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grimbough / rhdf5

Package providing an interface between HDF5 and R
http://bioconductor.org/packages/rhdf5
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rhdf5filters needs R 4.0 #74

Closed gouthamatla closed 3 years ago

gouthamatla commented 4 years ago

Hi I am trying to install rhdf5 using Bioconductor version 3.10 and R 3.6.1 in a fresh conda environment.

I am receiving the following error:

x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -shared -L/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib -Wl,-rpath-link,/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib -L/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib -L/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib -Wl,-rpath-link,/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o wrap.o Fatal error: creating temporary file for -e failed -L/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib/R/lib -lR
x86_64-conda_cos6-linux-gnu-c++: error: Fatal: No such file or directory
x86_64-conda_cos6-linux-gnu-c++: error: error:: No such file or directory
x86_64-conda_cos6-linux-gnu-c++: error: creating: No such file or directory
x86_64-conda_cos6-linux-gnu-c++: error: temporary: No such file or directory
x86_64-conda_cos6-linux-gnu-c++: error: file: No such file or directory
x86_64-conda_cos6-linux-gnu-c++: error: for: No such file or directory
make: *** [/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib/R/share/make/shlib.mk:6: rhdf5.so] Error 1
ERROR: compilation failed for package 'rhdf5'
* removing '/rds/general/user/gatla/home/anaconda3/envs/r361_cicero/lib/R/library/rhdf5'

The downloaded source packages are in
    '/rds/general/ephemeral/user/gatla/ephemeral/RtmpP7DfTS/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
  installation of package 'rhdf5' had non-zero exit status

I am not sure why the error message is a part of the command and seems like some permission issues.

So I tried to install manually using R CMD INSTALL. Seems like it depends on "rhdf5filters".

When I try to install rhdf5filters, it says that it is not available for R 3.6.1

> BiocManager::install("rhdf5filters") 
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'rhdf5filters'
Warning message:
package 'rhdf5filters' is not available (for R version 3.6.1)
grimbough commented 4 years ago

There's a few things going on here.

First off, what commands did you run that lead to the first error you've posted?

Regarding rhdf5filters, formally there are no restrictions on the versions of R it will work with. However because it's available from Bioconductor, which has a six monthly release cycle tied to specific R versions, there are some practical limitations that you might need to work around. *rhdf5filters** was only introduced in Bioconductor 3.11, and so as far as your R 3.6 / BioC 3.10 setup is concerned, the package isn't available via the repositories.

You can try installing via Github with BiocManager::install('grimbough/rhdf5filters') however, I don't know how well this will work in Anaconda. I have mixed experiences building packages from source when using R installed via conda.