Search
Question: mzR installation error: "unable to load shared object"
0
gravatar for Eugene
2.3 years ago by
Eugene0
United States
Eugene0 wrote:

First time I try to install mzR using Bioconductor or

  R CMD INSTALL --no-clean-on-error --no-multiarch mzR_2.3.1.tar.gz

and I always get message:

...

gcc -std=gnu99 -I/master/eugeneid/bin/R-3.2.1/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I"/master/eugeneid/bin/R-3.2.1/library/Rcpp/include" -I"/master/eugeneid/bin/R-3.2.1/library/zlibbioc/include"   -fpic  -g -O2  -c R_init_mzR.c -o R_init_mzR.o
g++ -shared -L/usr/local/lib64 -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/src/pthread/once.o ./boost/thread/src/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/Version.o ./pwiz/data/identdata/References.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o R_init_mzR.o -lpthread -L/net/corral2/vol0/master/eugeneid/bin/netcdf-4.3.3.1/myNetCDF/lib -lnetcdf
installing to /master/eugeneid/bin/R-3.2.1/library/mzR/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘close’ from package ‘base’ in package ‘mzR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so':
  libnetcdf.so.7: cannot open shared object file: No such file or directory
Error: loading failed

...
Both mzR.so and libnetcdf.so.7 exist.

Versions: R 3.2.1, mzR 2.2.1, Rcpp 0.11.6, netcdf-4.3.3.1, Bioconductor 3.1 (BiocInstaller 1.18.4)

Directories netcdf-4.3.3.1/myNetCDF/lib, netcdf-4.3.3.1/myNetCDF, and netcdf-4.3.3.1 are included in PATH

What could be wrong?

ADD COMMENTlink written 2.3 years ago by Eugene0
2

Diego is right, of course. Could you try the recommended installation using biocLite, and see it that works. Also, where is libnetcdf.so.7 - mine is in /usr/lib/libnetcdf.so.7. If it is in a non-standard location, maybe it is not found during compilation. 

 

ADD REPLYlink written 2.3 years ago by Laurent Gatto840

I do not have administrative rights, so I use files where they were located during installations.
As mzR uses NetCDR, I included its subdirectories bin/, lib/, and include/ in my PATH according to the installation instructions for ncdf ( https://cran.r-project.org/web/packages/ncdf/INSTALL ) and xcms, and previous error message "libnetcdf.so.7: cannot open shared object file: No such file or directory" disappeared.

But I got new error message for mzR.so:
>---------
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so':
  /master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so: undefined symbol: deflateInit2_
Error: loading failed
Execution halted
ERROR: loading failed
<---------------
In the case of error, "biocLite(<...>)" deletes installed files, that is why I use "R CMD INSTALL --no-clean-on-error  <...>.tar.gz" in such situations to keep installed files, getting the same error messages.
Now mzR.so exists:

> ldd -r /master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so
    linux-vdso.so.1 =>  (0x00007fffec53f000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aae7b82a000)
    libnetcdf.so.7 => /master/eugeneid/bin/netcdf-4.3.3.1/myNetCDF/lib/libnetcdf.so.7 (0x00002aae7ba47000)
    libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002aae7bd30000)
    libm.so.6 => /lib64/libm.so.6 (0x00002aae7c030000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aae7c2b4000)
    libc.so.6 => /lib64/libc.so.6 (0x00002aae7c4c2000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003eac400000)
undefined symbol: deflateInit2_    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: compress    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_ClassSymbol    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_findFun    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)

... and many others.

So, libnetcdf.so.7 is successively included in mzR.so, but it looks like now mzR.so can not get system variable deflateInit2_ ? What could be wrong?

 

ADD REPLYlink written 2.3 years ago by Eugene0

Some of these are spurious because they are defined by R; try R CMD ldd -r /master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so

ADD REPLYlink written 2.3 years ago by Martin Morgan ♦♦ 20k

I get exactly the  same, full output:

>----------------------

R CMD ldd -r /master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so
    linux-vdso.so.1 =>  (0x00007fff7f5fd000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ae6d8866000)
    libnetcdf.so.7 => /master/eugeneid/bin/netcdf-4.3.3.1/myNetCDF/lib/libnetcdf.so.7 (0x00002ae6d8a82000)
    libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002ae6d8d6b000)
    libm.so.6 => /lib64/libm.so.6 (0x00002ae6d906c000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002ae6d92ef000)
    libc.so.6 => /lib64/libc.so.6 (0x00002ae6d94fd000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003eac400000)
undefined symbol: R_NilValue    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_ClassSymbol    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_GlobalEnv    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_NaInt    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_UnboundValue    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_BaseNamespace    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_RowNamesSymbol    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_NaString    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_LevelsSymbol    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_NamesSymbol    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_lang2    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: deflateInit2_    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: compress    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_RegisterCFinalizerEx    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_PreserveObject    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: uncompress    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_findFun    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_mkCharCE    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_error    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: deflate    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_coerceVector    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_unprotect    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_isString    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: SET_STRING_ELT    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_ExternalPtrAddr    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: CAR    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_lang4    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: deflateEnd    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: REprintf    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_ProtectWithIndex    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: STRING_ELT    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_install    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_protect    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_setAttrib    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: crc32    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_mkChar    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_mkString    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflate    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_eval    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_ReleaseObject    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflateInit2_    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_Reprotect    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rprintf    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: compressBound    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_GetCCallable    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: S_realloc    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_isS4    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_inherits    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_length    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflateEnd    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: CDR    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflateCopy    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: REAL    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_xlength    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_onintr    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_ScalarString    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_lang1    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_CHAR    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: clock_gettime    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflateReset    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: deflateReset    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: INTEGER    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_isNull    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_allocVector    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: SET_VECTOR_ELT    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: S_alloc    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: PRINTNAME    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_SetExternalPtrTag    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: SET_TAG    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_getAttrib    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_registerRoutines    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: VECTOR_ELT    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: TYPEOF    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_MakeExternalPtr    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: Rf_lang3    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: CDDR    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_FlushConsole    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: R_SetExternalPtrProtected    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
<------------------------------------

ADD REPLYlink written 2.3 years ago by Eugene0

I'm not sure what is going on, but in case it's useful, I was expecting that R CMD ldd helped to include the libR.so, and that some of these symbols would resolve to it, as in

~/R/x86_64-unknown-linux-gnu-library/3.2-BiocDevel/mzR/libs$ R CMD ldd  -r mzR.so |grep libR
    libR.so => /home/mtmorgan/bin/R-3-2-branch/lib/libR.so (0x00007f6b679d9000)
    libRblas.so => /home/mtmorgan/bin/R-3-2-branch/lib/libRblas.so (0x00007f6b66220000)
~/R/x86_64-unknown-linux-gnu-library/3.2-BiocDevel/mzR/libs$ objdump -T mzR.so |grep Rf_install
0000000000000000      DF *UND*    0000000000000000              Rf_install
~/R/x86_64-unknown-linux-gnu-library/3.2-BiocDevel/mzR/libs$ objdump -T /home/mtmorgan/bin/R-3-2-branch/lib/libR.so|grep Rf_install
000000000017a716 g    DF .text    00000000000001e2  Base        Rf_install

 

ADD REPLYlink written 2.3 years ago by Martin Morgan ♦♦ 20k

Thank you for the idea: I found that I did not have libR.so, I reinstalled R with
   ./configure --enable-R-shlib --enable-R-static-lib --enable-BLAS-shlib
and now libR.so is presented in mzR.so.

The error message is the same, but the list of undefined symbols is much shorter:

dd -r /master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so
    linux-vdso.so.1 =>  (0x00007fffd7bfd000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b7891628000)
    libnetcdf.so.7 => /master/eugeneid/bin/netcdf-4.3.3.1/myNetCDF/lib/libnetcdf.so.7 (0x00002b7891845000)
    libR.so => /master/eugeneid/bin/R-3.2.1/lib/libR.so (0x00002b7891b2e000)
    libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b7892177000)
    libm.so.6 => /lib64/libm.so.6 (0x00002b7892478000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b78926fb000)
    libc.so.6 => /lib64/libc.so.6 (0x00002b7892909000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003eac400000)
    libRblas.so => /master/eugeneid/bin/R-3.2.1/lib/libRblas.so (0x00002b7892c63000)
    libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00002b7892e8e000)
    libreadline.so.5 => /usr/lib64/libreadline.so.5 (0x00002b7893125000)
    libncurses.so.5 => /usr/lib64/libncurses.so.5 (0x00002b7893363000)
    librt.so.1 => /lib64/librt.so.1 (0x00002b78935c0000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00002b78937c9000)
    libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00002b78939ce000)
undefined symbol: deflateInit2_    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: compress    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: uncompress    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: deflate    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: deflateEnd    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: crc32    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflate    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflateInit2_    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: compressBound    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflateEnd    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflateCopy    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: inflateReset    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)
undefined symbol: deflateReset    (/master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so)

Do I miss some compressing library?

ADD REPLYlink written 2.3 years ago by Eugene0
1

Maybe zlib?

ADD REPLYlink written 2.3 years ago by Laurent Gatto840

I installed zlib, included it in PATH and LD_LIBRARY_PATH, and got mzR.so of 73 MB containing 17 libraries with the same error message:

ldd /master/eugeneid/bin/R-3.2.1/library/mzR/libs/mzR.so
    linux-vdso.so.1 =>  (0x00007fffa21ff000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f529b314000)
    libnetcdf.so.7 => /master/eugeneid/bin/netcdf-4.3.3.1/myNetCDF/lib/libnetcdf.so.7 (0x00007f529b02a000)
    libR.so => /master/eugeneid/bin/R-3.2.1/lib/libR.so (0x00007f529a9e1000)
    libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f529a6db000)
    libm.so.6 => /lib64/libm.so.6 (0x00007f529a456000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f529a240000)
    libc.so.6 => /lib64/libc.so.6 (0x00007f5299eac000)
    /lib64/ld-linux-x86-64.so.2 (0x000000395b800000)
    libRblas.so => /master/eugeneid/bin/R-3.2.1/lib/libRblas.so (0x00007f5299c80000)
    libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00007f529999e000)
    libreadline.so.5 => /opt/rocks/lib/libreadline.so.5 (0x00007f5299762000)
    libncurses.so.5 => /lib64/libncurses.so.5 (0x00007f529953f000)
    librt.so.1 => /lib64/librt.so.1 (0x00007f5299337000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00007f5299133000)
    libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00007f5298f25000)
    libtinfo.so.5 => /lib64/libtinfo.so.5 (0x00007f5298d04000)
ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Eugene0

Did you do a clean installation, so all (sub) libraries were being re-built? I have

mzR/libs$ ls -lh mzR.so
-rwxr-xr-x 1 mtmorgan g_mtmorgan 56M May 10 14:10 mzR.so
mzR/libs$ R CMD ldd  mzR.so| wc -l
54

(even if ldd and R CMD ldd give you identical results at the moment, using R CMD ldd is correct -- R CMD sets up the environment to be consistent with the way R will run). I think you should rebuild R so that R knows about libz (not that this is the problem at the current stage). Also, I wouldn't mess with success but in principle at least I don't think you should need to tell R to be built with --enable-R-shlib; it seems like there is a mis-communication between the setting you used to build R and the settings you're using to compile packages; maybe you're selecting a different compiler or compiler options?

 

ADD REPLYlink written 2.3 years ago by Martin Morgan ♦♦ 20k

With zlib directories, included in PATH and LD_LIBRARY_PATH, I rebuilt R twice:
With --enable-R-shlib I have
   > ls -lh mzR.so
-rwxr-xr-x 1 eugeneid genetics 51M Aug  1 15:26 mzR.so
  > /R CMD ldd mzR.so | wc -l
  16
and undefined symbols are the same as previous.
Without --enable-R-shlib I got a lot of undefined symbols and
  > R CMD ldd  mzR.so| wc -l
  8

 

ADD REPLYlink written 2.3 years ago by Eugene0

OK. Finally, our system administrator reinstalled NetCDF from rpm, and I successively installed mzR.

ADD REPLYlink written 2.3 years ago by Eugene0
1

Why not use the official method for install (i.e. biocLite)? It seems you are trying to install the devel version of mzR on a Bioconductor release install. If so, this is not supported. Either:

# This will install mzR 2.2.1, which you seem to have already.
source("http://bioconductor.org/biocLite.R")
biocLite("mzR")

Or alternatively in a fresh R install:

# This will install mzR 2.3.1.
source("http://bioconductor.org/biocLite.R")
useDevel(TRUE) # change to the devel branch.
biocLite("mzR")

You cannot, in general, mix release and devel package versions in the same install.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Diego Diez700

Thank you for the fast response.

Sorry for misleading, I mixed output from two different attempts of installation: of mzR 2.2.1 and mzR 2.3.1. I tried several versions of mzR and R, result is the same - the same error messages.

 

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Eugene0

Could you clarify what you mean by "tried several versions" - have you tried using biocLite("mzR")? If that fails, please report the output of sessionInfo() in a new answer.

ADD REPLYlink written 2.3 years ago by Laurent Gatto840

Yes, I began with biocLite("mzR") ,  got that error message, and only after that I ran:

   R CMD INSTALL --no-clean-on-error  mzR_2.2.1.tar.gz.

sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Eugene0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 170 users visited in the last hour