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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 798/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomation 1.32.0  (landing page)
Altuna Akalin , Vedran Franke
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/genomation
git_branch: RELEASE_3_17
git_last_commit: f8dc939
git_last_commit_date: 2023-04-25 10:36:42 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for genomation on kjohnson2


To the developers/maintainers of the genomation package:
- 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: genomation
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomation_1.32.0.tar.gz
StartedAt: 2023-10-17 21:21:10 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 21:29:42 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 512.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: genomation.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomation_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/genomation.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.32.0’
* package encoding: latin1
* 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 ‘genomation’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/genomation.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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:
    in ScoreMatrixBin() function.
  Cannot process chunk/lines:
    NEW FUNCTIONS AND FEATURES
  Cannot process chunk/lines:
    The character vectors will label the x-axis of heatmaps. Examples: xcoords=c("-2kb","0","2kb")
  Cannot process chunk/lines:
    Implemented by Bozena Mika-Gospodorz.
  Cannot process chunk/lines:
    Implemented by Bozena Mika-Gospodorz.
  Cannot process chunk/lines:
    Implemented by Bozena Mika-Gospodorz.
  Cannot process chunk/lines:
    Implemented by Bozena Mika-Gospodorz.
* 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 object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  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 ... NOTE
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
  variable ‘id’
ScoreMatrixBin,RleList-GRangesList: no visible global function
  definition for ‘:=’
Undefined global functions or variables:
  := id
* checking Rd files ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
Examples with CPU (user + system) or elapsed time > 5s
                                                     user system elapsed
enrichmentMatrix-ScoreMatrixList-method             4.773  1.362  10.858
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 4.238  1.228   8.249
enrichmentMatrix-ScoreMatrix-method                 3.584  0.389   5.763
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘genomation_unit_tests.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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/genomation.Rcheck/00check.log’
for details.



Installation output

genomation.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘genomation’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c binSum.cpp -o binSum.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o genomation.so RcppExports.o binSum.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-genomation/00new/genomation/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (genomation)

Tests output

genomation.Rcheck/tests/genomation_unit_tests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> (require("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package")
Loading required package: genomation
Loading required package: grid
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 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: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    pattern

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

    strsplit

Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: readr
[1] TRUE
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
> genomation:::.test()
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
testing:min
testing:max
testing:median
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Rows: 2 Columns: 9
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): X1, X4, X6
dbl (5): X2, X3, X5, X7, X8
num (1): X9

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2 Columns: 9
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): X1, X4, X6
dbl (5): X2, X3, X5, X7, X8
num (1): X9

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.


RUNIT TEST PROTOCOL -- Tue Oct 17 21:29:23 2023 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
genomation RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In .local(target, windows, strand.aware) :
  1 windows fall off the target
2: In .local(target, windows, strand.aware) :
  2 windows fall off the target
3: In .local(target, windows, strand.aware) :
  2 windows fall off the target
4: In .local(target, windows, strand.aware) :
  2 windows fall off the target
5: In .local(target, windows, strand.aware) :
  2 windows fall off the target
6: In .local(target, windows, strand.aware) :
  2 windows fall off the target
7: In .local(target, windows, bin.num, bin.op, strand.aware) :
  2 windows fall off the target
8: In .local(target, windows, bin.num, bin.op, strand.aware) :
  2 windows fall off the target
> 
> proc.time()
   user  system elapsed 
 32.447   1.275  51.929 

Example timings

genomation.Rcheck/genomation-Ex.timings

nameusersystemelapsed
AnnotationByGeneParts-methods0.9550.0461.609
ScoreMatrix-methods2.3660.0593.525
ScoreMatrixBin-methods3.0090.0554.627
ScoreMatrixList-methods0.6000.0500.955
annotateWithFeature-methods0.0480.0030.082
annotateWithFeatureFlank-methods0.3910.0060.603
annotateWithFeatures-methods0.7260.0231.182
annotateWithGeneParts-methods0.5000.0350.857
binMatrix-methods0.2870.0210.481
convertBed2Exons-methods0.0620.0020.096
convertBed2Introns-methods0.0550.0020.085
enrichmentMatrix-ScoreMatrix-method3.5840.3895.763
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method4.2381.2288.249
enrichmentMatrix-ScoreMatrixList-method 4.773 1.36210.858
findFeatureComb-methods0.4240.0740.786
getFeatsWithTargetsStats-methods0.4280.0520.767
getFlanks-methods0.2070.0230.357
getRandomEnrichment-methods0.0050.0030.011
getTargetAnnotationStats-methods0.4200.0340.711
gffToGRanges0.1000.0100.165
heatMatrix0.3180.0440.585
heatMeta1.1160.1161.915
heatTargetAnnotation-methods0.7600.0291.220
intersectScoreMatrixList-methods0.3840.0120.600
multiHeatMatrix0.4070.0240.665
orderBy-methods0.6030.0230.998
patternMatrix-methods0.2330.0140.375
plotMeta0.4360.0260.714
plotTargetAnnotation-methods0.4480.0130.730
readBed0.1710.0130.315
readBroadPeak0.0400.0040.091
readFeatureFlank-methods0.2480.0060.383
readGeneric0.0410.0050.072
readNarrowPeak0.0380.0060.077
readTranscriptFeatures-methods0.2390.0100.403
scaleScoreMatrix-methods0.2600.0120.411
scaleScoreMatrixList0.6450.0231.000