nextflow
nextflow copied to clipboard
Unexpected warning message
After upgrading to JGit 6.1, the following warn message is reported in the log file.
Jun-08 19:01:52.220 [main] WARN org.eclipse.jgit.util.FS - Cannot run program "[?7h/usr/bin/git" (in directory "[?7h/usr/bin"): error=2, No such file or directory
It should be investigated the reason for this message and how to avoid it
it seems only to happen in Mac and if git is not in /usr/bin
in version 5 they only check if the file is present but from version 6 it seems the library is trying to execute before validating the path:
DEFAULT_GIT_LOCATION is a String = '/usr/bin/git'
protected File discoverGitExe() {
String path = SystemReader.getInstance().getenv("PATH"); //$NON-NLS-1$
File gitExe = searchPath(path, "git"); //$NON-NLS-1$
if (SystemReader.getInstance().isMacOS()) {
if (gitExe == null
|| DEFAULT_GIT_LOCATION.equals(gitExe.getPath())) {
if (searchPath(path, "bash") != null) { //$NON-NLS-1$
// On MacOSX, PATH is shorter when Eclipse is launched from the
// Finder than from a terminal. Therefore try to launch bash as a
// login shell and search using that.
try {
String w = readPipe(userHome(),
new String[]{"bash", "--login", "-c", "which git"}, // //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
....
} catch (CommandFailedException e) {
LOG.warn(e.getMessage());
}
Weird that jgit tries to use git
!
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.
Looks solved