Homebrew stop installation because openssl

[FF1683]

See screen with brew install gtDMMB/core/RNAStructViz this day

[maxieds]

Hello,

I'm Maxie, aka Christine's code goddess.

Try the following code snippets saved as the following in your current working directory: rnastructviz.rb. Then Run:

$ brew install rnastructviz.rb

If it works, I will push the change to main. It will be a few days before I can get back to you.

Files

(rnastructviz.rb)

class Rnastructviz < Formula
  desc "Graphical RNA secondary structure comparison multi-tool"
  homepage "https://github.com/gtDMMB/RNAStructViz/wiki"
  url "https://github.com/gtDMMB/RNAStructViz/archive/refs/tags/v2.4.18-beta.tar.gz"
  sha256 "f54e76af2683759204a0b9334bb3046ce8e49d289a4ce705e5a3bbb8e232a94d"
  version "v2.4.18-beta"
  revision 2
  
  depends_on "gtDMMB/core/fltkwithcairo"
  depends_on "gtDMMB/core/viennarna"
  depends_on "pkg-config"
  depends_on "curl"
  depends_on "coreutils"
  depends_on "grep"
  depends_on "gnu-sed"
  depends_on "openssl"
  depends_on "boost"

  # To maintainers: If this brew package becomes deprecated, replace the @12 with @MORE_RECENT_VERSION
  #                 throughout this formula.
  depends_on "llvm@12"
  depends_on :macos

  def install
    if MacOS.version >= :catalina
      llvm_path = "/usr/local/opt/llvm@12/"
      rsv_env = "STRUCTVIZ_COMPILER=\"" + llvm_path + "bin/clang++ -nostdinc++ -I" + llvm_path + "include/c++/v1\""
      # Add `brew` to the path (used in the RNAStructViz Makefile): 
      path_env = "PATH=\"/usr/local/bin:$PATH\" "
      system "/bin/bash -c '" + path_env + rsv_env + " make'"
    else
      system "CFLAGS=\"\" CXXFLAGS=\"\" LDFLAGS=\"\" make"
    end
    system "mv", "macos-application/RNAStructViz.app", "macos-application/RNAStructViz"
    system "cp", "src/RNAStructViz", "macos-application/RNAStructViz/Contents/MacOS/"
    system "cp", "-R", "macos-application/RNAStructViz", "macos-application/RNAStructViz.app"
    bin.install "src/RNAStructViz"
    prefix.install Dir["sample-structures"]
    prefix.install "macos-application/RNAStructViz.app"
  end
  
  def caveats; <<~EOS
    See RNAStructViz WIKI docs https://github.com/gtDMMB/RNAStructViz/wiki/FirstRunInstructions. 
    If your brew environment is configured correctly, you can now run `RNAStructViz` at your terminal.
  EOS
  end

  test do
    system "false"
  end
end

(rnastructviz.rb)

class Rnastructviz < Formula
  desc "Graphical RNA secondary structure comparison multi-tool"
  homepage "https://github.com/gtDMMB/RNAStructViz/wiki"
  url "https://github.com/gtDMMB/RNAStructViz/archive/refs/tags/v2.4.18-beta.tar.gz"
  sha256 "f54e76af2683759204a0b9334bb3046ce8e49d289a4ce705e5a3bbb8e232a94d"
  version "v2.4.18-beta"
  revision 2
  
  depends_on "gtDMMB/core/fltkwithcairo"
  depends_on "gtDMMB/core/viennarna"
  depends_on "pkg-config"
  depends_on "curl"
  depends_on "coreutils"
  depends_on "grep"
  depends_on "gnu-sed"
  depends_on "openssl@3.5"
  depends_on "boost"

  # To maintainers: If this brew package becomes deprecated, replace the @12 with @MORE_RECENT_VERSION
  #                 throughout this formula.
  depends_on "llvm@12"
  depends_on :macos

  def install
    if MacOS.version >= :catalina
      llvm_path = "/usr/local/opt/llvm@12/"
      rsv_env = "STRUCTVIZ_COMPILER=\"" + llvm_path + "bin/clang++ -nostdinc++ -I" + llvm_path + "include/c++/v1\""
      # Add `brew` to the path (used in the RNAStructViz Makefile): 
      path_env = "PATH=\"/usr/local/bin:$PATH\" "
      system "/bin/bash -c '" + path_env + rsv_env + " make'"
    else
      system "CFLAGS=\"\" CXXFLAGS=\"\" LDFLAGS=\"\" make"
    end
    system "mv", "macos-application/RNAStructViz.app", "macos-application/RNAStructViz"
    system "cp", "src/RNAStructViz", "macos-application/RNAStructViz/Contents/MacOS/"
    system "cp", "-R", "macos-application/RNAStructViz", "macos-application/RNAStructViz.app"
    bin.install "src/RNAStructViz"
    prefix.install Dir["sample-structures"]
    prefix.install "macos-application/RNAStructViz.app"
  end
  
  def caveats; <<~EOS
    See RNAStructViz WIKI docs https://github.com/gtDMMB/RNAStructViz/wiki/FirstRunInstructions. 
    If your brew environment is configured correctly, you can now run `RNAStructViz` at your terminal.
  EOS
  end

  test do
    system "false"
  end
end

[FF1683]

 Hello,

Thank you for fast reply. I work on Mac intel with Sequoia.
I never used ruby so maybe I’m wrong.
Instruction brew install rnastructviz.rb does not work with error Failed to load cask: rnastructviz.rb.
I don’t understand this instruction brew not using your snippet.

So, I tried Mac OSX install using Homebrew FLTK (with-cairo)
I have got fltkwithcairo/fltk-1.3.8-source-patched_15 not 1.4.x-r13071.
Nevertheless fltk-1.3 and fltk-1.4 work well both.

But before make clean && make && make run it’s necessary to comment or to delete the definition of static inline char* strchrnul(const char *s, int ch) in BuildTargetInfo.h.in. Clang gives strchrnul exists in string.h at line 198.
And now RNAStructViz runs very well with Sequoia !

I suggest to add in your wiki at the paragraph Completing the from-source install  between “Now we are ready to build the source:” an “make clean && make && make run”

Please verify your path as changing terminal window lost PATH.

Congratulations for your interesting software and his structure. I was searching an example in FLTK LINKS and I saw RNAStructViz v2.4.1-testing !

    François  

[maxieds]

@FF1683
Thank you for the compliments. RNAStructViz became my baby since 2018 while working with Christine getting my doctorate.

I do not have access to MacOS of the version you are using. Please humor us by testing a few things:

Try the following lines to see what gets reported. Note that MacOS C/C++ is spotty:

# Optional:
$ cd ~
$ mkdir RSV107Test
$ cd RSV107Test
# Run no matter what:
$ git clone https://github.com/gtDMMB/RNAStructViz
$ cd RNAStructViz
$ checkout issue107-testing
$ make clean && make && make run

Does this work on Sequoia?

[maxieds]

Hello,

I enclose `BuildTargetInfo.h.in` adding lines 37 and 52.

Without these two lines here it is the log with error at line 32.

Best regards,

François

Hello, the files you attached suggest that the build problem is with MacOS string functionality (which has changed over the years).

Please try to replace [BuildTargetInfo.h.in](http://buildtargetinfo.h.in/) with the following code, then build with your modifications. Note that it seems to be the strchrnull function definition that causes the error:

/* BuildTargetInfo.h(.in) : Local platform specific definitions inserted at compile time; 
 * Author: Maxie D. Schmidt (maxieds@gmail.com)
 * Created: 2018.10.31
 */

#ifndef __BUILD_TARGET_INFO_H__
#define __BUILD_TARGET_INFO_H__

#ifdef TARGETOS_LINUX
     #define __TARGETOS_LINUX__
     #define TARGETOS "GNU/Linux"
#elif defined(TARGETOS_OPENBSD)
     #define __TARGETOS_OPENBSD__
     #define TARGETOS "OpenBSD"
#elif defined(TARGETOS_FREEBSD) 
     #define __TARGETOS_FREEBSD__
     #define TARGETOS "FreeBSD"
#elif defined(TARGETOS_GNUHURD) 
     #define __TARGETOS_GNUHURD__
     #define TARGETOS "GNU/Hurd"
#elif defined(TARGETOS_MACOSX)
     #define __TARGETOS_APPLE__
     #define TARGETOS "MacOSX/Darwin"
#else 
     #define TARGETOS_GENERIC_UNIX
     #define __TARGETOS_UNIX__
     #define TARGETOS "Generic Unix (Unknown Build Target)"
#endif

#ifdef TARGETOS_MACOSX
     #ifndef __APPLE__
          #define __APPLE__
     #endif
     #ifndef strchrnul && !HAVE_STRCHRNUL
          #include <string.h>
          /* Mac OSX apparently does not support the strchrnul function: */
          //*
          static inline char* strchrnul(const char *s, int ch) 
          {
               if(s == NULL) 
               {
                    return NULL;
		       }
               char *strchrResult = (char *) strchr(s, ch);
               if(strchrResult == NULL) 
               {
                    size_t slen = strnlen(s, 2048);
                    return (char *) (s + slen);
               }
               return strchrResult;
          }
          //*/
     #else
          extern char *strchrnul(const char *s, int c);
     #endif
#endif

#ifdef __LOCAL_NOUSE_THREADS
     #undef _GLIBCXX__PTHREADS
     #undef _GLIBCXX_HAS_GTHREADS
     #ifdef __STDC_NO_THREADS__
          #undef __STDC_NO_THREADS__
     #endif
     #define __STDC_NO_THREADS__ (1)
#endif

#ifndef _GNU_SOURCE
     #define _GNU_SOURCE
#endif

#if __GNUC__ > 5
     #define GNU_CONST_STATIC_DECLARATION constexpr
#else
     #define GNU_CONST_STATIC_DECLARATION const
#endif

// Debugging settings with the -fsanitize=address flag:
#ifndef __RNASTRUCTVIZ_LOCAL_FSANITIZE_CONFIG
     #define __RNASTRUCTVIZ_LOCAL_FSANITIZE_CONFIG          (1)
     static inline const char* __asan_default_options() { 
          return "verbosity=1:malloc_context_size=20:detect_leaks=0:"
		 "detect_stack_use_after_return=1:print_stats=1:log_threads=1"; 
     }
#endif

#define FLTK_USE_CAIRO  1
#define FLTK_HAVE_CAIRO 1

#define ERRORS_TO_ISO8859_1   1      /* FLTK Unicode character encoding */

#ifndef BOOST_FILESYSTEM_NO_DEPRECATED
#define BOOST_FILESYSTEM_NO_DEPRECATED
#endif

#define __STRUCTVIZ_INSTALL_SIGNAL_HANDLERS
#define __STRUCTVIZ_INSTALL_SIGSEGV_HANDLER     1
#define __STRUCTVIZ_INSTALL_CTRLC_HANDLER       1

#define RNASTRUCTVIZ_VSTRING         ("🧬  RNAStructViz  v2.4.18-beta -- RNA Secondary Structure Comparison Multi-Tool")

#define HUGE_BUFFER_LINE_SIZE        (2048)

#include <stdlib.h>
#include <stdio.h>

#include <FL/Fl.H>
#include <FL/fl_ask.H>

#include <string>
using std::string;

class ApplicationBuildInfo {

     protected:
          inline static const char *GIT_RELEASE_TYPE      = "BETA-TESTING"; //"##__GIT_RELEASE_TYPE__##";
	      inline static const char *GIT_COMMIT_HASH       = "##__GIT_COMMITREV_HASHNUM__##";
          inline static const char *GIT_COMMIT_HASH_SHORT = "##__GIT_COMMITREV_HASHNUM_SHORT__##";
          inline static const char *GIT_COMMIT_DATE       = "##__GIT_COMMITREV_DATE__##";
          inline static const char *GIT_BRANCH_REVSTRING  = "##__GIT_DESCRIBE_REVSTRING__##";
          inline static const char *BUILD_PLATFORM_ID     = "##__BUILD_PLATFORM_ID__##";
          inline static const char *BUILD_DATETIME        = "##__LOCAL_BUILD_TIME__##";
          inline static const char *BUILD_FLTK_CONFIG     = "##__BUILD_FLTK_CONFIG__##";

     public:
       static inline string RNAStructVizFigletTextLogo() {
            static const char *figletTextLogoLines[] = {
                 "+-+-+-+-+-+-+-+-+-+-+-+-+",
                 "|R|N|A|S|t|r|u|c|t|V|i|z|",
                 "+-+-+-+-+-+-+-+-+-+-+-+-+",
	        };
            std::string figletTextLogo = std::string("");
            int numLogoLines = sizeof(figletTextLogoLines) / sizeof(figletTextLogoLines[0]);
            for(int line = 0; line < numLogoLines; line++) {
                 figletTextLogo += std::string(figletTextLogoLines[line]) + std::string("\n");
            }
            return figletTextLogo.substr(0, figletTextLogo.length() - 1);
       }
          
       static inline string UserManualWikiLink() {
               return string("User Manual: https://github.com/gtDMMB/RNAStructViz/wiki");
       }

       static inline string GitReleaseType() {
            string releaseDesc = string("Git Release Type: ") + string(GIT_RELEASE_TYPE);
	    return releaseDesc;
       }

       static inline string GitRevisionInfoFull() {
               char revString[HUGE_BUFFER_LINE_SIZE];
               snprintf(revString, HUGE_BUFFER_LINE_SIZE, 
                     "Git Revision: %s (%s) [%s]", 
                     GIT_COMMIT_HASH_SHORT, GIT_COMMIT_HASH, GIT_BRANCH_REVSTRING);
               revString[HUGE_BUFFER_LINE_SIZE - 1] = '\0';
               return string(revString);
       }

       static inline string GitRevisionInfo() {
               char revString[HUGE_BUFFER_LINE_SIZE];
               snprintf(revString, HUGE_BUFFER_LINE_SIZE, 
                     "Git Revision: %s [%s]", 
                     GIT_COMMIT_HASH_SHORT, GIT_BRANCH_REVSTRING);
               revString[HUGE_BUFFER_LINE_SIZE - 1] = '\0';
               return string(revString);
       }

       static inline string GitRevisionDate() {
               return string("Revision Date: ") + string(GIT_COMMIT_DATE);
       }

       static inline string BuildPlatform() {
            return string("Target Platform: ") + string(BUILD_PLATFORM_ID);
       }

       static inline string LocalBuildDateTime() {
            return string("Local Build Time: ") + string(BUILD_DATETIME);
       }

       static inline string BuildFLTKConfig() {
               return string("FLTK-Config: ") + 
                string(BUILD_FLTK_CONFIG);
       }

       static inline string CairoVersionString() {
               return string("Cairo Library: ") + string(CAIRO_VERSION_STRING);
       }

       static inline string FLTKVersionString() {
            char fltkVersionStr[HUGE_BUFFER_LINE_SIZE];
            snprintf(fltkVersionStr, HUGE_BUFFER_LINE_SIZE - 1, 
                     "%d.%d.%d (API #%d)", 
                     FL_MAJOR_VERSION, FL_MINOR_VERSION, FL_PATCH_VERSION, FL_API_VERSION);
            fltkVersionStr[HUGE_BUFFER_LINE_SIZE - 1] = '\0';
            return string("FLTK Library: ") + string(fltkVersionStr);
       }

       static inline void PrintAboutListing(const char *aboutStr = NULL, FILE *whichOut = stderr) {
            if(whichOut == NULL) {
                    whichOut = stderr;
            }
            fprintf(whichOut, "%s\n\n", RNAStructVizFigletTextLogo().c_str());
            fprintf(whichOut, "==== %s ====\n\n", RNASTRUCTVIZ_VSTRING);
            fprintf(whichOut, "ABOUT THIS APPLICATION:\n");
            if(aboutStr == NULL) {
                    fprintf(whichOut, "   >>%s\n   >> %s\n   >> %s\n   >> %s\n   >> %s\n   >> %s\n   >> %s\n   >> %s\n   >> %s\n\n", 
                                      UserManualWikiLink().c_str(), 
				      GitReleaseType().c_str(), GitRevisionInfoFull().c_str(), 
                                      GitRevisionDate().c_str(), FLTKVersionString().c_str(),
                                      BuildFLTKConfig().c_str(),  
                                      CairoVersionString().c_str(), BuildPlatform().c_str(), 
                                      LocalBuildDateTime().c_str());
            }
            else {
                 fprintf(whichOut, "%s\n\n", aboutStr);
            }
	    for(unsigned int chi = 0; chi < strlen(RNASTRUCTVIZ_VSTRING); chi++) {
	         fprintf(whichOut, "=");
	    }
	    fprintf(whichOut, "\n\n");
            const char *bugReportMsg = "Please include a screenshot along with this information in any bug report you submit.\n"
                                       "   New issues with the application can be submitted by following the instructions at\n" 
                                       "   « https://github.com/gtDMMB/RNAStructViz/wiki/BugReportingAndErrors »";
            fprintf(whichOut, "BUG REPORT INFORMATION:\n** %s **\n", bugReportMsg);
       }

};

#endif

Original files:

Log RSV107Test.txt
BuildTargetInfo.h.in.txt.txt

[maxieds]

@FF1683 @ceheitsch
Did that change let you build RNAStructViz? It's important that you let me know because you might eventually need to re-clone the source, in which case we need to have everything patched.