private void checkMirrors(final Change event) {
if ((fRequireLoad & (REQUIRE_CRAN | REQUIRE_BIOC)) != 0) {
return;
}
SelectedRepos selected = fSelectedRepos;
fAllCRAN = ConstArrayList.concat(fCustomCRAN, fRCRAN);
RRepo selectedCRAN = selected.getCRANMirror();
if (selected.getCRANMirror() != null) {
selectedCRAN = Util.findRepo(fAllCRAN, selectedCRAN);
} else if (fFirstTime && fSelectedCRANInR != null) {
selectedCRAN = Util.getRepoByURL(fAllCRAN, fSelectedCRANInR);
}
if (selectedCRAN == null) {
fRequireConfirm |= REQUIRE_CRAN;
selectedCRAN = PreferencesUtil.getInstancePrefs().getPreferenceValue(LAST_CRAN_PREF);
if (selectedCRAN != null) {
selectedCRAN = Util.findRepo(fAllCRAN, selectedCRAN);
}
if (!fCustomCRAN.isEmpty()
&& (selectedCRAN == null || !selectedCRAN.getId().startsWith(RRepo.CUSTOM_PREFIX))) {
selectedCRAN = fCustomCRAN.get(0);
}
if (fFirstTime && selectedCRAN == null) {
selectedCRAN = fRCRANByCountry;
}
}
RRepo selectedBioC = selected.getBioCMirror();
fAllBioC = ConstArrayList.concat(fCustomBioC, fRBioC);
if (selectedBioC != null) {
selectedBioC = Util.findRepo(fAllBioC, selectedBioC);
} else if (fFirstTime && fSelectedBioCInR != null) {
selectedBioC = RPkgUtil.getRepoByURL(fAllBioC, fSelectedBioCInR);
}
if (selectedBioC == null) {
fRequireConfirm |= REQUIRE_BIOC;
selectedBioC = PreferencesUtil.getInstancePrefs().getPreferenceValue(LAST_BIOC_PREF);
if (!fCustomBioC.isEmpty()
&& (selectedBioC == null || !selectedBioC.getId().startsWith(RRepo.CUSTOM_PREFIX))) {
selectedBioC = fCustomBioC.get(0);
}
if (fFirstTime && selectedBioC == null) {
selectedBioC = Util.getRepoByURL(fAllBioC, "http://www.bioconductor.org"); // $NON-NLS-1$
}
}
selected = new SelectedRepos(selected.getRepos(), selectedCRAN, fBioCVersion, selectedBioC);
if ((fRequireLoad & (REQUIRE_REPOS)) == 0) {
for (final RRepo repo : fAllRepos) {
if (repo instanceof RVarRepo) {
((RVarRepo) repo).updateURL(selected);
}
}
}
fSelectedRepos = selected;
event.fPkgs = 1;
}
private void setPkgs() {
final Change event = fRTaskEvent;
if (event.fNewPkgs instanceof FullRPkgSet) {
fPkgsExt = (FullRPkgSet) event.fNewPkgs;
fPkgsLight = null;
} else if (event.fNewPkgs instanceof RPkgSet) {
fPkgsExt = null;
fPkgsLight = (RPkgSet) event.fNewPkgs;
}
if (event.fInstalledPkgs != null) {
event.fPkgs |= INSTALLED;
}
}
private void runLoadPkgs(
final ISelectedRepos repoSettings, final RService r, final IProgressMonitor monitor)
throws CoreException {
final boolean loadRepoPkgs =
(fRequireLoad & (REQUIRE_REPO_PKGS)) != 0 && getReposStatus(repoSettings).isOK();
final boolean loadInstPkgs = ((fRequireLoad & (REQUIRE_INST_PKGS)) != 0);
FullRPkgSet pkgs = null;
if (loadRepoPkgs) {
fRTaskEvent.fOldPkgs = getRPkgSet();
fRTaskEvent.fNewPkgs = pkgs = fPkgScanner.loadAvailable(repoSettings, r, monitor);
}
if (loadInstPkgs) {
if (pkgs == null) {
if (fPkgsExt != null) {
pkgs = fPkgsExt.cloneAvailable();
} else {
pkgs = new FullRPkgSet(0);
}
}
checkInstalled(pkgs, r, monitor);
updateRViews(repoSettings, pkgs, r, monitor);
}
if (pkgs != null) {
getWriteLock().lock();
try {
setPkgs();
if (loadRepoPkgs) {
fRequireLoad &= ~REQUIRE_REPO_PKGS;
fPkgsStamp = fRTaskEvent.fStamp;
fRTaskEvent.fPkgs |= AVAILABLE;
}
if (loadInstPkgs) {
fRequireLoad &= ~REQUIRE_INST_PKGS;
}
} finally {
getWriteLock().unlock();
}
}
}
