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This page was generated on 2024-05-04 11:40:20 -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 kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CAGEr
Version: 2.10.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings CAGEr_2.10.0.tar.gz
StartedAt: 2024-05-04 05:37:03 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 05:51:53 -0000 (Sat, 04 May 2024)
EllapsedTime: 889.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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       47.645  0.938  48.676
exportToTrack              48.036  0.283  48.408
clusterCTSS                47.444  0.259  47.803
scoreShift                 37.580  0.550  38.207
cumulativeCTSSdistribution 35.427  1.237  36.738
quantilePositions          34.796  0.719  35.584
annotateCTSS               34.578  0.811  35.457
CustomConsensusClusters    17.077  0.455  17.565
getExpressionProfiles      15.824  0.407  16.267
plotExpressionProfiles     13.192  0.232  13.451
expressionClasses           7.171  0.168   7.353
distclu-functions           6.695  0.148   6.852
consensusClustersDESeq2     6.022  0.124   6.159
getShiftingPromoters        5.770  0.079   5.861
* 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: 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/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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-class2.5690.1162.714
CAGEr_Multicore4.0810.0564.146
CTSS-class0.3840.0040.389
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0990.0040.103
CTSSnormalizedTpm1.0050.0441.051
CTSStagCount1.1760.1271.309
CTSStoGenes0.4900.0320.523
CustomConsensusClusters17.077 0.45517.565
GeneExpDESeq20.6700.0040.676
GeneExpSE0.0060.0000.006
QuantileWidthFunctions0.1850.0040.189
aggregateTagClusters47.645 0.93848.676
annotateCTSS34.578 0.81135.457
byCtss0.020.000.02
clusterCTSS47.444 0.25947.803
consensusClusters0.1620.0200.182
consensusClustersDESeq26.0220.1246.159
consensusClustersTpm0.0080.0000.008
coverage-functions2.9930.1043.102
cumulativeCTSSdistribution35.427 1.23736.738
distclu-functions6.6950.1486.852
exampleCAGEexp000
exportToTrack48.036 0.28348.408
expressionClasses7.1710.1687.353
genomeName0.0010.0000.001
getCTSS1.3480.0161.367
getExpressionProfiles15.824 0.40716.267
getShiftingPromoters5.7700.0795.861
hanabi0.3310.0080.339
hanabiPlot0.4160.0040.421
import.CAGEscanMolecule000
import.CTSS0.1140.0000.114
import.bam000
import.bedCTSS0.0010.0000.000
import.bedScore000
import.bedmolecule0.0000.0000.001
inputFiles0.0020.0000.002
inputFilesType0.0020.0000.002
librarySizes0.0020.0000.002
mapStats0.0700.0040.074
mergeCAGEsets2.9130.0202.939
mergeSamples0.6580.0000.659
moleculesGR2CTSS0.1800.0040.184
normalizeTagCount0.6500.0040.652
parseCAGEscanBlocksToGrangeTSS0.0300.0000.031
plotAnnot3.2110.0163.235
plotCorrelation0.3560.0120.369
plotExpressionProfiles13.192 0.23213.451
plotInterquantileWidth4.0820.1284.218
plotReverseCumulatives0.4150.0030.410
quantilePositions34.796 0.71935.584
quickEnhancers000
ranges2annot0.5020.0000.503
ranges2genes0.1020.0000.103
ranges2names0.0770.0000.077
resetCAGEexp0.4360.0000.437
rowSums.RleDataFrame0.0290.0000.028
rowsum.RleDataFrame0.0320.0000.031
sampleLabels0.0050.0000.005
scoreShift37.580 0.55038.207
seqNameTotalsSE0.0040.0000.004
setColors0.3980.0000.398
strandInvaders0.8850.0160.911
summariseChrExpr0.4950.0000.496
tagClusters0.280.000.28