you have to install a new version of gcc (or find an updated version that's already on your machine, which is probably the case if you're working on a shared computing resource ...
written 14 months ago by daniel.gaffney20 • updated 14 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Beachmat install / compile issue
... Solved! Your final point was the key - libstdc++.so.6 is found in lib64 not lib. (Argh). It seems it is sufficient to include the library in LD_LIBRARY_PATH for the compilation to succeed. Thanks again for your help! (I will post the solution as a reply to the main question). ...
written 14 months ago by daniel.gaffney20
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Comment: C: Beachmat install / compile issue
... Thanks again. I rebuilt R-3.4.3 with the following flags: ./configure --prefix=$HOME/local LDFLAGS="-L/software/gcc-6.2.0/lib -L$HOME/local/lib" --disable-openmp (I had some issues with compiling with openmp enabled, so I switched it off). I had the following env variables set: echo $LD_LIBRARY_PAT ...
written 14 months ago by daniel.gaffney20
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Comment: C: Beachmat install / compile issue
... So I removed and reinstalled Rhdf5lib as follows: source("https://bioconductor.org/biocLite.R") remove.packages("Rhdf5lib") biocLite("Rhdf5lib") This works fine, now I get the following error when installing beachmat:   Error: package or namespace load failed for ‘beachmat’ in dyn.load(file, DLLpa ...
written 14 months ago by daniel.gaffney20
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Answer: A: Beachmat install / compile issue
... I've also tried changing various environmental variables :PATH, LD_LIBRARY_PATH, CC and CXX to point to the correct gcc version, so I get: echo $LD_LIBRARY_PATH;echo $CC; echo $CXX /software/gcc-6.2.0/lib64/:/usr/local/lsf/9.1/linux2.6-glibc2.3-x86_64/lib:/nfs/users/nfs_d/dg13/local/lib /software/ ...
written 14 months ago by daniel.gaffney20
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Comment: C: Beachmat install / compile issue
... Apologies - the output of sessionInfo is:   sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit)   Matrix products: default BLAS: /nfs/teams/team170/Daniel/local/lib/R/lib/libRblas.so LAPACK: /nfs/teams/team170/Daniel/local/lib/R/lib/libRlapack.so   locale: [1 ...
written 14 months ago by daniel.gaffney20
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Beachmat install / compile issue
... Hi, I am getting a compilation error when installing beachmat on a clean install (i.e. downloaded and compiled the 3.4.3 source, reinstalled all packages from scratch) of R-3.4.3. My gcc version is 4.6.3. (Ubuntu/Linaro 4.6.3-1ubuntu5). Compilation seems to fail when it reaches the compilation step ...
compilation error beachmat written 14 months ago by daniel.gaffney20

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