From 1f3032e1730aee9c123a8938364f90bf5ae0e10b Mon Sep 17 00:00:00 2001
From: Mick Jordan <mick.jordan@oracle.com>
Date: Wed, 23 Sep 2015 15:58:33 -0700
Subject: [PATCH] more compression support for package installation
---
.../r/nodes/builtin/base/BasePackage.java | 1 +
.../builtin/base/HiddenInternalFunctions.java | 49 ++++--
.../r/nodes/builtin/base/LoadFunctions.java | 76 ++++++++-
.../truffle/r/runtime/RCompression.java | 158 +++++++++++++++++-
.../com/oracle/truffle/r/runtime/RError.java | 6 +-
.../r/runtime/conn/GZIPConnections.java | 48 +++++-
.../r/install.cran.packages.R | 6 +-
7 files changed, 309 insertions(+), 35 deletions(-)
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/BasePackage.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/BasePackage.java
index c3a5f2e4c4..c41434b4ae 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/BasePackage.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/BasePackage.java
@@ -344,6 +344,7 @@ public class BasePackage extends RBuiltinPackage {
add(Length.class, LengthNodeGen::create);
add(License.class, LicenseNodeGen::create);
add(ListBuiltin.class, ListBuiltinNodeGen::create);
+ add(LoadFunctions.Load.class, LoadFunctionsFactory.LoadNodeGen::create);
add(LoadFunctions.LoadFromConn2.class, LoadFunctionsFactory.LoadFromConn2NodeGen::create);
add(LocaleFunctions.BindTextDomain.class, LocaleFunctionsFactory.BindTextDomainNodeGen::create);
add(LocaleFunctions.Enc2Native.class, LocaleFunctionsFactory.Enc2NativeNodeGen::create);
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/HiddenInternalFunctions.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/HiddenInternalFunctions.java
index 5b44f6fdeb..8d521d3671 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/HiddenInternalFunctions.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/HiddenInternalFunctions.java
@@ -365,7 +365,7 @@ public class HiddenInternalFunctions {
@TruffleBoundary
private RIntVector lazyLoadDBinsertValueInternal(MaterializedFrame frame, Object value, RAbstractStringVector file, byte asciiL, int compression, RFunction hook) {
- if (compression != 1) {
+ if (!(compression == 1 || compression == 3)) {
throw RError.error(this, Message.GENERIC, "unsupported compression");
}
@@ -378,16 +378,35 @@ public class HiddenInternalFunctions {
try {
byte[] data = RSerialize.serialize(value, RRuntime.fromLogical(asciiL), false, RSerialize.DEFAULT_VERSION, callHook);
- byte[] cdata = new byte[data.length + 20];
- long[] cdatalen = new long[1];
- cdatalen[0] = cdata.length;
- int rc = RFFIFactory.getRFFI().getBaseRFFI().compress(cdata, cdatalen, data);
- if (rc != 0) {
- throw RError.error(this, Message.GENERIC, "zlib uncompress error");
+ // See comment in LazyLoadDBFetch for format
+ int outLen;
+ int offset;
+ RCompression.Type type;
+ byte[] cdata;
+ if (compression == 1) {
+ type = RCompression.Type.GZIP;
+ offset = 4;
+ outLen = (int) (1.001 * data.length) + 20;
+ cdata = new byte[outLen];
+ boolean rc = RCompression.compress(type, data, cdata);
+ if (!rc) {
+ throw RError.error(this, Message.GENERIC, "zlib compress error");
+ }
+ } else if (compression == 3) {
+ type = RCompression.Type.LZMA;
+ offset = 5;
+ outLen = data.length;
+ cdata = new byte[outLen];
+ boolean rc = RCompression.compress(type, data, cdata);
+ if (!rc) {
+ throw RError.error(this, Message.GENERIC, "lzma compress error");
+ }
+ } else {
+ throw RInternalError.shouldNotReachHere();
}
int[] intData = new int[2];
- intData[1] = (int) cdatalen[0] + 4; // include outlen
- intData[0] = appendFile(file.getDataAt(0), cdata, data.length, (int) cdatalen[0]);
+ intData[1] = outLen + offset; // include length + type (compression == 3)
+ intData[0] = appendFile(file.getDataAt(0), cdata, data.length, type);
return RDataFactory.createIntVector(intData, RDataFactory.COMPLETE_VECTOR);
} catch (Throwable ex) {
// Exceptions have been observed that were masked and very hard to find
@@ -407,12 +426,11 @@ public class HiddenInternalFunctions {
* int in the first four bytes of the data. See {@link LazyLoadDBFetch}.
*
* @param path path of file
- * @param data the compressed data
+ * @param cdata the compressed data
* @param ulen length of uncompressed data
- * @param len length of compressed data
* @return offset in file of appended data
*/
- private int appendFile(String path, byte[] data, int ulen, int len) {
+ private int appendFile(String path, byte[] cdata, int ulen, RCompression.Type type) {
File file = new File(path);
try (BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(file, true))) {
int result = (int) file.length();
@@ -422,7 +440,10 @@ public class HiddenInternalFunctions {
byte[] ulenData = new byte[4];
dataLengthBuf.get(ulenData);
out.write(ulenData);
- out.write(data, 0, len);
+ if (type == RCompression.Type.LZMA) {
+ out.write(RCompression.Type.LZMA.typeByte);
+ }
+ out.write(cdata);
return result;
} catch (IOException ex) {
throw RError.error(this, Message.GENERIC, "lazyLoadDBinsertValue file append error");
@@ -433,7 +454,7 @@ public class HiddenInternalFunctions {
/*
* Created as primitive function to avoid incrementing reference count for the argument.
- *
+ *
* returns -1 for non-shareable, 0 for private, 1 for temp, 2 for shared and
* SHARED_PERMANENT_VAL for permanent shared
*/
diff --git a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/LoadFunctions.java b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/LoadFunctions.java
index 0b8f166b20..55f49aab8d 100644
--- a/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/LoadFunctions.java
+++ b/com.oracle.truffle.r.nodes.builtin/src/com/oracle/truffle/r/nodes/builtin/base/LoadFunctions.java
@@ -25,6 +25,8 @@ import com.oracle.truffle.r.runtime.env.*;
import com.oracle.truffle.r.runtime.env.REnvironment.PutException;
import com.oracle.truffle.r.runtime.ops.na.*;
+// from src/main/saveload.c
+
public class LoadFunctions {
@RBuiltin(name = "loadFromConn2", kind = RBuiltinKind.INTERNAL, parameterNames = {"con", "envir", "verbose"})
@@ -32,8 +34,6 @@ public class LoadFunctions {
private final NACheck naCheck = NACheck.create();
- // from src/main/saveload.c
-
@Specialization
@TruffleBoundary
protected RStringVector load(RConnection con, REnvironment envir, @SuppressWarnings("unused") RAbstractLogicalVector verbose) {
@@ -76,4 +76,76 @@ public class LoadFunctions {
}
}
}
+
+ @RBuiltin(name = "load", kind = RBuiltinKind.INTERNAL, parameterNames = {"con", "envir"})
+ public abstract static class Load extends RInvisibleBuiltinNode {
+ // now deprecated but still used by some packages
+
+ private static final int R_MAGIC_EMPTY = 999;
+ private static final int R_MAGIC_CORRUPT = 998;
+ private static final int R_MAGIC_TOONEW = 997;
+ private static final int R_MAGIC_ASCII_V1 = 1001;
+ private static final int R_MAGIC_BINARY_V1 = 1002;
+ private static final int R_MAGIC_XDR_V1 = 1003;
+ private static final int R_MAGIC_ASCII_V2 = 2001;
+ private static final int R_MAGIC_BINARY_V2 = 2002;
+ private static final int R_MAGIC_XDR_V2 = 2003;
+
+ @Specialization
+ @TruffleBoundary
+ protected RStringVector load(RAbstractStringVector fileVec, @SuppressWarnings("unused") REnvironment envir) {
+ controlVisibility();
+ String path = Utils.tildeExpand(fileVec.getDataAt(0));
+ try (BufferedInputStream bs = new BufferedInputStream(new FileInputStream(path))) {
+ int magic = readMagic(bs);
+ switch (magic) {
+ case R_MAGIC_EMPTY:
+ throw RError.error(this, RError.Message.MAGIC_EMPTY);
+ case R_MAGIC_TOONEW:
+ throw RError.error(this, RError.Message.MAGIC_TOONEW);
+ case R_MAGIC_CORRUPT:
+ throw RError.error(this, RError.Message.MAGIC_CORRUPT);
+ default:
+
+ }
+
+ } catch (IOException ex) {
+ throw RError.error(this, RError.Message.FILE_OPEN_ERROR);
+ }
+ throw RError.nyi(this, "load");
+ }
+
+ private static int readMagic(BufferedInputStream bs) throws IOException {
+ byte[] buf = new byte[5];
+ int count = bs.read(buf, 0, 5);
+ if (count != 5) {
+ if (count == 0) {
+ return R_MAGIC_EMPTY;
+ } else {
+ return R_MAGIC_CORRUPT;
+ }
+ }
+ String magic = new String(buf);
+ switch (magic) {
+ case "RDA1\n":
+ return R_MAGIC_ASCII_V1;
+ case "RDB1\n":
+ return R_MAGIC_BINARY_V1;
+ case "RDX1\n":
+ return R_MAGIC_XDR_V1;
+ case "RDA2\n":
+ return R_MAGIC_ASCII_V2;
+ case "RDB2\n":
+ return R_MAGIC_BINARY_V2;
+ case "RDX2\n":
+ return R_MAGIC_XDR_V2;
+ default:
+ if (buf[0] == 'R' && buf[1] == 'D') {
+ return R_MAGIC_TOONEW;
+ } else {
+ return R_MAGIC_CORRUPT;
+ }
+ }
+ }
+ }
}
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RCompression.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RCompression.java
index 436641ff91..1edb9f7205 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RCompression.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RCompression.java
@@ -26,6 +26,8 @@ import java.io.IOException;
import java.io.OutputStream;
import java.io.InputStream;
import java.lang.ProcessBuilder.Redirect;
+
+import com.oracle.truffle.r.runtime.conn.GZIPConnections.GZIPRConnection;
import com.oracle.truffle.r.runtime.ffi.RFFIFactory;
/**
@@ -53,6 +55,19 @@ public class RCompression {
}
return null;
}
+
+ /**
+ * Decode the compression type from the bytes in buf (which must be at least length 5).
+ */
+ public static Type decodeBuf(byte[] buf) {
+ if (buf[0] == 'B' && buf[1] == 'Z' && buf[2] == 'h') {
+ return RCompression.Type.BZIP2;
+ } else if (buf[0] == (byte) 0xFD && buf[1] == '7' && buf[2] == 'z' && buf[3] == 'X' && buf[4] == 'Z') {
+ return RCompression.Type.LZMA;
+ } else {
+ return RCompression.Type.NONE;
+ }
+ }
}
public static boolean uncompress(Type type, byte[] udata, byte[] cdata) {
@@ -72,6 +87,31 @@ public class RCompression {
}
}
+ public static boolean compress(Type type, byte[] udata, byte[] cdata) {
+ switch (type) {
+ case NONE:
+ System.arraycopy(udata, 0, cdata, 0, udata.length);
+ return true;
+ case GZIP:
+ return gzipCompress(udata, cdata);
+ case BZIP2:
+ throw RInternalError.unimplemented("BZIP2 compression");
+ case LZMA:
+ return lzmaCompress(udata, cdata);
+ default:
+ assert false;
+ return false;
+ }
+
+ }
+
+ private static boolean gzipCompress(byte[] udata, byte[] cdata) {
+ long[] cdatalen = new long[1];
+ cdatalen[0] = cdata.length;
+ int rc = RFFIFactory.getRFFI().getBaseRFFI().compress(cdata, cdatalen, udata);
+ return rc == 0;
+ }
+
private static boolean gzipUncompress(byte[] udata, byte[] data) {
long[] destlen = new long[1];
destlen[0] = udata.length;
@@ -79,6 +119,30 @@ public class RCompression {
return rc == 0;
}
+ private static boolean lzmaCompress(byte[] udata, byte[] cdata) {
+ int rc;
+ ProcessBuilder pb = new ProcessBuilder("xz", "--compress", "--format=raw", "--lzma2", "--stdout");
+ pb.redirectError(Redirect.INHERIT);
+ try {
+ Process p = pb.start();
+ OutputStream os = p.getOutputStream();
+ InputStream is = p.getInputStream();
+ ProcessOutputThread readThread = new ProcessOutputThreadFixed(is, cdata);
+ readThread.start();
+ os.write(udata);
+ os.close();
+ rc = p.waitFor();
+ if (rc == 0) {
+ readThread.join();
+ return true;
+ }
+ } catch (InterruptedException | IOException ex) {
+ return false;
+ }
+ return rc == 0;
+
+ }
+
private static boolean lzmaUncompress(byte[] udata, byte[] data) {
int rc;
ProcessBuilder pb = new ProcessBuilder("xz", "--decompress", "--format=raw", "--lzma2", "--stdout");
@@ -87,7 +151,7 @@ public class RCompression {
Process p = pb.start();
OutputStream os = p.getOutputStream();
InputStream is = p.getInputStream();
- ProcessOutputThread readThread = new ProcessOutputThread(is, udata);
+ ProcessOutputThread readThread = new ProcessOutputThreadFixed(is, udata);
readThread.start();
os.write(data);
os.close();
@@ -99,33 +163,109 @@ public class RCompression {
}
}
} catch (InterruptedException | IOException ex) {
- rc = 127;
+ return false;
}
return rc == 0;
}
- private static final class ProcessOutputThread extends Thread {
- private byte[] udata;
- private InputStream is;
- private int totalRead;
+ /**
+ * This is used by {@link GZIPRConnection}.
+ */
+ public static byte[] lzmaUncompressFromFile(String path) {
+ return genericUncompressFromFile(new String[]{"xz", "--decompress", "--lzma2", "--stdout", path});
+ }
+
+ public static byte[] bzipUncompressFromFile(String path) {
+ return genericUncompressFromFile(new String[]{"bzip2", "-dc", path});
+ }
+
+ private static byte[] genericUncompressFromFile(String[] command) {
+ int rc;
+ ProcessBuilder pb = new ProcessBuilder(command);
+ pb.redirectError(Redirect.INHERIT);
+ try {
+ Process p = pb.start();
+ InputStream is = p.getInputStream();
+ ProcessOutputThreadVariable readThread = new ProcessOutputThreadVariable(is);
+ readThread.start();
+ rc = p.waitFor();
+ if (rc == 0) {
+ readThread.join();
+ return readThread.getData();
+ }
+ } catch (InterruptedException | IOException ex) {
+ // fall through
+ }
+ return null;
+
+ }
- private ProcessOutputThread(InputStream is, byte[] udata) {
+ private abstract static class ProcessOutputThread extends Thread {
+ protected final InputStream is;
+ protected int totalRead;
+
+ ProcessOutputThread(InputStream is) {
super("XZProcessOutputThread");
this.is = is;
- this.udata = udata;
+ }
+
+ }
+
+ /**
+ * Reads until the expected length or EOF (which is an error).
+ */
+ private static final class ProcessOutputThreadFixed extends ProcessOutputThread {
+ protected byte[] data;
+
+ private ProcessOutputThreadFixed(InputStream is, byte[] data) {
+ super(is);
+ this.data = data;
+ }
+
+ @Override
+ public void run() {
+ int n;
+ try {
+ while (totalRead < data.length && (n = is.read(data, totalRead, data.length - totalRead)) != -1) {
+ totalRead += n;
+ }
+ } catch (IOException ex) {
+ return;
+ }
+ }
+ }
+
+ /**
+ * Reads a variable sized amount of data into a growing array.
+ *
+ */
+ private static final class ProcessOutputThreadVariable extends ProcessOutputThread {
+ private byte[] data;
+
+ private ProcessOutputThreadVariable(InputStream is) {
+ super(is);
+ this.data = new byte[8192];
}
@Override
public void run() {
int n;
try {
- while (totalRead < udata.length && (n = is.read(udata, totalRead, udata.length - totalRead)) != -1) {
+ while ((n = is.read(data, totalRead, data.length - totalRead)) != -1) {
totalRead += n;
+ if (totalRead == data.length) {
+ byte[] udataNew = new byte[data.length * 2];
+ System.arraycopy(data, 0, udataNew, 0, data.length);
+ data = udataNew;
+ }
}
} catch (IOException ex) {
return;
}
+ }
+ private byte[] getData() {
+ return data;
}
}
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
index 94a2e6a723..8568d3de27 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RError.java
@@ -617,6 +617,7 @@ public final class RError extends RuntimeException {
FILE_CANNOT_REMOVE(" cannot remove file '%s'"),
FILE_CANNOT_RENAME(" cannot rename file '%s' to '%s'"),
FILE_COPY_RECURSIVE_IGNORED("'recursive' will be ignored as 'to' is not a single existing directory"),
+ FILE_OPEN_ERROR("unable to open file"),
DIR_CANNOT_CREATE("cannot create dir '%s'"),
IMPOSSIBLE_SUBSTITUTE("substitute result cannot be represented"),
PACKAGE_AVAILABLE("'%s' may not be available when loading"),
@@ -630,7 +631,10 @@ public final class RError extends RuntimeException {
REG_FINALIZER_FIRST("first argument must be environment or external pointer"),
REG_FINALIZER_SECOND("second argument must be a function"),
REG_FINALIZER_THIRD("third argument must be 'TRUE' or 'FALSE'"),
- LAZY_LOAD_DB_CORRUPT("lazy-load database '%s' is corrupt");
+ LAZY_LOAD_DB_CORRUPT("lazy-load database '%s' is corrupt"),
+ MAGIC_EMPTY("restore file may be empty -- no data loaded"),
+ MAGIC_TOONEW("restore file may be from a newer version of R -- no data loaded"),
+ MAGIC_CORRUPT("bad restore file magic number (file may be corrupted) -- no data loaded");
public final String message;
final boolean hasArgs;
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/conn/GZIPConnections.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/conn/GZIPConnections.java
index 2b3e8f1347..2000cc8321 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/conn/GZIPConnections.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/conn/GZIPConnections.java
@@ -35,7 +35,9 @@ public class GZIPConnections {
public static final int GZIP_BUFFER_SIZE = (2 << 20);
/**
- * Base class for all modes of gzfile connections.
+ * Base class for all modes of gzfile connections. N.B. gzfile is defined to be able to read
+ * gzip, bzip, lzma and uncompressed files, which has to be implemented by reading the first few
+ * bytes of the file and detecting the type of the file.
*/
public static class GZIPRConnection extends BasePathRConnection {
public GZIPRConnection(String path, String modeString) throws IOException {
@@ -49,10 +51,33 @@ public class GZIPConnections {
switch (getOpenMode().abstractOpenMode) {
case Read:
case ReadBinary:
- try {
- delegate = new GZIPInputRConnection(this);
- } catch (ZipException ex) {
- delegate = new FileConnections.FileReadTextRConnection(this);
+ RCompression.Type cType = RCompression.Type.NONE;
+ try (InputStream is = new FileInputStream(path)) {
+ byte[] buf = new byte[5];
+ int count = is.read(buf);
+ if (count == 5) {
+ cType = RCompression.Type.decodeBuf(buf);
+ }
+ }
+ switch (cType) {
+ case NONE:
+ delegate = new FileConnections.FileReadTextRConnection(this);
+ break;
+ case GZIP:
+ delegate = new GZIPInputRConnection(this);
+ break;
+ case LZMA:
+ /*
+ * no lzma support in Java. For now we use RCompression to a byte array
+ * and return a ByteArrayInputStream on that.
+ */
+ byte[] lzmaUdata = RCompression.lzmaUncompressFromFile(path);
+ delegate = new ByteGZipInputRConnection(this, new ByteArrayInputStream(lzmaUdata));
+ break;
+ case BZIP2:
+ // ditto
+ byte[] bzipUdata = RCompression.bzipUncompressFromFile(path);
+ delegate = new ByteGZipInputRConnection(this, new ByteArrayInputStream(bzipUdata));
}
break;
case Write:
@@ -75,13 +100,18 @@ public class GZIPConnections {
}
private static class GZIPInputRConnection extends DelegateReadRConnection implements ReadWriteHelper {
- private GZIPInputStream inputStream;
+ private InputStream inputStream;
GZIPInputRConnection(GZIPRConnection base) throws IOException {
super(base);
inputStream = new GZIPInputStream(new FileInputStream(base.path), GZIP_BUFFER_SIZE);
}
+ protected GZIPInputRConnection(GZIPRConnection base, InputStream is) {
+ super(base);
+ this.inputStream = is;
+ }
+
@Override
public String readChar(int nchars, boolean useBytes) throws IOException {
return readCharHelper(nchars, inputStream, useBytes);
@@ -120,6 +150,12 @@ public class GZIPConnections {
}
+ private static class ByteGZipInputRConnection extends GZIPInputRConnection {
+ ByteGZipInputRConnection(GZIPRConnection base, ByteArrayInputStream is) {
+ super(base, is);
+ }
+ }
+
private static class GZIPOutputRConnection extends DelegateWriteRConnection implements ReadWriteHelper {
private GZIPOutputStream outputStream;
diff --git a/com.oracle.truffle.r.test.cran/r/install.cran.packages.R b/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
index a7badc434a..deb6359c9b 100644
--- a/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
+++ b/com.oracle.truffle.r.test.cran/r/install.cran.packages.R
@@ -75,7 +75,7 @@ create.blacklist.iter <- function(blacklist) {
# known to be uninstallable
# uses C++
cplusplus <- c("Rcpp", "Segmentor3IsBack", "QUIC", "kernlab", "adaptivetau", "geepack", "caTools", "amap", "rgenoud", "stringi", "rjson", "ars",
- "e1071", "aylmer")
+ "e1071", "aylmer", "cpm")
# tcltk
tcltk <- c("AnnotLists", "tcltk2", "aplpack")
# parser bugs
@@ -88,13 +88,13 @@ trufflevisitor.nyi <- c("colorspace")
# problems with native code
nativeinstall <- c("Rglpk", "overlap", "adimpro", "deSolve")
# S4 anything using S4 objects
-s4 <- c("matrixStats", "AcceptanceSampling", "biglm", "analyz", "RCurl", "anfis", "aod", "ascii")
+s4 <- c("matrixStats", "AcceptanceSampling", "biglm", "analyz", "RCurl", "anfis", "aod", "ascii", "childsds")
# graphics
graphics <- c("Cairo", "rgl")
# incomplete definitions from Rmath.h
math <- c("mvtnorm")
# serialize
-serialize <- c("actuar", "spam", "codetools", "iterators", "apc", "apsrtable", "assertthat")
+serialize <- c("actuar", "spam", "codetools", "iterators", "apc", "apsrtable", "assertthat", "citbcmst", "cubfits")
# fortran related
fortran <- c("appell", "blockmodeling", "clues", "rootSolve", "cts", "bayesQR", "cvplogistic")
initial.blacklist <- c(cplusplus, tcltk, parserbug, core, math, trufflevisitor.nyi, nativeinstall, s4, graphics, serialize, fortran)
--
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