private void checkInit(final int flags, final RService r, final IProgressMonitor monitor)
throws CoreException {
if ((flags & INITIAL) == INITIAL || fRPlatform == null) {
checkRVersion(r.getPlatform());
final IREnvConfiguration config = fREnv.getConfig();
if (config != null && config.isRemote()) {
fRLibGroups = REnvLibGroups.loadFromR(r, monitor);
}
}
}
private void runApplyRepo(
final ISelectedRepos repos, final RService r, final IProgressMonitor monitor)
throws CoreException {
monitor.subTask("Setting repository configuration...");
try {
if (repos.getBioCMirror() != null) {
final FunctionCall call = r.createFunctionCall("options");
call.addChar("BioC_mirror", repos.getBioCMirror().getURL());
call.evalVoid(monitor);
}
{
final List<RRepo> selectedRepos = (List<RRepo>) repos.getRepos();
final String[] ids = new String[selectedRepos.size()];
final String[] urls = new String[selectedRepos.size()];
for (int i = 0; i < urls.length; i++) {
final RRepo repo = selectedRepos.get(i);
ids[i] = repo.getId();
urls[i] = repo.getURL();
}
final RVector<RCharacterStore> data =
new RVectorImpl<RCharacterStore>(
new RCharacterDataImpl(urls), RObject.CLASSNAME_CHARACTER, ids);
final FunctionCall call = r.createFunctionCall("options");
call.add("repos", data);
call.evalVoid(monitor);
}
} catch (final CoreException e) {
throw new CoreException(
new Status(
IStatus.ERROR,
RCore.PLUGIN_ID,
"An error occurred when setting repository configuration in R.",
e));
}
}
private ISelectedRepos runLoadRepos(final RService r, final IProgressMonitor monitor)
throws CoreException {
try {
String bioCVersion;
{
final RObject data =
r.evalData("as.character(tools:::.BioC_version_associated_with_R_version)", monitor);
bioCVersion = RDataUtil.checkSingleCharValue(data);
}
final boolean loadRMirrors = ((fRequireLoad & (REQUIRE_CRAN | REQUIRE_BIOC)) != 0);
final boolean loadRRepos = ((fRequireLoad & (REQUIRE_REPOS)) != 0);
List<RRepo> rCRAN = null;
List<RRepo> rBioC = null;
String selectedCRAN = null;
RRepo rCRANByCountry = null;
String selectedBioC = null;
if (loadRMirrors) {
monitor.subTask("Fetching available mirrors...");
final String region = Locale.getDefault().getCountry().toLowerCase();
{
final RObject data =
r.evalData(
"getCRANmirrors()[c('Name', 'URL', 'CountryCode')]", monitor); // $NON-NLS-1$
final RDataFrame df = RDataUtil.checkRDataFrame(data);
final RCharacterStore names =
RDataUtil.checkRCharVector(df.get("Name")).getData(); // $NON-NLS-1$
final RCharacterStore urls =
RDataUtil.checkRCharVector(df.get("URL")).getData(); // $NON-NLS-1$
final RCharacterStore regions =
RDataUtil.checkRCharVector(df.get("CountryCode")).getData(); // $NON-NLS-1$
final int l = RDataUtil.checkIntLength(names);
rCRAN = new ArrayList<>(l);
for (int i = 0; i < l; i++) {
final String url = Util.checkURL(urls.getChar(i));
if (!url.isEmpty()) {
final RRepo repo = new RRepo(RRepo.R_PREFIX + url, names.getChar(i), url, null);
rCRAN.add(repo);
if (rCRANByCountry == null
&& !region.isEmpty()
&& region.equals(regions.getChar(i))) {
rCRANByCountry = repo;
}
}
}
}
{
final String[][] fix =
new String[][] {
{"Seattle (USA)", "http://www.bioconductor.org"},
{"Bethesda (USA)", "http://watson.nci.nih.gov/bioc_mirror"},
{"Dortmund (Germany)", "http://bioconductor.statistik.tu-dortmund.de"},
{"Bergen (Norway)", "http://bioconductor.uib.no"},
{"Cambridge (UK)", "http://mirrors.ebi.ac.uk/bioconductor"}
};
rBioC = new ArrayList<>(fix.length);
for (int i = 0; i < fix.length; i++) {
final String url = Util.checkURL(fix[i][1]);
if (!url.isEmpty()) {
rBioC.add(new RRepo(RRepo.R_PREFIX + url, fix[i][0], url, null));
}
}
}
}
List<RRepo> rrepos = null;
List<RRepo> selected = null;
if (loadRRepos) {
monitor.subTask("Fetching available repositories...");
{
final RObject data = r.evalData("options('repos')[[1L]]", monitor); // $NON-NLS-1$
if (data.getRObjectType() != RObject.TYPE_NULL) {
final RCharacterStore urls = RDataUtil.checkRCharVector(data).getData();
final RStore ids = ((RVector<?>) data).getNames();
final int l = RDataUtil.checkIntLength(urls);
selected = new ArrayList<>(l);
for (int i = 0; i < l; i++) {
final String id = (ids != null) ? ids.getChar(i) : null;
final String url = urls.getChar(i);
final RRepo repo = Util.createRepoFromR(id, null, url);
if (repo != null) {
selected.add(repo);
}
}
} else {
selected = new ArrayList<>(4);
}
}
final RObject data =
r.evalData(
"local({"
+ //$NON-NLS-1$
"p <- file.path(Sys.getenv('HOME'), '.R', 'repositories')\n"
+ //$NON-NLS-1$
"if (!file.exists(p)) p <- file.path(R.home('etc'), 'repositories')\n"
+ //$NON-NLS-1$
"r <- utils::read.delim(p, header = TRUE, comment.char = '#', colClasses = c(rep.int('character', 3L), rep.int('logical', 4L)))\n"
+ //$NON-NLS-1$
"r[c(names(r)[1L], 'URL', 'default')]\n"
+ //$NON-NLS-1$
"})",
monitor); //$NON-NLS-1$
final RDataFrame df = RDataUtil.checkRDataFrame(data);
final RStore ids = df.getRowNames();
final RCharacterStore labels = RDataUtil.checkRCharVector(df.get(0)).getData();
final RCharacterStore urls =
RDataUtil.checkRCharVector(df.get("URL")).getData(); // $NON-NLS-1$
final RLogicalStore isDefault =
(selected.isEmpty())
? RDataUtil.checkRLogiVector(df.get("default")).getData()
: null; //$NON-NLS-1$
{
final int l = RDataUtil.checkIntLength(labels);
rrepos = new ArrayList<>(l + 4);
for (int i = 0; i < l; i++) {
final String id = (ids != null) ? ids.getChar(i) : null;
final String url = urls.getChar(i);
final RRepo repo = Util.createRepoFromR(id, labels.getChar(i), url);
if (repo != null) {
rrepos.add(repo);
if (isDefault != null && isDefault.getLogi(i)) {
selected.add(repo);
}
}
}
}
for (int i = 0; i < selected.size(); i++) {
final RRepo repo = selected.get(i);
RRepo rrepo = null;
if (!repo.getURL().isEmpty()) {
rrepo = RPkgUtil.getRepoByURL(rrepos, repo.getURL());
}
if (rrepo != null) {
selected.set(i, rrepo);
continue;
}
if (!repo.getId().isEmpty()) {
final int j = rrepos.indexOf(repo); // by id
if (j >= 0) {
rrepo = rrepos.get(j);
if (!RVarRepo.hasVars(rrepo.getURL())) {
rrepo.setURL(repo.getURL());
}
selected.set(i, rrepo);
continue;
}
}
repo.setName(RRepo.hintName(repo));
continue;
}
}
if (loadRMirrors) {
if (loadRRepos) {
final RRepo repo = RPkgUtil.getRepoById(rrepos, RRepo.CRAN_ID);
if (repo != null && !repo.getURL().isEmpty() && !RVarRepo.hasVars(repo.getURL())) {
selectedCRAN = repo.getURL();
}
} else {
final RObject data = r.evalData("options('repos')[[1L]]['CRAN']", monitor); // $NON-NLS-1$
if (data.getRObjectType() != RObject.TYPE_NULL) {
final String url = Util.checkURL(RDataUtil.checkSingleChar(data));
if (!url.isEmpty() && !RVarRepo.hasVars(url)) {
selectedCRAN = url;
}
}
}
{
final RObject data = r.evalData("options('BioC_mirror')[[1L]]", monitor); // $NON-NLS-1$
if (data.getRObjectType() != RObject.TYPE_NULL) {
selectedBioC = RDataUtil.checkSingleChar(data);
}
}
}
getWriteLock().lock();
try {
fBioCVersion = bioCVersion;
if (loadRMirrors) {
fRequireLoad &= ~(REQUIRE_CRAN | REQUIRE_BIOC);
fRCRAN = rCRAN;
fRCRANByCountry = rCRANByCountry;
fSelectedCRANInR = selectedCRAN;
fRBioC = rBioC;
fSelectedBioCInR = selectedBioC;
fMirrorsStamp = fRTaskEvent.fStamp;
checkMirrors(fRTaskEvent);
}
if (loadRRepos) {
fRequireLoad &= ~(REQUIRE_REPOS);
fRRepos = rrepos;
fSelectedReposInR = selected;
checkRepos(fRTaskEvent);
}
fFirstTime = false;
if (getReposStatus(fSelectedRepos, fSelectedRepos, fRequireConfirm).isOK()) {
return fSelectedRepos;
}
return null;
} finally {
getWriteLock().unlock();
}
} catch (final Exception e) {
throw new CoreException(
new Status(
IStatus.ERROR,
RCore.PLUGIN_ID,
0,
"An error occurred when loading data for package manager.",
e));
}
}
private void checkInstalled(
final FullRPkgSet pkgs, final RService r, final IProgressMonitor monitor)
throws CoreException {
RVector<RNumericStore> libs = null;
boolean[] update = null;
try {
libs =
RDataUtil.checkRNumVector(r.evalData("rj:::.renv.checkLibs()", monitor)); // $NON-NLS-1$
final int l = RDataUtil.checkIntLength(libs.getData());
ITER_LIBS:
for (int idxLib = 0; idxLib < l; idxLib++) {
final String libPath = libs.getNames().getChar(idxLib);
if (fLibs != null) {
final int idx = (int) fLibs.getNames().indexOf(libPath);
if (idx >= 0) {
if (fLibs.getData().getNum(idx) == libs.getData().getNum(idxLib)) {
continue ITER_LIBS;
}
}
}
if (update == null) {
update = new boolean[l];
}
update[idxLib] = true;
}
fLibs = libs;
} catch (final UnexpectedRDataException | CoreException e) {
throw new CoreException(
new Status(
IStatus.ERROR,
RCore.PLUGIN_ID,
"An error occurred when checking for changed R libraries.",
e));
}
if (update != null || pkgs != null) {
if (fRTaskEvent == null) {
fRTaskEvent = new Change(fREnv);
}
if (fRTaskEvent.fOldPkgs == null) {
fRTaskEvent.fOldPkgs = getRPkgSet();
}
if (fPkgsExt != null || pkgs != null) {
final FullRPkgSet newPkgs = (pkgs != null) ? pkgs : fPkgsExt.cloneAvailable();
fRTaskEvent.fNewPkgs = newPkgs;
fRLibPaths = RLibPaths.create(getRLibGroups(), libs, r, monitor);
fPkgScanner.updateInstFull(fRLibPaths, update, newPkgs, fRTaskEvent, r, monitor);
} else {
final RPkgSet newPkgs = new RPkgSet((int) libs.getLength());
fRTaskEvent.fNewPkgs = newPkgs;
fRLibPaths = RLibPaths.createLight(getRLibGroups(), libs);
fPkgScanner.updateInstLight(fRLibPaths, update, newPkgs, fRTaskEvent, r, monitor);
}
if (fRTaskEvent.fInstalledPkgs != null && fRTaskEvent.fInstalledPkgs.names.isEmpty()) {
fRTaskEvent.fInstalledPkgs = null;
}
if (pkgs == null) {
setPkgs();
}
if (fRTaskEvent.fInstalledPkgs != null && fDB != null) {
fDB.updatePkgs(fRTaskEvent);
}
}
}