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Troubleshooting

Problem 1: Error Message "undefined reference to lzma" Is Reported During Cufflinks Compilation

Symptom

An error message "undefined reference to'lzma_stream_buffer_bound'" is reported when Cufflinks is compiled.

Possible Causes

The LZMA dependency package is not installed.

Procedure

Run the following command to install xz-devel.aarch64:

yum install xz-devel.aarch64

Problem 2: Error Message "could not detect bam" Is Displayed During Cufflinks Compilation

Symptom

An error message "error:we cand not detect bam"is reported when Cufflinks is compiled.

Possible Causes

  • The configure file is incorrectly configured.
  • <bam/version.hpp> is used to determine the BAM version in the configure file.

Procedure

  • If the configure file is incorrectly configured:
    Run the following commands to modify the configure file:
    1. Open configure.
      vi configure
    2. Press i to enter the insert mode and change no to yes in line 5380 of the file.
      succeeded=yes
    3. Press Esc, type :wq!, and press Enter to save the file and exit.
  • If <bam/version.hpp> is used to determine the BAM version in the configure file (actually version.h is the version file of the BAM):
    Run the following commands to modify the configure file:
    1. Open configure.
      vi configure
    2. Press i to enter the insert mode and change bam/version.hpp to bam/version.h.
      bam/version.h
    3. Press Esc, type :wq!, and press Enter to save the file and exit.

Problem 3: Error Message "could not find htslib" Is Displayed During Cufflinks Compilation

Symptom

An error message "could not find htslib"is reported when Cufflinks is compiled.

Possible Causes

The built-in HTSlib of SAMtools is used, which is not supported in the current version.

Procedure

Install HTSlib independently and copy the generated libhts.* file to the lib directory.

Run the following commands to install HTSlib:

tar -xvf htslib-1.9.tar.bz2
cd htslib-1.9
make
cp libhts.* /usr/local/lib

Problem 4: Error Message "GHash.hh:91:44: error" Is Displayed During Cufflinks Compilation

Symptom

An error is reported when Cufflinks is compiled. The error information is as follows:

GHash.hh:91:44: error: type/value mismatch at argument 1 in template parameter list for 'template<class _Tp> struct std::hash'
91 |     while (pos<fCapacity && hash[pos].hash<0) pos++;
|                                            ^

Possible Causes

The Cufflinks source code has a bug, which has been fixed in the latest master release.

Procedure

Download the latest Cufflinks installation package.

https://codeload.github.com/cole-trapnell-lab/cufflinks/zip/master

Problem 5: Error Message "error while loading shared libraries" Is Displayed During the Test

Symptom

An error message similar to "error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory" is displayed during the test.

Possible Causes

The HTSlib environment variables have not been added.

Procedure

  1. Use PuTTY to log in to the server as the root user.
  2. Run the following command to specify the HTSlib address:
    export LD_LIBRARY_PATH=/path/to/HTSLIB/htslib-1.9:$LD_LIBRARY_PATH