##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicRanges_1.63.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/GenomicRanges.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.63.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicRanges’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    DEPRECATED AND DEFUNCT
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GPos-class.Rd: IRanges, IntegerRanges
  GRanges-class.Rd: strand, Seqinfo, DataFrame, seqlevels, List
  GRangesList-class.Rd: RleList, CharacterList, CompressedIRangesList,
    IntegerRangesList, DataFrame, Seqinfo, seqlevels, Rle, AtomicList
  absoluteRanges.Rd: IntegerRanges, Seqinfo, seqlengths
  findOverlaps-methods.Rd: Hits
  strand-utils.Rd: RleList
  tileGenome.Rd: Seqinfo, seqlengths
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomicRanges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeGRangesFromDataFrame
> ### Title: Make a GRanges object from a data.frame or DataFrame
> ### Aliases: makeGRangesFromDataFrame coerce,data.frame,GRanges-method
> ###   coerce,DataFrame,GRanges-method makeGPosFromDataFrame
> ###   coerce,data.frame,GPos-method coerce,DataFrame,GPos-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## BASIC makeGRangesFromDataFrame() EXAMPLES
> ## ---------------------------------------------------------------------
> 
> df <- data.frame(chr="chr1", start=11:15, end=12:16,
+                  strand=c("+","-","+","*","."), score=1:5)
> df
   chr start end strand score
1 chr1    11  12      +     1
2 chr1    12  13      -     2
3 chr1    13  14      +     3
4 chr1    14  15      *     4
5 chr1    15  16      .     5
> makeGRangesFromDataFrame(df)  # strand value "." is replaced with "*"
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      +
  [2]     chr1     12-13      -
  [3]     chr1     13-14      +
  [4]     chr1     14-15      *
  [5]     chr1     15-16      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## With NAs in range-defining columns:
> df$start[5] <- df$end[2] <- NA
> df
   chr start end strand score
1 chr1    11  12      +     1
2 chr1    12  NA      -     2
3 chr1    13  14      +     3
4 chr1    14  15      *     4
5 chr1    NA  16      .     5
> #makeGRangesFromDataFrame(df)  # error!
> makeGRangesFromDataFrame(df, na.rm=TRUE)  # rows with NAs got dropped
GRanges object with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      +
  [2]     chr1     13-14      +
  [3]     chr1     14-15      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## The strand column is optional:
> df <- data.frame(chr="chr1", start=11:15, end=12:16, score=1:5)
> makeGRangesFromDataFrame(df)
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      *
  [2]     chr1     12-13      *
  [3]     chr1     13-14      *
  [4]     chr1     14-15      *
  [5]     chr1     15-16      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> gr <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)
> gr2 <- as(df, "GRanges")  # equivalent to the above
> stopifnot(identical(gr, gr2))
> gr2 <- GRanges(df)        # equivalent to the above
> stopifnot(identical(gr, gr2))
> 
> makeGRangesFromDataFrame(df, ignore.strand=TRUE)
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      *
  [2]     chr1     12-13      *
  [3]     chr1     13-14      *
  [4]     chr1     14-15      *
  [5]     chr1     15-16      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
+                              ignore.strand=TRUE)
GRanges object with 5 ranges and 1 metadata column:
      seqnames    ranges strand |     score
         <Rle> <IRanges>  <Rle> | <integer>
  [1]     chr1     11-12      * |         1
  [2]     chr1     12-13      * |         2
  [3]     chr1     13-14      * |         3
  [4]     chr1     14-15      * |         4
  [5]     chr1     15-16      * |         5
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> makeGRangesFromDataFrame(df, seqinfo=paste0("chr", 4:1))
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      *
  [2]     chr1     12-13      *
  [3]     chr1     13-14      *
  [4]     chr1     14-15      *
  [5]     chr1     15-16      *
  -------
  seqinfo: 4 sequences from an unspecified genome; no seqlengths
> makeGRangesFromDataFrame(df, seqinfo=c(chrM=NA, chr1=500, chrX=100))
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      *
  [2]     chr1     12-13      *
  [3]     chr1     13-14      *
  [4]     chr1     14-15      *
  [5]     chr1     15-16      *
  -------
  seqinfo: 3 sequences from an unspecified genome
> makeGRangesFromDataFrame(df, seqinfo=Seqinfo(paste0("chr", 4:1)))
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      *
  [2]     chr1     12-13      *
  [3]     chr1     13-14      *
  [4]     chr1     14-15      *
  [5]     chr1     15-16      *
  -------
  seqinfo: 4 sequences from an unspecified genome; no seqlengths
> 
> ## ---------------------------------------------------------------------
> ## BASIC makeGPosFromDataFrame() EXAMPLES
> ## ---------------------------------------------------------------------
> 
> df <- data.frame(
+     rsids=    c("rs7927381", "rs79273813", "rs79273815",
+                 "rs79273819", "rs79273817", "rs79273811", "rs79273814"),
+     seqnames= c("11", "1", "11", "1", "5", "8", "8"),
+     positions=c("67579271", "179599437", "70746832",
+                 "5066529", "107006951", "95077418", "43582071"),
+     alleles=  c("T/C", "A/G", "C/G, C/T", "G/A, G/C", "T/C, T/G",
+                 "G/A, G/T", "G/A, G/T"),
+     genes=    c(NA, "TDRD5", "SHANK2", NA, "LOC102467213", "NDUFAF6", NA),
+     row.names=letters[1:7]
+ )
> 
> makeGPosFromDataFrame(df)
UnstitchedGPos object with 7 positions and 0 metadata columns:
    seqnames       pos strand
       <Rle> <integer>  <Rle>
  a       11  67579271      *
  b        1 179599437      *
  c       11  70746832      *
  d        1   5066529      *
  e        5 107006951      *
  f        8  95077418      *
  g        8  43582071      *
  -------
  seqinfo: 4 sequences from an unspecified genome; no seqlengths
> makeGPosFromDataFrame(df, keep.extra.columns=TRUE)
UnstitchedGPos object with 7 positions and 3 metadata columns:
    seqnames       pos strand |       rsids     alleles        genes
       <Rle> <integer>  <Rle> | <character> <character>  <character>
  a       11  67579271      * |   rs7927381         T/C         <NA>
  b        1 179599437      * |  rs79273813         A/G        TDRD5
  c       11  70746832      * |  rs79273815    C/G, C/T       SHANK2
  d        1   5066529      * |  rs79273819    G/A, G/C         <NA>
  e        5 107006951      * |  rs79273817    T/C, T/G LOC102467213
  f        8  95077418      * |  rs79273811    G/A, G/T      NDUFAF6
  g        8  43582071      * |  rs79273814    G/A, G/T         <NA>
  -------
  seqinfo: 4 sequences from an unspecified genome; no seqlengths
> as(df, "GPos")  # same as above
UnstitchedGPos object with 7 positions and 3 metadata columns:
    seqnames       pos strand |       rsids     alleles        genes
       <Rle> <integer>  <Rle> | <character> <character>  <character>
  a       11  67579271      * |   rs7927381         T/C         <NA>
  b        1 179599437      * |  rs79273813         A/G        TDRD5
  c       11  70746832      * |  rs79273815    C/G, C/T       SHANK2
  d        1   5066529      * |  rs79273819    G/A, G/C         <NA>
  e        5 107006951      * |  rs79273817    T/C, T/G LOC102467213
  f        8  95077418      * |  rs79273811    G/A, G/T      NDUFAF6
  g        8  43582071      * |  rs79273814    G/A, G/T         <NA>
  -------
  seqinfo: 4 sequences from an unspecified genome; no seqlengths
> 
> ## With missing positions:
> df$positions[2L] <- NA
> df
       rsids seqnames positions  alleles        genes
a  rs7927381       11  67579271      T/C         <NA>
b rs79273813        1      <NA>      A/G        TDRD5
c rs79273815       11  70746832 C/G, C/T       SHANK2
d rs79273819        1   5066529 G/A, G/C         <NA>
e rs79273817        5 107006951 T/C, T/G LOC102467213
f rs79273811        8  95077418 G/A, G/T      NDUFAF6
g rs79273814        8  43582071 G/A, G/T         <NA>
> #makeGPosFromDataFrame(df)  # error!
> makeGPosFromDataFrame(df, na.rm=TRUE)  # rows with NAs got dropped
UnstitchedGPos object with 6 positions and 0 metadata columns:
    seqnames       pos strand
       <Rle> <integer>  <Rle>
  a       11  67579271      *
  c       11  70746832      *
  d        1   5066529      *
  e        5 107006951      *
  f        8  95077418      *
  g        8  43582071      *
  -------
  seqinfo: 4 sequences from an unspecified genome; no seqlengths
> 
> ## ---------------------------------------------------------------------
> ## ABOUT AUTOMATIC DETECTION OF THE seqnames/start/end/strand COLUMNS
> ## ---------------------------------------------------------------------
> 
> ## Automatic detection of the seqnames/start/end/strand columns is
> ## case insensitive:
> df <- data.frame(ChRoM="chr1", StarT=11:15, stoP=12:16,
+                  STRAND=c("+","-","+","*","."), score=1:5)
> makeGRangesFromDataFrame(df)
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      +
  [2]     chr1     12-13      -
  [3]     chr1     13-14      +
  [4]     chr1     14-15      *
  [5]     chr1     15-16      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## It also ignores a common prefix between the start and end columns:
> df <- data.frame(seqnames="chr1", tx_start=11:15, tx_end=12:16,
+                  strand=c("+","-","+","*","."), score=1:5)
> makeGRangesFromDataFrame(df)
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1     11-12      +
  [2]     chr1     12-13      -
  [3]     chr1     13-14      +
  [4]     chr1     14-15      *
  [5]     chr1     15-16      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## The common prefix between the start and end columns is used to
> ## disambiguate between more than one seqnames column:
> df <- data.frame(chrom="chr1", tx_start=11:15, tx_end=12:16,
+                  tx_chr="chr2", score=1:5)
> makeGRangesFromDataFrame(df)
GRanges object with 5 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr2     11-12      *
  [2]     chr2     12-13      *
  [3]     chr2     13-14      *
  [4]     chr2     14-15      *
  [5]     chr2     15-16      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## ---------------------------------------------------------------------
> ## 0-BASED VS 1-BASED START POSITIONS
> ## ---------------------------------------------------------------------
> 
> if (require(rtracklayer)) {
+   session <- browserSession()
+   genome(session) <- "sacCer2"
+   query <- ucscTableQuery(session, "Assembly")
+   df <- getTable(query)
+   head(df)
+ 
+   ## A common pitfall is to forget that the UCSC Table Browser uses the
+   ## "0-based start" convention:
+   gr0 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
+                                       start.field="chromStart",
+                                       end.field="chromEnd")
+   head(gr0)
+ 
+   ## The start positions need to be converted into 1-based positions,
+   ## to adhere to the convention used in Bioconductor:
+   gr1 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
+                                       start.field="chromStart",
+                                       end.field="chromEnd",
+                                       starts.in.df.are.0based=TRUE)
+   head(gr1)
+ }
Loading required package: rtracklayer
Warning in .local(x, ...) :
  'track' parameter is deprecated now you go by the 'table' instead
                Use ucscTables(genome, track) to retrieve the list of tables for a track
Error in if (file == "" || length(file) == 0) stop("empty or no content specified") : 
  missing value where TRUE/FALSE needed
Calls: ucscTableQuery ... .local -> ucscTables -> rtracklayerGET -> htmlParse
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
genomicvars 22.184  3.505  27.300
GPos-class  16.755  0.919  18.635
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicRanges
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘GenomicRanges’ ...
** this is package ‘GenomicRanges’ version ‘1.63.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c transcript_utils.c -o transcript_utils.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-GenomicRanges/00new/GenomicRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicRanges)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
[1] TRUE
> GenomicRanges:::.test()


RUNIT TEST PROTOCOL -- Fri Nov 14 20:08:24 2025 
*********************************************** 
Number of test functions: 74 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicRanges RUnit Tests - 74 test functions, 0 errors, 0 failures
Number of test functions: 74 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 13.314   0.119  14.549