[R-package] miscellaneous changes to comply with CRAN requirements (#3338)

* [R-package] update DESCRIPTION per CRAN comments

* newlines

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* more fixes

* update Rbuildignore

* more changes

* more changes per CRAN response

* add email

* run examples in CI

* add newest CRAN response

* add Solaris patch

* update patch

* another attempt at ifaddrs patch

* fix unnecessary comment

* update configure

* comments

* bump version

* tabs

* fix address alignment, required by cran (#3415)

* fix dataset binary file alignment

* many fixes

* fix warnings

* fix bug

* Update file_io.cpp

* Update file_io.cpp

* simplify code

* Apply suggestions from code review

* general

* remove unneeded alignment

* Update file_io.h

* int32 to byte8 alignment

* Apply suggestions from code review

* Apply suggestions from code review

* [R-package] add new copyright holder in DESCRIPTION (#3409)

* [R-package] add new copyright holder in DESCRIPTION

* fix role

* fixing conflicts

* [R-package] add new copyright holder in DESCRIPTION (#3409)

* [R-package] add new copyright holder in DESCRIPTION

* fix role

* trying to fix conflicts

* more fixes

* this will work

* update cran-comments

* simplify solaris, add more testing docs

* stuff

* remove rchck docs

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* remove extra use of cat()

* change solaris check

* update docs

* remove testing code

* fix warning about cleanup not having execute permissions

* fix cmake builds

* remove blank line
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: Guolin Ke <guolin.ke@outlook.com>

R-package/man/lgb.model.dt.tree.Rd

@@ -39,7 +39,7 @@ The columns of the \code{data.table} are:
 Parse a LightGBM model json dump into a \code{data.table} structure.
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.plot.importance.Rd

@@ -37,7 +37,7 @@ The graph represents each feature as a horizontal bar of length proportional to
 Features are shown ranked in a decreasing importance order.
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.plot.interpretation.Rd

@@ -34,7 +34,7 @@ The graph represents each feature as a horizontal bar of length proportional to
 contribution of a feature. Features are shown ranked in a decreasing contribution order.
 }
 \examples{
-\dontrun{
+\donttest{
 Logit <- function(x) {
   log(x / (1.0 - x))
 }

R-package/man/lgb.prepare.Rd

@@ -9,6 +9,9 @@ lgb.prepare(...)
 \arguments{
 \item{...}{catch-all to match old calls}
 }
+\value{
+Nothing. This function always raises an exception
+}
 \description{
 removed functions
 }

R-package/man/lgb.prepare2.Rd

@@ -9,6 +9,9 @@ lgb.prepare2(...)
 \arguments{
 \item{...}{catch-all to match old calls}
 }
+\value{
+Nothing. This function always raises an exception
+}
 \description{
 removed functions
 }

R-package/man/lgb.prepare_rules.Rd

@@ -9,6 +9,9 @@ lgb.prepare_rules(...)
 \arguments{
 \item{...}{catch-all to match old calls}
 }
+\value{
+Nothing. This function always raises an exception
+}
 \description{
 removed functions
 }

R-package/man/lgb.prepare_rules2.Rd

@@ -9,6 +9,9 @@ lgb.prepare_rules2(...)
 \arguments{
 \item{...}{catch-all to match old calls}
 }
+\value{
+Nothing. This function always raises an exception
+}
 \description{
 removed functions
 }

R-package/man/lgb.save.Rd

@@ -20,7 +20,7 @@ lgb.Booster
 Save LightGBM model
 }
 \examples{
-\dontrun{
+\donttest{
 library(lightgbm)
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train

R-package/man/lgb.train.Rd

@@ -132,7 +132,7 @@ Logic to train with LightGBM
 }
 
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.unloader.Rd

@@ -26,7 +26,7 @@ Attempts to unload LightGBM packages so you can remove objects cleanly without
              apparent reason and you do not want to restart R to fix the lost object.
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lightgbm.Rd

@@ -70,6 +70,9 @@ If early stopping occurs, the model will have 'best_iter' field.}
                         CPU using hyper-threading to generate 2 threads per CPU core).}
 }}
 }
+\value{
+a trained \code{lgb.Booster}
+}
 \description{
 Simple interface for training a LightGBM model.
 }

R-package/man/predict.lgb.Booster.Rd

@@ -61,7 +61,7 @@ For regression or binary classification, it returns a vector of length \code{nro
 Predicted values based on class \code{lgb.Booster}
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/readRDS.lgb.Booster.Rd

@@ -12,13 +12,13 @@ readRDS.lgb.Booster(file = "", refhook = NULL)
 \item{refhook}{a hook function for handling reference objects.}
 }
 \value{
-\code{lgb.Booster}.
+\code{lgb.Booster}
 }
 \description{
 Attempts to load a model stored in a \code{.rds} file, using \code{\link[base]{readRDS}}
 }
 \examples{
-\dontrun{
+\donttest{
 library(lightgbm)
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train

R-package/man/saveRDS.lgb.Booster.Rd

@@ -42,7 +42,7 @@ Attempts to save a model using RDS. Has an additional parameter (\code{raw})
              which decides whether to save the raw model or not.
 }
 \examples{
-\dontrun{
+\donttest{
 library(lightgbm)
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train

R-package/man/setinfo.Rd

@@ -19,7 +19,9 @@ setinfo(dataset, ...)
 \item{info}{the specific field of information to set}
 }
 \value{
-passed object
+the dataset you passed in
+
+the dataset you passed in
 }
 \description{
 Set one attribute of a \code{lgb.Dataset}
@@ -38,7 +40,7 @@ The \code{name} field can be one of the following:
 }
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/slice.Rd

@@ -17,6 +17,8 @@ slice(dataset, ...)
 \item{idxset}{an integer vector of indices of rows needed}
 }
 \value{
+constructed sub dataset
+
 constructed sub dataset
 }
 \description{
@@ -24,7 +26,7 @@ Get a new \code{lgb.Dataset} containing the specified rows of
              original \code{lgb.Dataset} object
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/src/Makevars.in

@@ -40,6 +40,7 @@ OBJECTS = \
     metric/dcg_calculator.o \
     metric/metric.o \
     objective/objective_function.o \
+    network/ifaddrs_patch.o \
     network/linker_topo.o \
     network/linkers_mpi.o \
     network/linkers_socket.o \

R-package/src/Makevars.win.in

@@ -41,6 +41,7 @@ OBJECTS = \
     metric/dcg_calculator.o \
     metric/metric.o \
     objective/objective_function.o \
+    network/ifaddrs_patch.o \
     network/linker_topo.o \
     network/linkers_mpi.o \
     network/linkers_socket.o \

src/network/ifaddrs_patch.cpp

+/*!
+* Copyright (c) 2009, Jay Loden, Dave Daeschler, Giampaolo Rodola.
+ * Licensed under the BSD 3-Clause License.
+ * See https://github.com/giampaolo/psutil/blob/master/LICENSE
+ */
+#if (defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))
+
+#include <string.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <net/if.h>
+#include <netinet/in.h>
+#include <sys/ioctl.h>
+#include <sys/types.h>
+#include <sys/socket.h>
+#include <sys/sockio.h>
+
+#include "ifaddrs_patch.h"
+
+#define MAX(x, y) ((x) > (y)?(x):(y))
+#define SIZE(p) MAX((p).ss_len, sizeof(p))
+
+
+static struct sockaddr *
+sa_dup(struct sockaddr_storage *sa1) {
+    struct sockaddr *sa2;
+    size_t sz = sizeof(struct sockaddr_storage);
+    sa2 = (struct sockaddr *) calloc(1, sz);
+    memcpy(sa2, sa1, sz);
+    return(sa2);
+}
+
+
+void freeifaddrs(struct ifaddrs *ifp) {
+    if (NULL == ifp) return;
+    free(ifp->ifa_name);
+    free(ifp->ifa_addr);
+    free(ifp->ifa_netmask);
+    free(ifp->ifa_dstaddr);
+    freeifaddrs(ifp->ifa_next);
+    free(ifp);
+}
+
+
+int getifaddrs(struct ifaddrs **ifap) {
+    int sd = -1;
+    char *ccp, *ecp;
+    struct lifconf ifc;
+    struct lifreq *ifr;
+    struct lifnum lifn;
+    struct ifaddrs *cifa = NULL; /* current */
+    struct ifaddrs *pifa = NULL; /* previous */
+    const size_t IFREQSZ = sizeof(struct lifreq);
+
+    sd = socket(AF_INET, SOCK_STREAM, 0);
+    if (sd < 0)
+        goto error;
+
+    ifc.lifc_buf = NULL;
+    *ifap = NULL;
+    /* find how much memory to allocate for the SIOCGLIFCONF call */
+    lifn.lifn_family = AF_UNSPEC;
+    lifn.lifn_flags = 0;
+    if (ioctl(sd, SIOCGLIFNUM, &lifn) < 0)
+        goto error;
+
+    /* Sun and Apple code likes to pad the interface count here in case interfaces
+     * are coming up between calls */
+    lifn.lifn_count += 4;
+
+    ifc.lifc_family = AF_UNSPEC;
+    ifc.lifc_len = lifn.lifn_count * sizeof(struct lifreq);
+    ifc.lifc_buf = static_cast<char*>(calloc(1, ifc.lifc_len));
+    if (ioctl(sd, SIOCGLIFCONF, &ifc) < 0)
+        goto error;
+
+    ccp = reinterpret_cast<char *>(ifc.lifc_req);
+    ecp = ccp + ifc.lifc_len;
+
+    while (ccp < ecp) {
+        ifr = (struct lifreq *) ccp;
+        cifa = (struct ifaddrs *) calloc(1, sizeof(struct ifaddrs));
+        cifa->ifa_next = NULL;
+        cifa->ifa_name = strdup(ifr->lifr_name);
+
+        if (pifa == NULL) {
+            *ifap = cifa; /* first one */
+        } else {
+            pifa->ifa_next = cifa;
+        }
+
+        if (ioctl(sd, SIOCGLIFADDR, ifr, IFREQSZ) < 0)
+            goto error;
+        cifa->ifa_addr = sa_dup(&ifr->lifr_addr);
+
+        if (ioctl(sd, SIOCGLIFNETMASK, ifr, IFREQSZ) < 0)
+            goto error;
+        cifa->ifa_netmask = sa_dup(&ifr->lifr_addr);
+
+        cifa->ifa_flags = 0;
+        cifa->ifa_dstaddr = NULL;
+
+        if (0 == ioctl(sd, SIOCGLIFFLAGS, ifr)) /* optional */
+            cifa->ifa_flags = ifr->lifr_flags;
+
+        if (ioctl(sd, SIOCGLIFDSTADDR, ifr, IFREQSZ) < 0) {
+            if (0 == ioctl(sd, SIOCGLIFBRDADDR, ifr, IFREQSZ))
+                cifa->ifa_dstaddr = sa_dup(&ifr->lifr_addr);
+        } else {
+            cifa->ifa_dstaddr = sa_dup(&ifr->lifr_addr);
+        }
+
+        pifa = cifa;
+        ccp += IFREQSZ;
+    }
+    free(ifc.lifc_buf);
+    close(sd);
+    return 0;
+error:
+    if (ifc.lifc_buf != NULL)
+        free(ifc.lifc_buf);
+    if (sd != -1)
+        close(sd);
+    freeifaddrs(*ifap);
+    return (-1);
+}
+
+#endif  // (defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))

src/network/ifaddrs_patch.h

+/*!
+ * Copyright (c) 2009, Jay Loden, Dave Daeschler, Giampaolo Rodola.
+ * Licensed under the BSD 3-Clause License.
+ * See https://github.com/giampaolo/psutil/blob/master/LICENSE
+ */
+
+/*
+ * - https://lists.samba.org/archive/samba-technical/2009-February/063079.html
+ * - https://github.com/giampaolo/psutil/blob/master/psutil/arch/solaris/v10/ifaddrs.h
+ */
+
+#ifndef LIGHTGBM_NETWORK_IFADDRS_PATCH_H_
+#define LIGHTGBM_NETWORK_IFADDRS_PATCH_H_
+
+#include <sys/socket.h>
+#include <net/if.h>
+
+#undef  ifa_dstaddr
+#undef  ifa_broadaddr
+#define ifa_broadaddr ifa_dstaddr
+
+struct ifaddrs {
+    struct ifaddrs  *ifa_next;
+    char            *ifa_name;
+    unsigned int     ifa_flags;
+    struct sockaddr *ifa_addr;
+    struct sockaddr *ifa_netmask;
+    struct sockaddr *ifa_dstaddr;
+};
+
+extern int getifaddrs(struct ifaddrs **);
+extern void freeifaddrs(struct ifaddrs *);
+
+#endif  // LIGHTGBM_NETWORK_IFADDRS_PATCH_H_