Trouble installing Bioconductor packages inside a conda environment.

Question

[TonyCN]

I would appreciate some assistance resolving Bioconductor R package installation problems within a conda environment.

I have an Ubuntu machine with three accounts: root, user 1 with sudo privileges and part of group 1001, and user 2 also part of group 1001. This machine has a fresh installation of Ubuntu, please don't presume I have all the necessary dependencies.

As sudo, user 1 (me) installed Anaconda, which then becomes executable by user 2. Then user 2 set up a conda environment and install R-base and R-essentials. They then access R from the terminal and begin the process of installing Bioconductor's biocmanager. All is going well until they try to install any of the R bioconductor packages. For example,

BiocManager::install("missMethyl")

Throws up several errors. Here are a collection of them:

cp: cannot stat 'hdf5/c++/src/.libs/libhdf5_cpp.a': No such file or directory
make: *** [Makevars:36: copying] Error 1
ERROR: compilation failed for package ‘Rhdf5lib’

........

Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... no
checking for xmlParseFile in -lxml... no
configure: error: "libxml not found"
ERROR: configuration failed for package ‘XML’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/XML’
ERROR: dependency ‘XML’ is not available for package ‘rtracklayer’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/rtracklayer’
ERROR: dependency ‘XML’ is not available for package ‘biomaRt’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/biomaRt’
ERROR: dependency ‘Rhdf5lib’ is not available for package ‘rhdf5’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/rhdf5’
ERROR: dependency ‘XML’ is not available for package ‘annotate’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/annotate’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/GenomicFeatures’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/genefilter’
ERROR: dependencies ‘rhdf5’, ‘Rhdf5lib’ are not available for package ‘HDF5Array’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/HDF5Array’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/TxDb.Hsapiens.UCSC.hg19.knownGene’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘bumphunter’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/bumphunter’
ERROR: dependency ‘HDF5Array’ is not available for package ‘DelayedMatrixStats’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/DelayedMatrixStats’
ERROR: dependencies ‘GenomicFeatures’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ are not available for package ‘FDb.InfiniumMethylation.hg19’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/FDb.InfiniumMethylation.hg19’
ERROR: dependencies ‘bumphunter’, ‘DelayedMatrixStats’, ‘genefilter’, ‘HDF5Array’ are not available for package ‘minfi’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/minfi’
ERROR: dependencies ‘FDb.InfiniumMethylation.hg19’, ‘minfi’, ‘annotate’, ‘genefilter’ are not available for package ‘methylumi’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/methylumi’
ERROR: dependency ‘minfi’ is not available for package ‘IlluminaHumanMethylation450kmanifest’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/IlluminaHumanMethylation450kmanifest’
ERROR: dependency ‘minfi’ is not available for package ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/IlluminaHumanMethylation450kanno.ilmn12.hg19’
ERROR: dependency ‘minfi’ is not available for package ‘IlluminaHumanMethylationEPICmanifest’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/IlluminaHumanMethylationEPICmanifest’
ERROR: dependency ‘minfi’ is not available for package ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
ERROR: dependencies ‘minfi’, ‘methylumi’, ‘IlluminaHumanMethylation450kmanifest’, ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’, ‘IlluminaHumanMethylationEPICmanifest’, ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’ are not available for package ‘missMethyl’
* removing ‘/home/npaudel/.conda/envs/r_env/lib/R/library/missMethyl’

......

make[3]: Entering directory '/tmp/RtmpnsAIx5/R.INSTALL3753b2ffeadb1/Rhdf5lib/src/hdf5/c++/src'
  CXX      H5Exception.lo
  CXX      H5IdComponent.lo
  CXX      H5DataSpace.lo
H5DataSpace.cpp:15:10: fatal error: iostream.h: No such file or directory
 #include <iostream.h>
          ^~~~~~~~~~~~
compilation terminated.

I have a feeling HDF5 might be an issue so here's the Summary Information during the failed attempt at installing missMethyl:

        *SUMMARY OF THE HDF5 CONFIGURATION
        =================================
General Information:
-------------------
                   HDF5 Version: 1.10.5
                  Configured on: Wed Nov  3 18:12:21 GMT 2021
                  Configured by: npaudel@anthony-desktop
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux anthony-desktop 5.11.0-37-generic #41~20.04.2-Ubuntu SMP Fri Sep 24 09:06:38 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /tmp/RtmpnsAIx5/R.INSTALL3753b2ffeadb1/Rhdf5lib/src/hdf5/hdf5
Compiling Options:
------------------
                     Build Mode: production
              Debugging Symbols: no
                        Asserts: no
                      Profiling: no
             Optimization Level: high
Linking Options:
----------------
                      Libraries: static
  Statically Linked Executables: 
                        LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/npaudel/.conda/envs/r_env/lib -Wl,-rpath-link,/home/npaudel/.conda/envs/r_env/lib -L/home/npaudel/.conda/envs/r_env/lib
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/tmp/RtmpnsAIx5/R.INSTALL3753b2ffeadb1/Rhdf5lib/src/hdf5/szip/szip/lib
                Extra libraries: -lrt -lsz -lz -ldl -lm 
                       Archiver: /home/npaudel/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-ar
                       AR_FLAGS: cr
                         Ranlib: /home/npaudel/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-ranlib
Languages:
----------
                              C: yes
                     C Compiler: /home/npaudel/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-cc
                       CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/npaudel/.conda/envs/r_env/include
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/tmp/RtmpnsAIx5/R.INSTALL3753b2ffeadb1/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/npaudel/.conda/envs/r_env/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1589917437985/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/npaudel/.conda/envs/r_env=/usr/local/src/conda-prefix -w -fpic
                     H5 C Flags:  -std=c99  -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -O
                     AM C Flags: 
               Shared C Library: no
               Static C Library: yes
                        Fortran: no
                            C++: yes
                   C++ Compiler: /home/npaudel/.conda/envs/r_env/bin/x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11
                      C++ Flags: -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/npaudel/.conda/envs/r_env/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1589917437985/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/home/npaudel/.conda/envs/r_env=/usr/local/src/conda-prefix -w -fpic
                   H5 C++ Flags:   -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O
                   AM C++ Flags:  -DOLD_HEADER_FILENAME -DHDF_NO_NAMESPACE -DNO_STATIC_CAST
             Shared C++ Library: no
             Static C++ Library: yes
                           Java: no
Features:
---------
                   Parallel HDF5: no
Parallel Filtered Dataset Writes: no
              Large Parallel I/O: no
              High-level library: yes
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib),szip(encoder)
                             MPE: no
                      Direct VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
          Function stack tracing: no
       Strict file format checks: no
    Optimization instrumentation: no*

Thanks.

[Ram]

If you're using conda to manage an R environment (which I do not recommend for your main R environment), do not install packages from within R. Instead, use conda and bioconductor-* conda packages from the bioconda channel. Package managers do not play well together, and R's internal package manager/conda are no exception.

I personally prefer to install and manage my principal R installation outside all package managers - no homebrew, no conda. I use conda to only set up specific environments on demand, such as an R 3.4.1 env, one for cnvs/bams (with Rsamtools & copywriteR) or paper-specific environments so I can flash-freeze a setup.

[GenoMax]

You seem to be missing libxml. Since you have sudo privileges you can install (libxml-dev) outside of conda.