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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 822/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.58.0  (landing page)
H. Pagès
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/GenomicFeatures
git_branch: RELEASE_3_20
git_last_commit: a6e2405
git_last_commit_date: 2024-10-29 09:32:22 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for GenomicFeatures on lconway

To the developers/maintainers of the GenomicFeatures package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFeatures.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: GenomicFeatures
Version: 1.58.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicFeatures_1.58.0.tar.gz
StartedAt: 2024-11-19 22:26:49 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 22:38:05 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 676.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicFeatures.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicFeatures_1.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicFeatures.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.58.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GenomicFeatures’ can be installed ... OK
* 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 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’
  ‘AnnotationDbi:::.valid.metadata.table’
  ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
  ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
  ‘BiocGenerics:::testPackage’
  ‘GenomeInfoDb:::getSeqlevelsReplacementMode’
  ‘GenomeInfoDb:::normarg_new2old’
  ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
  ‘GenomicRanges:::unsafe.transcriptWidths’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’
  ‘S4Vectors:::decodeRle’ ‘S4Vectors:::extract_data_frame_rows’
  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 ... NOTE
checkRd: (-1) coordinate-mapping-methods.Rd:144-168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coordinate-mapping-methods.Rd:169-194: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nearest-methods.Rd:43-61: Lost braces in \itemize; meant \describe ?
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
coverageByTranscript       60.331  4.238  64.955
coordinate-mapping-methods 56.029  3.046  67.406
exonicParts                35.049  1.939  37.209
extractTranscriptSeqs      10.092  0.322  10.515
transcriptLocs2refLocs      6.056  0.901   7.020
getPromoterSeq-methods      2.663  1.248   6.133
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.


Installation output

GenomicFeatures.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘GenomicFeatures’ ...
** using staged installation
** 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 (GenomicFeatures)

Tests output

GenomicFeatures.Rcheck/tests/run_unitTests.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: GenomicRanges
Loading required package: AnnotationDbi
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")'.

[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK


RUNIT TEST PROTOCOL -- Tue Nov 19 22:37:56 2024 
*********************************************** 
Number of test functions: 67 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 67 test functions, 0 errors, 0 failures
Number of test functions: 67 
Number of errors: 0 
Number of failures: 0 
There were 11 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 54.357   1.420  57.306 

Example timings

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings

nameusersystemelapsed
FeatureDb-class0.0610.0040.066
TxDb-class1.7160.1231.845
as-format-methods1.0450.0181.068
coordinate-mapping-methods56.029 3.04667.406
coverageByTranscript60.331 4.23864.955
exonicParts35.049 1.93937.209
extendExonsIntoIntrons2.2550.1152.534
extractTranscriptSeqs10.092 0.32210.515
extractUpstreamSeqs1.2570.2391.676
features0.0470.0020.050
getPromoterSeq-methods2.6631.2486.133
id2name0.1540.0040.159
mapIdsToRanges0.7340.2981.038
mapRangesToIds0.5760.0080.590
microRNAs0.0000.0010.001
nearest-methods0.5790.0330.615
proteinToGenome1.3330.0141.354
select-methods0.1580.0060.165
transcriptLengths3.5610.0443.626
transcriptLocs2refLocs6.0560.9017.020
transcripts2.1070.0682.197
transcriptsBy0.6840.0120.699
transcriptsByOverlaps0.2220.0030.225