mzR installation error: "unable to load shared object"
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Entering edit mode
Eugene • 0
@eugene-8477
Last seen 9.4 years ago
United States

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?
mzR installation • 6.6k views
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2
Entering edit mode

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. 

 

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Entering edit mode

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?

 

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Entering edit mode

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

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Entering edit mode

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)
<------------------------------------

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0
Entering edit mode

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

 

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0
Entering edit mode

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?

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1
Entering edit mode

Maybe zlib?

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0
Entering edit mode

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)
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0
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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?

 

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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

 

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

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1
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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.

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0
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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.

 

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0
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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.

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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

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