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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 823/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.59.1  (landing page)
Hervé Pagès
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/GenomicRanges
git_branch: devel
git_last_commit: efa80fa
git_last_commit_date: 2024-11-15 06:05:50 -0500 (Fri, 15 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for GenomicRanges on palomino7

To the developers/maintainers of the GenomicRanges package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicRanges.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GenomicRanges
Version: 1.59.1
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicRanges.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GenomicRanges_1.59.1.tar.gz
StartedAt: 2024-12-24 01:06:47 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 01:11:36 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 289.0 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicRanges.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicRanges.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GenomicRanges_1.59.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GenomicRanges.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.59.1'
* 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 whether package 'GenomicRanges' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* 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 ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/GenomicRanges/libs/x64/GenomicRanges.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'GRanges_and_GRangesList_slides.pdf' from 507Kb to 256Kb
     compacted 'Ten_things_slides.pdf' from 277Kb to 150Kb
  consider running tools::compactPDF() on these files,
  or build the source package with --compact-vignettes
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
genomicvars              50.54  11.29   61.84
GPos-class               42.00   4.31   48.01
makeGRangesFromDataFrame  0.88   0.07    5.80
* 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: 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/GenomicRanges.Rcheck/00check.log'
for details.


Installation output

GenomicRanges.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GenomicRanges
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'GenomicRanges' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c transcript_utils.c -o transcript_utils.o
In function 'tloc2rloc',
    inlined from 'tlocs2rlocs' at transcript_utils.c:208:26:
transcript_utils.c:143:45: warning: 'start' may be used uninitialized [-Wmaybe-uninitialized]
  143 |         return on_minus_strand ? end - tloc : start + tloc;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:120:24: note: 'start' was declared here
  120 |         int nexons, j, start, end, width;
      |                        ^~~~~
In function 'tloc2rloc',
    inlined from 'tlocs2rlocs' at transcript_utils.c:208:26:
transcript_utils.c:143:45: warning: 'end' may be used uninitialized [-Wmaybe-uninitialized]
  143 |         return on_minus_strand ? end - tloc : start + tloc;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:120:31: note: 'end' was declared here
  120 |         int nexons, j, start, end, width;
      |                               ^~~
gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicRanges)

Tests output

GenomicRanges.Rcheck/tests/run_unitTests.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Attaching package: 'IRanges'

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

    windows

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


RUNIT TEST PROTOCOL -- Tue Dec 24 01:11:19 2024 
*********************************************** 
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 
  52.01    0.73   52.96 

Example timings

GenomicRanges.Rcheck/GenomicRanges-Ex.timings

nameusersystemelapsed
GNCList-class0.700.030.73
GPos-class42.00 4.3148.01
GRanges-class1.050.031.08
GRangesFactor-class0.620.000.62
GRangesList-class0.640.010.67
GenomicRanges-comparison0.220.020.24
absoluteRanges1.930.092.08
constraint0.890.071.03
coverage-methods0.250.000.25
findOverlaps-methods1.860.031.89
genomic-range-squeezers000
genomicvars50.5411.2961.84
inter-range-methods2.560.292.85
intra-range-methods0.760.110.87
makeGRangesFromDataFrame0.880.075.80
makeGRangesListFromDataFrame0.110.000.11
nearest-methods1.950.031.98
phicoef000
setops-methods3.920.023.94
strand-utils0.130.000.12
subtract-methods0.290.000.30
tile-methods0.130.000.13
tileGenome0.300.020.31