Confirming build works with blank (standard user) account settings on my home Mac mini

[maxieds]

@ceheitsch
I used the SOM support instructions to setup a new blank (standard user) account on my home Mac mini (as I indicated in the GTFoldPython issue on this topic -- GH Enterprise). I was able to build gtfold (this repo) using the following command:

$ cmake -v . -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER="/usr/local/opt/llvm/bin/clang" \
     -DCMAKE_CXX_COMPILER="/usr/local/opt/llvm/bin/clang++" \
     -DCMAKE_C_LINK_EXECUTABLE="/usr/local/opt/llvm/bin/ld.lld" \
     -DMACOS_OFFICE_BOX=1
$ make
$ echo "aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaaca
> caugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacgaguggcggacggg
> ugaguaaugucugggaaacugccugauggagggggauaacuacuggaaacgguagcuaau
> accgcauaacgucgcaagaccaaagagggggaccuucgggccucuugccaucggaugugc
> ccagaugggauuagcuaguaggugggguaacggcucaccuaggcgacgaucccuagcugg
> ucugagaggaugaccagccacacuggaacugagacacgguccagacuccuacgggaggca
> gcaguggggaauauugcacaaugggcgcaagccugaugcagccaugccgcguguaugaag
> aaggccuucggguuguaaaguacuuucagcggggaggaagggaguaaaguuaauaccuuu
> gcucauugacguuacccgcagaagaagcaccggcuaacuccgugccagcagccgcgguaa
> uacggagggugcaagcguuaaucggaauuacugggcguaaagcgcacgcaggcgguuugu
> uaagucagaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaagcuu
> gagucucguagagggggguagaauuccagguguagcggugaaaugcguagagaucuggag
> gaauaccgguggcgaaggcggcccccuggacgaagacugacgcucaggugcgaaagcgug
> gggagcaaacaggauuagauacccugguaguccacgccguaaacgaugucgacuuggagg
> uugugcccuugaggcguggcuuccggagcuaacgcguuaagucgaccgccuggggaguac
> ggccgcaagguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaugug
> guuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccacggaaguuuucag
> agaugagaaugugccuucgggaaccgugagacaggugcugcauggcugucgucagcucgu
> guugugaaauguuggguuaagucccgcaacgagcgcaacccuuauccuuuguugccagcg
> guccggccgggaacucaaaggagacugccagugauaaacuggaggaagguggggaugacg
> ucaagucaucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaag
> agaagcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccggauuggagu
> cugcaacucgacuccaugaagucggaaucgcuaguaaucguggaucagaaugccacggug
> aauacguucccgggccuuguacacaccgcccgucacaccaugggaguggguugcaaaaga
> aguagguagcuuaaccuucgggagggcgcuuaccacuuugugauucaugacuggggugaa
> gucguaacaagguaaccguaggggaaccugcgguuggaucaccuccuua" > ecoli.txt
$ ./bin/gtmfe ecoli.txt 
GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction
(c) 2007-2011  D.A. Bader, C.E. Heitsch, S.C. Harvey
Georgia Institute of Technology

Run Configuration:
- standard
- thermodynamic parameters: /Users/maxieds-gtdmmb/GTDMMBSoftwareProjects/gtfold/gtfold-mfe/data/Turner99/
- input file: ecoli.txt
- sequence length: 1542
- output file: ecoli.ct

Computing minimum free energy structure...
Done.

Results:
- Minimum Free Energy:    -618.2000 kcal/mol
- MFE runtime:  4.272769 seconds


AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
........((((((...(.(((((..(((....((((((((((((..........(((.(.(((..((((.....(((((((....))))))))))).))).).)))...(((((((....(((((((..((...(((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).)))))))..)).)))))))((((((.(((..((((((((.......)))))))))))...))))))..(((.((.((.(.((((((((..((((.(((((.(((.....)))))))).((((....))))......))))..((((((.((((((.(((....))).(((((((((((((.((..........((((.(((((.((((((..(((((..(.(((((..(..((.((((((((.......)))))))).))..)....))))).......(((((......(((((((((.((....)))))...)))))))))))..(((...((((......((((((((...((....))....(((((((((.((((((((((...((((.((......)).))))..))))))))))..)))))))))..((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)))))))).((((...(((((((..((...((((.........))))))..)))))))))))..))))((((((((((((((..((((.....))))..))))))...((....))...)))))))))))...)..))))).(((....)))...........(((((((((((....)))((((.((......)).))))..)))))))).)))))).)))))..))))(((((.(((.......(((((..(((((((....)))))))...((....))..))))))))))))))).))))))))).)))).......)))))).)))))).))))..))))).)))).)))......))))))).))))))))))))))).)))))))))))).((((((.((.(((((.....))))))).(((((((.((((((.....))))))...(((((..(((..((((((((...((..((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))..))..........(((((((((..((((((.....((((.((.((...(((((((.........)))))))...))))))))(((((..((....))..)))))......))))))..)))))))))..........)))))....))))))..))))).....)))))))(((((((..((((.......))))..........(((((((((....)))))))))))))))))))))).

MFE structure saved in .ct format to ecoli.ct

I also wanted to test the secondary configuration for cmake we came up with for another one of your spare Mac boxes. To do this I ran the following:

$ rm -rf CMakeFiles/
$ cmake -v . -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER="/usr/local/opt/llvm/bin/clang" \
     -DCMAKE_CXX_COMPILER="/usr/local/opt/llvm/bin/clang++" \
     -DCMAKE_C_LINK_EXECUTABLE="/usr/local/opt/llvm/bin/ld.lld" \
     -DMAC_ISYSROOT_PATH="/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr" 
$ make
$ ./bin/gtmfe ecoli.txt 
GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction
(c) 2007-2011  D.A. Bader, C.E. Heitsch, S.C. Harvey
Georgia Institute of Technology

Run Configuration:
- standard
- thermodynamic parameters: /Users/maxieds-gtdmmb/GTDMMBSoftwareProjects/gtfold/gtfold-mfe/data/Turner99/
- input file: ecoli.txt
- sequence length: 1542
- output file: ecoli.ct

Computing minimum free energy structure...
Done.

Results:
- Minimum Free Energy:    -618.2000 kcal/mol
- MFE runtime:  4.192864 seconds


AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
........((((((...(.(((((..(((....((((((((((((..........(((.(.(((..((((.....(((((((....))))))))))).))).).)))...(((((((....(((((((..((...(((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).)))))))..)).)))))))((((((.(((..((((((((.......)))))))))))...))))))..(((.((.((.(.((((((((..((((.(((((.(((.....)))))))).((((....))))......))))..((((((.((((((.(((....))).(((((((((((((.((..........((((.(((((.((((((..(((((..(.(((((..(..((.((((((((.......)))))))).))..)....))))).......(((((......(((((((((.((....)))))...)))))))))))..(((...((((......((((((((...((....))....(((((((((.((((((((((...((((.((......)).))))..))))))))))..)))))))))..((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)))))))).((((...(((((((..((...((((.........))))))..)))))))))))..))))((((((((((((((..((((.....))))..))))))...((....))...)))))))))))...)..))))).(((....)))...........(((((((((((....)))((((.((......)).))))..)))))))).)))))).)))))..))))(((((.(((.......(((((..(((((((....)))))))...((....))..))))))))))))))).))))))))).)))).......)))))).)))))).))))..))))).)))).)))......))))))).))))))))))))))).)))))))))))).((((((.((.(((((.....))))))).(((((((.((((((.....))))))...(((((..(((..((((((((...((..((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))..))..........(((((((((..((((((.....((((.((.((...(((((((.........)))))))...))))))))(((((..((....))..)))))......))))))..)))))))))..........)))))....))))))..))))).....)))))))(((((((..((((.......))))..........(((((((((....)))))))))))))))))))))).

MFE structure saved in .ct format to ecoli.ct

Therefore, I conclude that both are sane cmake configuration files for Mac/Mojave/10.14. I am not sure what is going on with the systems that you are not able to build on. Can you make yourself a new account using these instructions, and then run the following (to see if it works):

$ su - mynewusername && source ~/.bash_profile
$ mkdir GTDMMBSoftwareProjects && cd GTDMMBSoftwareProjects
$ git clone https://github.com/gtDMMB/gtfold.git
$ cd gtfold

Then follow the build instructions I created here?