more CRAN updates, minor high-chromcode update

chrchang · May 27, 2024 · 0df8e2a · 0df8e2a
1 parent eff1264
commit 0df8e2a
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Showing 7 changed files with 43 additions and 16 deletions.
diff --git a/2.0/include/plink2_bgzf.cc b/2.0/include/plink2_bgzf.cc
@@ -852,20 +852,21 @@ PglErr InitBgzfCompressStreamEx(const char* out_fname, uint32_t do_append, uint3
     return kPglRetThreadCreateFail;
   }
 #else
-  if (unlikely(pthread_create(&(bgzfp->threads[compressor_thread_ct]),
 #  ifdef __cplusplus
+  if (unlikely(pthread_create(&(bgzfp->threads[compressor_thread_ct]),
                               &g_thread_startup.smallstack_thread_attr,
+                              BgzfCompressWriterThread, bgzfp))) {
+    bgzfp->unfinished_init_state = (kMaxBgzfSlotCt << 4) | compressor_thread_ct;
+    return kPglRetThreadCreateFail;
+  }
 #  else
+  if (unlikely(pthread_create(&(bgzfp->threads[compressor_thread_ct]),
                               &smallstack_thread_attr,
-#  endif
                               BgzfCompressWriterThread, bgzfp))) {
-#  ifndef __cplusplus
     pthread_attr_destroy(&smallstack_thread_attr);
-#  endif
     bgzfp->unfinished_init_state = (kMaxBgzfSlotCt << 4) | compressor_thread_ct;
     return kPglRetThreadCreateFail;
   }
-#  if !defined(__cplusplus)
   pthread_attr_destroy(&smallstack_thread_attr);
 #  endif
 #endif

diff --git a/2.0/pgenlibr/DESCRIPTION b/2.0/pgenlibr/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pgenlibr
 Type: Package
 Title: PLINK 2 Binary (.pgen) Reader
 Version: 0.3.6
-Date: 2024-05-26
+Date: 2024-05-27
 Authors@R: c(person(given = "Christopher",
                     family = "Chang",
                     role = c("aut", "cre"),
@@ -33,6 +33,7 @@ Authors@R: c(person(given = "Christopher",
 Description: A thin wrapper over PLINK 2's core libraries which provides an R
     interface for reading .pgen files.  A minimal .pvar loader is also
     included.  Chang et al. (2015) \doi{10.1186/s13742-015-0047-8}.
+Encoding: UTF-8
 License: LGPL (>= 3)
 Copyright: This package includes sources of the libdeflate library owned by
     Eric Biggers, sources of the SIMDe library owned by Evan Nemerson, sources
@@ -41,4 +42,4 @@ Copyright: This package includes sources of the libdeflate library owned by
 BugReports: https://github.com/chrchang/plink-ng/issues
 Imports: Rcpp (>= 1.0.1)
 LinkingTo: Rcpp
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/2.0/pgenlibr/NAMESPACE b/2.0/pgenlibr/NAMESPACE
@@ -1,3 +1,28 @@
+# Generated by roxygen2: do not edit by hand
+
+export(AlleleCodeBuf)
+export(BoolBuf)
+export(Buf)
+export(ClosePgen)
+export(ClosePvar)
+export(GetAlleleCode)
+export(GetAlleleCt)
+export(GetMaxAlleleCt)
+export(GetRawSampleCt)
+export(GetVariantCt)
+export(GetVariantId)
+export(GetVariantsById)
+export(HardcallPhasePresent)
+export(IntAlleleCodeBuf)
+export(IntBuf)
+export(NewPgen)
+export(NewPvar)
+export(Read)
+export(ReadAlleles)
+export(ReadHardcalls)
+export(ReadIntList)
+export(ReadList)
+export(VariantScores)
+import(Rcpp)
+importFrom(Rcpp,evalCpp)
 useDynLib(pgenlibr, .registration=TRUE)
-exportPattern("^[[:alpha:]]+")
-importFrom(Rcpp, evalCpp)
diff --git a/2.0/pgenlibr/R/RcppExports.R b/2.0/pgenlibr/R/RcppExports.R
@@ -117,7 +117,7 @@ BoolBuf <- function(pgen) {
     .Call(`_pgenlibr_BoolBuf`, pgen)
 }
 
-#' Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA}
+#' Loads the variant_numth variant, and then fills buf with \{0, 1, 2, NA\}
 #' values indicating the number of copies of the first ALT (or user-specified)
 #' allele each sample has.
 #'
@@ -187,7 +187,7 @@ ReadAlleles <- function(pgen, acbuf, variant_num, phasepresent_buf = NULL) {
 #' @param variant_subset Integer vector containing 1-based indexes of variants
 #' to load.
 #' @return Integer matrix, where rows correspond to samples, columns
-#' correspond to variant_subset, and values are in {0, 1, 2, NA} indicating
+#' correspond to variant_subset, and values are in \{0, 1, 2, NA\} indicating
 #' the number of hardcall ALT allele copies.  For multiallelic variants, all
 #' ALT alleles are combined.
 #' @export

diff --git a/2.0/pgenlibr/src/pgenlibr.cpp b/2.0/pgenlibr/src/pgenlibr.cpp
@@ -915,7 +915,7 @@ LogicalVector BoolBuf(List pgen) {
   return LogicalVector(rp->GetSubsetSize());
 }
 
-//' Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA}
+//' Loads the variant_numth variant, and then fills buf with \{0, 1, 2, NA\}
 //' values indicating the number of copies of the first ALT (or user-specified)
 //' allele each sample has.
 //'
@@ -1023,7 +1023,7 @@ void ReadAlleles(List pgen, SEXP acbuf, int variant_num, Nullable<LogicalVector>
 //' @param variant_subset Integer vector containing 1-based indexes of variants
 //' to load.
 //' @return Integer matrix, where rows correspond to samples, columns
-//' correspond to variant_subset, and values are in {0, 1, 2, NA} indicating
+//' correspond to variant_subset, and values are in \{0, 1, 2, NA\} indicating
 //' the number of hardcall ALT allele copies.  For multiallelic variants, all
 //' ALT alleles are combined.
 //' @export

diff --git a/2.0/plink2.cc b/2.0/plink2.cc
@@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.00a6"
 #elif defined(USE_AOCL)
   " AMD"
 #endif
-  " (26 May 2024)";
+  " (27 May 2024)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""

diff --git a/2.0/plink2_common.h b/2.0/plink2_common.h
@@ -744,9 +744,9 @@ CONSTI32(kMaxChrTextnumSlen, 2);
 CONSTI32(kMaxChrTextnum, 995);
 
 #  ifdef __LP64__
-CONSTI32(kChrExcludeWords, 32);
+CONSTI32(kChrExcludeWords, 16);
 #  else
-CONSTI32(kChrExcludeWords, 64);
+CONSTI32(kChrExcludeWords, 32);
 #  endif
 
 CONSTI32(kMaxChrTextnumSlen, 3);