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This page was generated on 2024-05-31 17:02:51 -0400 (Fri, 31 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 264/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.10.0  (landing page)
Charles Plessy
Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_19
git_last_commit: 6c8b145
git_last_commit_date: 2024-04-30 10:30:39 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

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: 2.10.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CAGEr_2.10.0.tar.gz
StartedAt: 2024-05-31 01:54:41 -0400 (Fri, 31 May 2024)
EndedAt: 2024-05-31 02:10:25 -0400 (Fri, 31 May 2024)
EllapsedTime: 944.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CAGEr_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.10.0’
* 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 ‘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 ... NOTE
checkRd: (-1) inputFiles.Rd:28: Lost braces
    28 | code{\link{CAGEexp}} objects.
       |     ^
checkRd: (-1) inputFilesType.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inputFilesType.Rd:53-55: 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 ... NOTE
S3 methods shown with full name in Rd file 'rowsum.RleDataFrame.Rd':
  'rowsum.RleDataFrame'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
aggregateTagClusters       31.504  3.504  35.010
exportToTrack              28.957  0.628  29.587
clusterCTSS                28.470  0.512  28.973
cumulativeCTSSdistribution 20.201  4.248  24.449
annotateCTSS               21.741  2.383  24.127
scoreShift                 21.010  1.420  22.431
quantilePositions          18.342  2.024  20.367
CustomConsensusClusters    11.170  1.220  12.390
getExpressionProfiles       8.424  0.820   9.247
plotExpressionProfiles      8.152  0.537   8.688
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck/00check.log’
for details.


Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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-class2.9690.1003.073
CAGEr_Multicore3.5670.1313.698
CTSS-class0.2660.0000.266
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0770.0040.081
CTSSnormalizedTpm0.7440.0520.796
CTSStagCount0.7960.1200.917
CTSStoGenes0.4020.0280.430
CustomConsensusClusters11.17 1.2212.39
GeneExpDESeq20.4480.0120.460
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1180.0080.127
aggregateTagClusters31.504 3.50435.010
annotateCTSS21.741 2.38324.127
byCtss0.0180.0000.017
clusterCTSS28.470 0.51228.973
consensusClusters0.1440.0040.148
consensusClustersDESeq23.5270.4393.967
consensusClustersTpm0.0060.0000.006
coverage-functions1.6070.3351.943
cumulativeCTSSdistribution20.201 4.24824.449
distclu-functions3.4060.7244.087
exampleCAGEexp0.0010.0000.001
exportToTrack28.957 0.62829.587
expressionClasses3.1980.4123.610
genomeName0.0010.0000.001
getCTSS0.8810.0040.885
getExpressionProfiles8.4240.8209.247
getShiftingPromoters3.3220.3883.711
hanabi0.1920.0240.215
hanabiPlot0.2650.0200.285
import.CAGEscanMolecule0.0010.0000.000
import.CTSS0.0770.0000.077
import.bam0.0000.0000.001
import.bedCTSS0.0000.0010.000
import.bedScore000
import.bedmolecule000
inputFiles0.0000.0020.001
inputFilesType0.0010.0000.001
librarySizes0.0010.0000.002
mapStats0.0550.0000.054
mergeCAGEsets1.8470.0041.851
mergeSamples0.4370.0000.437
moleculesGR2CTSS0.1140.0000.114
normalizeTagCount0.4310.0040.414
parseCAGEscanBlocksToGrangeTSS0.0220.0000.021
plotAnnot2.1460.0312.179
plotCorrelation0.2320.0040.237
plotExpressionProfiles8.1520.5378.688
plotInterquantileWidth1.7240.0321.756
plotReverseCumulatives0.3540.0000.292
quantilePositions18.342 2.02420.367
quickEnhancers000
ranges2annot0.3290.0040.333
ranges2genes0.0520.0000.052
ranges2names0.0500.0030.054
resetCAGEexp0.2890.0010.289
rowSums.RleDataFrame0.0190.0000.020
rowsum.RleDataFrame0.0220.0000.023
sampleLabels0.0040.0000.004
scoreShift21.010 1.42022.431
seqNameTotalsSE0.0030.0000.004
setColors0.2930.0000.293
strandInvaders0.6600.0920.725
summariseChrExpr0.3910.0000.392
tagClusters0.2070.0040.210