Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-12-24 11:39 -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 260/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.13.0  (landing page)
Charles Plessy
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: devel
git_last_commit: cdfe2b1
git_last_commit_date: 2024-10-29 09:44:43 -0500 (Tue, 29 Oct 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  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for CAGEr on nebbiolo1

To the developers/maintainers of the CAGEr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.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: CAGEr
Version: 2.13.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CAGEr_2.13.0.tar.gz
StartedAt: 2024-12-23 20:19:58 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 20:32:09 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 731.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CAGEr_2.13.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘CAGEr’ 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 loading without being on the library search path ... 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:
  CAGEexp-class.Rd: MultiAssayExperiment, DataFrame, Rle
  CAGEr-class.Rd: MultiAssayExperiment
  CTSStagCount.Rd: DataFrame, Rle, RangedSummarizedExperiment
  CTSStoGenes.Rd: SummarizedExperiment
  CustomConsensusClusters.Rd: GRanges, RangedSummarizedExperiment
  TSSlogo.Rd: BSgenome
  aggregateTagClusters.Rd: RangedSummarizedExperiment
  annotateCTSS.Rd: GRanges, TxDb
  bam2CTSS.Rd: GRanges
  byCtss.Rd: data.table
  consensusClusters.Rd: GRanges, SummarizedExperiment
  distclu.Rd: GRangesList
  dot-ctss_summary_for_clusters.Rd: GRanges
  expressionClasses.Rd: Rle
  flagLowExpCTSS.Rd: Rle
  getCTSS.Rd: RangedSummarizedExperiment
  import.CAGEscanMolecule.Rd: GRanges
  import.CTSS.Rd: GPos
  loadFileIntoGPos.Rd: GPos
  moleculesGR2CTSS.Rd: GRanges
  paraclu.Rd: RangedSummarizedExperiment, GRangesList
  plotCorrelation.Rd: SummarizedExperiment, DataFrame
  quantilePositions.Rd: RangedSummarizedExperiment
  ranges2annot.Rd: rowRanges, Rle
  ranges2names.Rd: Rle
  strandInvaders.Rd: Rle
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
paraclu                44.581  0.083  44.670
exportToTrack          35.578  0.054  35.633
aggregateTagClusters   20.278  0.007  20.285
scoreShift             17.774  0.264  18.038
quantilePositions      13.276  0.077  13.353
annotateCTSS           11.570  0.004  11.574
distclu                 9.276  0.005   9.285
plotExpressionProfiles  7.320  0.085   7.405
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CAGEr.Rcheck/00check.log’
for details.


Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CAGEr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (CAGEr)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class1.8440.0441.894
CAGEr_Multicore3.4740.0053.479
CTSS-class0.2490.0020.251
CTSScoordinates0.0750.0030.079
CTSSnormalizedTpm0.6590.0440.704
CTSStagCount0.6130.1070.721
CTSStoGenes0.3640.0360.400
CustomConsensusClusters4.6510.0074.659
GeneExpDESeq20.4810.0030.485
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1280.0010.129
TSSlogo2.5410.0182.560
aggregateTagClusters20.278 0.00720.285
annotateCTSS11.570 0.00411.574
byCtss0.0130.0010.015
consensusClusters0.1640.0000.166
consensusClustersDESeq21.9120.0001.913
consensusClustersTpm0.0050.0010.006
cumulativeCTSSdistribution3.4400.0543.495
distclu9.2760.0059.285
dot-ctss_summary_for_clusters0.8230.0020.825
exampleCAGEexp0.0000.0000.001
exportToTrack35.578 0.05435.633
expressionClasses1.8690.0011.870
filteredCTSSidx0.0100.0000.009
flagLowExpCTSS0.0330.0000.032
genomeName0.0010.0000.000
getCTSS0.8700.0060.875
getExpressionProfiles4.9200.0154.935
getShiftingPromoters1.9680.0001.968
hanabi0.2270.0020.229
hanabiPlot0.2640.0290.293
import.CAGEscanMolecule000
import.CTSS0.0730.0030.077
import.bam0.0000.0010.001
import.bedCTSS000
import.bedScore0.0010.0000.000
import.bedmolecule0.0000.0010.001
importPublicData0.0000.0010.001
inputFiles0.0020.0000.002
inputFilesType0.0020.0000.002
librarySizes0.0010.0010.002
mapStats0.0520.0020.055
mergeCAGEsets2.0280.0042.032
mergeSamples0.4480.0010.449
moleculesGR2CTSS0.1160.0010.117
normalizeTagCount0.4660.0000.445
paraclu44.581 0.08344.670
parseCAGEscanBlocksToGrangeTSS0.0240.0000.024
plotAnnot2.3730.0512.425
plotCorrelation0.2370.0050.243
plotExpressionProfiles7.3200.0857.405
plotInterquantileWidth2.1390.0452.184
plotReverseCumulatives2.3640.0042.306
quantilePositions13.276 0.07713.353
quickEnhancers0.0010.0000.000
ranges2annot0.3610.0000.360
ranges2genes0.060.000.06
ranges2names0.0560.0000.056
resetCAGEexp0.3220.0010.322
rowSums.RleDataFrame0.0210.0000.021
rowsum.RleDataFrame0.0240.0010.025
sampleLabels0.0050.0000.004
scoreShift17.774 0.26418.038
seqNameTotalsSE0.0040.0000.004
setColors0.30.00.3
strandInvaders0.6300.0950.711
summariseChrExpr0.4070.0000.408
tagClusters0.4000.0040.404