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This page was generated on 2023-02-07 11:06:51 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

CHECK results for GenomicTuples on merida1


To the developers/maintainers of the GenomicTuples package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicTuples.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 783/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicTuples 1.33.0  (landing page)
Peter Hickey
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/GenomicTuples
git_branch: master
git_last_commit: 2d72eeb
git_last_commit_date: 2022-11-01 11:10:31 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GenomicTuples
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicTuples.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicTuples_1.33.0.tar.gz
StartedAt: 2023-02-07 01:51:20 -0500 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 01:56:30 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 309.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenomicTuples.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicTuples.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicTuples_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GenomicTuples.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicTuples/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicTuples’ version ‘1.33.0’
* 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 ‘GenomicTuples’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used 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 ... OK
* checking R 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘GenomicRanges:::extraColumnSlots’
  ‘GenomicRanges:::extraColumnSlotsAsDF’ ‘S4Vectors:::VH_recycle’
  ‘S4Vectors:::orderBy’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
checkRd: (5) GTuples-class.Rd:127-155: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:181-189: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:190-205: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:206-211: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:212-218: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:227-230: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:232-234: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:236-240: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:242-246: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:248-258: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:260-263: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:265-269: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:271-280: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:282-286: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:288-292: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:294-302: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:304-309: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:311-316: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:318-323: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:325-330: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:332-335: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:346-352: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:354-360: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:362-367: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:369-377: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:385-389: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:391-396: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:398-406: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:408-417: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:426-431: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:433-436: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:438-443: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:445-465: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:467-471: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:473-478: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:480-490: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:491-504: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:506-520: \item in \describe must have non-empty label
checkRd: (5) GTuples-class.Rd:527-541: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:120-134: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:135-141: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:142-149: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:150-155: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:156-161: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:162-166: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:167-171: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:172-179: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:180-184: \item in \describe must have non-empty label
checkRd: (5) GTuples-comparison.Rd:185-190: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:65-69: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:78-81: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:82-85: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:86-89: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:90-94: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:95-101: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:102-107: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:108-119: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:120-129: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:130-136: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:137-141: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:142-146: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:147-155: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:156-162: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:163-168: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:169-174: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:175-180: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:181-184: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:196-202: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:204-210: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:212-218: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:220-228: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:236-242: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:243-245: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:248-254: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:262-268: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:269-273: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:274-278: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:279-285: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:286-298: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:299-304: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:305-311: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:319-325: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:326-331: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:332-335: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:343-347: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:348-355: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:356-360: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:361-367: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:368-373: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:374-386: \item in \describe must have non-empty label
checkRd: (5) GTuplesList-class.Rd:387-393: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/GenomicTuples.Rcheck/00check.log’
for details.



Installation output

GenomicTuples.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘GenomicTuples’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c IPD.cpp -o IPD.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c allTuplesSorted.cpp -o allTuplesSorted.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c pcompareGTuples.cpp -o pcompareGTuples.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GenomicTuples.so IPD.o RcppExports.o allTuplesSorted.o pcompareGTuples.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-GenomicTuples/00new/GenomicTuples/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 (GenomicTuples)

Tests output

GenomicTuples.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

> library(testthat)
> test_check("GenomicTuples")
Loading required package: GenomicTuples
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 1085 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 1085 ]
> 
> proc.time()
   user  system elapsed 
 76.007   0.793 101.832 

Example timings

GenomicTuples.Rcheck/GenomicTuples-Ex.timings

nameusersystemelapsed
GTuples-class0.6300.0400.878
GTuples-comparison0.9020.0101.186
GTuplesList-class0.7960.0081.058
findOverlaps-methods0.8870.0071.154
illdefined-methods0.0330.0000.039
intra-tuple-methods0.2400.0020.305
nearest-methods1.2500.0051.587
tuples-squeezers0.0010.0000.000