Back to Multiple platform build/check report for BioC 3.19:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:36:21 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 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
palomino3Windows 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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 2024-05-03 21:24:56 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:40:47 -0400 (Fri, 03 May 2024)
EllapsedTime: 950.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEr.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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       31.760  3.308  35.068
exportToTrack              28.895  0.504  29.399
clusterCTSS                28.306  0.535  28.831
cumulativeCTSSdistribution 19.751  4.432  24.183
annotateCTSS               21.803  2.219  24.024
scoreShift                 20.801  1.364  22.166
quantilePositions          18.050  1.988  20.039
CustomConsensusClusters    11.010  0.992  12.002
getExpressionProfiles       8.194  0.884   9.077
plotExpressionProfiles      8.019  0.580   8.600
* 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

##############################################################################
##############################################################################
###
### 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-class3.2870.2913.584
CAGEr_Multicore3.5120.1323.644
CTSS-class0.2480.0040.252
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.070.000.07
CTSSnormalizedTpm0.6650.0480.712
CTSStagCount0.7760.1240.900
CTSStoGenes0.3480.0520.401
CustomConsensusClusters11.010 0.99212.002
GeneExpDESeq20.4450.0040.449
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1230.0000.123
aggregateTagClusters31.760 3.30835.068
annotateCTSS21.803 2.21924.024
byCtss0.0190.0000.019
clusterCTSS28.306 0.53528.831
consensusClusters0.1540.0000.154
consensusClustersDESeq23.7460.4044.151
consensusClustersTpm0.0050.0000.005
coverage-functions1.7390.4162.156
cumulativeCTSSdistribution19.751 4.43224.183
distclu-functions3.5590.7404.251
exampleCAGEexp0.0010.0000.000
exportToTrack28.895 0.50429.399
expressionClasses3.2590.4843.743
genomeName000
getCTSS0.8850.0080.893
getExpressionProfiles8.1940.8849.077
getShiftingPromoters3.2010.4043.605
hanabi0.2070.0080.215
hanabiPlot0.2720.0080.281
import.CAGEscanMolecule000
import.CTSS0.0700.0040.074
import.bam0.0010.0000.000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
inputFiles0.0000.0010.001
inputFilesType0.0000.0010.001
librarySizes0.0010.0000.002
mapStats0.0520.0000.052
mergeCAGEsets1.8330.0041.838
mergeSamples0.4220.0000.422
moleculesGR2CTSS0.1130.0000.113
normalizeTagCount0.4410.0120.430
parseCAGEscanBlocksToGrangeTSS0.0220.0000.023
plotAnnot2.1550.0682.224
plotCorrelation0.230.000.23
plotExpressionProfiles8.0190.5808.600
plotInterquantileWidth1.7390.0041.743
plotReverseCumulatives0.3490.0040.303
quantilePositions18.050 1.98820.039
quickEnhancers0.0010.0000.000
ranges2annot0.3210.0040.325
ranges2genes0.0520.0000.052
ranges2names0.0510.0000.051
resetCAGEexp0.2970.0000.297
rowSums.RleDataFrame0.0210.0000.021
rowsum.RleDataFrame0.0230.0000.023
sampleLabels0.0040.0000.004
scoreShift20.801 1.36422.166
seqNameTotalsSE0.0000.0030.003
setColors0.2760.0040.280
strandInvaders0.6500.1040.731
summariseChrExpr0.3750.0040.379
tagClusters0.2150.0040.220