text: user4595: I am trying to installing Vep on Linux but an error is permanent
  [fi1d18@cyan01 ensembl-vep-release-95]$ perl INSTALL.pl
  
  Hello! This installer is configured to install v95 of the Ensembl API for use by the VEP.
  It will not affect any existing installations of the Ensembl API that you may have.
  
  It will also download and install cache files from Ensembl's FTP server.
  
  Checking for installed versions of the Ensembl API...done
  
  Setting up directories
  Destination directory ./Bio already exists.
  Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
   - fetching BioPerl
   - unpacking ./Bio/tmp/release-1-6-924.zip
   - moving files
  Attempting to install Bio::DB::HTS and htslib.
  
  >>> If this fails, try re-running with --NO_HTSLIB
  
   - checking out HTSLib
  fatal: destination path 'htslib' already exists and is not an empty directory.
   - building HTSLIB in ./htslib
  In /home/fi1d18/ensembl-vep/ensembl-vep-release-95/htslib
  gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_io.o cram/cram_io.c
  cram/cram_io.c:61:18: error: lzma.h: No such file or directory
  cram/cram_io.c: In function 'lzma_mem_deflate':
  cram/cram_io.c:679: warning: implicit declaration of function 'lzma_stream_buffer_bound'
  cram/cram_io.c:685: error: 'LZMA_OK' undeclared (first use in this function)
  cram/cram_io.c:685: error: (Each undeclared identifier is reported only once
  cram/cram_io.c:685: error: for each function it appears in.)
  cram/cram_io.c:685: warning: implicit declaration of function 'lzma_easy_buffer_encode'
  cram/cram_io.c:685: error: 'LZMA_CHECK_CRC32' undeclared (first use in this function)
  cram/cram_io.c: In function 'lzma_mem_inflate':
  cram/cram_io.c:695: error: 'lzma_stream' undeclared (first use in this function)
  cram/cram_io.c:695: error: expected ';' before 'strm'
  cram/cram_io.c:701: error: 'LZMA_OK' undeclared (first use in this function)
  cram/cram_io.c:701: warning: implicit declaration of function 'lzma_stream_decoder'
  cram/cram_io.c:701: error: 'strm' undeclared (first use in this function)
  cram/cram_io.c:701: warning: implicit declaration of function 'lzma_easy_decoder_memusage'
  cram/cram_io.c:719: warning: implicit declaration of function 'lzma_code'
  cram/cram_io.c:719: error: 'LZMA_RUN' undeclared (first use in this function)
  cram/cram_io.c:720: error: 'LZMA_STREAM_END' undeclared (first use in this function)
  cram/cram_io.c:732: error: 'LZMA_FINISH' undeclared (first use in this function)
  cram/cram_io.c:743: warning: implicit declaration of function 'lzma_end'
  At top level:
  cc1: warning: unrecognized command line option "-Wno-unused-result"
  make: *** [cram/cram_io.o] Error 1
  Compile didn't complete. No libhts.a library file found at INSTALL.pl line 820.
  [fi1d18@cyan01 ensembl-vep-release-95]$
  
  And
  [fi1d18@cyan01 ensembl-vep]$ perl INSTALL.pl --NO_HTSLIB
  
  Hello! This installer is configured to install v95 of the Ensembl API for use by the VEP.
  It will not affect any existing installations of the Ensembl API that you may have.
  
  It will also download and install cache files from Ensembl's FTP server.
  
  Checking for installed versions of the Ensembl API...done
  
  Setting up directories
  Destination directory ./Bio already exists.
  Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
   - fetching BioPerl
   - unpacking ./Bio/tmp/release-1-6-924.zip
   - moving files
  
  Downloading required Ensembl API files
   - fetching ensembl
   - unpacking ./Bio/tmp/ensembl.zip
   - moving files
   - getting version information
   - fetching ensembl-variation
   - unpacking ./Bio/tmp/ensembl-variation.zip
   - moving files
   - getting version information
   - fetching ensembl-funcgen
   - unpacking ./Bio/tmp/ensembl-funcgen.zip
   - moving files
   - getting version information
   - fetching ensembl-io
   - unpacking ./Bio/tmp/ensembl-io.zip
   - moving files
   - getting version information
  
  Testing VEP installation
  ERROR: Testing VEP script failed with the following error
  Can't locate Time/HiRes.pm in @INC (@INC contains: /home/fi1d18/ensembl-vep/modules /home/fi1d18/ensembl-vep ./Bio /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/Utils/SqlHelper.pm line 93.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/Utils/SqlHelper.pm line 93.
  Compilation failed in require at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm line 81.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm line 81.
  Compilation failed in require at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/DBSQL/DBAdaptor.pm line 69.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/DBSQL/DBAdaptor.pm line 69.
  Compilation failed in require at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/Registry.pm line 137.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/Registry.pm line 137.
  Compilation failed in require at /home/fi1d18/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
  Compilation failed in require at (eval 7) line 3.
          ...propagated at /usr/share/perl5/base.pm line 94.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
  Compilation failed in require at (eval 6) line 3.
          ...propagated at /usr/share/perl5/base.pm line 94.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
  Compilation failed in require at ./vep line 20.
  BEGIN failed--compilation aborted at ./vep line 20.
  
  [fi1d18@cyan01 ensembl-vep]$
  
  
  user1310: What you can try is stated out in the message:
  
  If this fails, try re-running with --NO_HTSLIB
  
  
original_text: 4595: <p>I am trying to installing Vep on Linux but an error is permanent</p>
  
  <pre><code>[fi1d18@cyan01 ensembl-vep-release-95]$ perl INSTALL.pl
  
  Hello! This installer is configured to install v95 of the Ensembl API for use by the VEP.
  It will not affect any existing installations of the Ensembl API that you may have.
  
  It will also download and install cache files from Ensembl's FTP server.
  
  Checking for installed versions of the Ensembl API...done
  
  Setting up directories
  Destination directory ./Bio already exists.
  Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
   - fetching BioPerl
   - unpacking ./Bio/tmp/release-1-6-924.zip
   - moving files
  Attempting to install Bio::DB::HTS and htslib.
  
  &gt;&gt;&gt; If this fails, try re-running with --NO_HTSLIB
  
   - checking out HTSLib
  fatal: destination path 'htslib' already exists and is not an empty directory.
   - building HTSLIB in ./htslib
  In /home/fi1d18/ensembl-vep/ensembl-vep-release-95/htslib
  gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I.  -c -o cram/cram_io.o cram/cram_io.c
  cram/cram_io.c:61:18: error: lzma.h: No such file or directory
  cram/cram_io.c: In function 'lzma_mem_deflate':
  cram/cram_io.c:679: warning: implicit declaration of function 'lzma_stream_buffer_bound'
  cram/cram_io.c:685: error: 'LZMA_OK' undeclared (first use in this function)
  cram/cram_io.c:685: error: (Each undeclared identifier is reported only once
  cram/cram_io.c:685: error: for each function it appears in.)
  cram/cram_io.c:685: warning: implicit declaration of function 'lzma_easy_buffer_encode'
  cram/cram_io.c:685: error: 'LZMA_CHECK_CRC32' undeclared (first use in this function)
  cram/cram_io.c: In function 'lzma_mem_inflate':
  cram/cram_io.c:695: error: 'lzma_stream' undeclared (first use in this function)
  cram/cram_io.c:695: error: expected ';' before 'strm'
  cram/cram_io.c:701: error: 'LZMA_OK' undeclared (first use in this function)
  cram/cram_io.c:701: warning: implicit declaration of function 'lzma_stream_decoder'
  cram/cram_io.c:701: error: 'strm' undeclared (first use in this function)
  cram/cram_io.c:701: warning: implicit declaration of function 'lzma_easy_decoder_memusage'
  cram/cram_io.c:719: warning: implicit declaration of function 'lzma_code'
  cram/cram_io.c:719: error: 'LZMA_RUN' undeclared (first use in this function)
  cram/cram_io.c:720: error: 'LZMA_STREAM_END' undeclared (first use in this function)
  cram/cram_io.c:732: error: 'LZMA_FINISH' undeclared (first use in this function)
  cram/cram_io.c:743: warning: implicit declaration of function 'lzma_end'
  At top level:
  cc1: warning: unrecognized command line option "-Wno-unused-result"
  make: *** [cram/cram_io.o] Error 1
  Compile didn't complete. No libhts.a library file found at INSTALL.pl line 820.
  [fi1d18@cyan01 ensembl-vep-release-95]$
  </code></pre>
  
  <p>And</p>
  
  <pre><code>[fi1d18@cyan01 ensembl-vep]$ perl INSTALL.pl --NO_HTSLIB
  
  Hello! This installer is configured to install v95 of the Ensembl API for use by the VEP.
  It will not affect any existing installations of the Ensembl API that you may have.
  
  It will also download and install cache files from Ensembl's FTP server.
  
  Checking for installed versions of the Ensembl API...done
  
  Setting up directories
  Destination directory ./Bio already exists.
  Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
   - fetching BioPerl
   - unpacking ./Bio/tmp/release-1-6-924.zip
   - moving files
  
  Downloading required Ensembl API files
   - fetching ensembl
   - unpacking ./Bio/tmp/ensembl.zip
   - moving files
   - getting version information
   - fetching ensembl-variation
   - unpacking ./Bio/tmp/ensembl-variation.zip
   - moving files
   - getting version information
   - fetching ensembl-funcgen
   - unpacking ./Bio/tmp/ensembl-funcgen.zip
   - moving files
   - getting version information
   - fetching ensembl-io
   - unpacking ./Bio/tmp/ensembl-io.zip
   - moving files
   - getting version information
  
  Testing VEP installation
  ERROR: Testing VEP script failed with the following error
  Can't locate Time/HiRes.pm in @INC (@INC contains: /home/fi1d18/ensembl-vep/modules /home/fi1d18/ensembl-vep ./Bio /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/Utils/SqlHelper.pm line 93.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/Utils/SqlHelper.pm line 93.
  Compilation failed in require at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm line 81.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/DBSQL/DBConnection.pm line 81.
  Compilation failed in require at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/DBSQL/DBAdaptor.pm line 69.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/DBSQL/DBAdaptor.pm line 69.
  Compilation failed in require at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/Registry.pm line 137.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/Bio/EnsEMBL/Registry.pm line 137.
  Compilation failed in require at /home/fi1d18/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 58.
  Compilation failed in require at (eval 7) line 3.
          ...propagated at /usr/share/perl5/base.pm line 94.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
  Compilation failed in require at (eval 6) line 3.
          ...propagated at /usr/share/perl5/base.pm line 94.
  BEGIN failed--compilation aborted at /home/fi1d18/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
  Compilation failed in require at ./vep line 20.
  BEGIN failed--compilation aborted at ./vep line 20.
  
  [fi1d18@cyan01 ensembl-vep]$
  </code></pre>
   1310: <p>What you can try is stated out in the message:</p>
  
  <blockquote>
    <p>If this fails, try re-running with --NO_HTSLIB</p>
  </blockquote>
  