Troubleshooting

Problem 1: "std::unique_ptr" Is Reported During CMake Compilation

Symptom

"std::unique_ptr" is reported during CMake compilation, and the error message is "CMake Error at CMakeLists.txt:92 (message):

The C++ compiler does not support C++11 (e.g. std::unique_ptr)."

Possible Cause

This error is related to the system time setting.

Procedure

• After the system time is set correctly, decompress the source code package again for compilation.
• Run the following command to modify the CmakeCache.txt file:
  1. Open CmakeCache.txt.

     vi CmakeCache.txt

  2. Press i to enter the insert mode and modify line 362 of the file.

     CMake_HAVE_CXX_UNIQUE_PTR:INTERNAL=ON

  3. Press Esc, type :wq!, and press Enter to save the file and exit.
  4. Perform compilation and installation.

     make

Problem 2: "CMake Error at TBB-stamp" Is Reported During ROOT Compilation

Symptom

"CMake Error at TBB-stamp" is reported during ROOT compilation. The error information is similar to the following:

CMake Error at TBB-stamp/TBB-download-RelWithDebInfo.cmake:49 (message):

Command failed: 1

'/storage/softwares/TaiShan/CNVnator/CMAKE/bin/cmake' '-Dmake=' '-Dconfig=' '-P' '/storage/softwares/TaiShan/CNVnator/ROOT-6.18/TBB-prefix/src/TBB-stamp/TBB-download-RelWithDebInfo-impl.cmake'

Possible Cause

Such a failure to find the file is caused by the cluster's failure to connect to the network.

Procedure

Save the downloaded installation packages to the folder generated after CMake is installed. For details, see Installing CMake.

Problem 3: "[cnvnator] Error 1" Is Reported During CNVnator Compilation

Symptom

"[cnvnator] Error 1" is reported during CNVnator compilation. The error information is similar to the following:

/usr/bin/ld: samtools/htslib-1.9/libhts.a(hfile_s3.o): undefined reference to symbol 'HMAC@@libcrypto.so.10'

//usr/lib64/libcrypto.so.10: error adding symbols: DSO missing from command line

collect2: error: ld returned 1 exit status

make: *** [cnvnator] Error 1

Possible Cause

An error occurs during compilation and linking.

Procedure

Run the following make command:

make LIBS="-lcrypto"