Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-03 11:08:44 -0500 (Sat, 03 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4152
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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

CHECK results for chipseq on merida1


To the developers/maintainers of the chipseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chipseq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 310/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipseq 1.49.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-12-02 14:00:12 -0500 (Fri, 02 Dec 2022)
git_url: https://git.bioconductor.org/packages/chipseq
git_branch: master
git_last_commit: 5a0e94e
git_last_commit_date: 2022-11-01 11:04:29 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'ShortRead' which is not available

Summary

Package: chipseq
Version: 1.49.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chipseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chipseq_1.49.0.tar.gz
StartedAt: 2022-12-02 23:36:58 -0500 (Fri, 02 Dec 2022)
EndedAt: 2022-12-02 23:44:53 -0500 (Fri, 02 Dec 2022)
EllapsedTime: 475.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: chipseq.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:chipseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings chipseq_1.49.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/chipseq.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chipseq/DESCRIPTION’ ... OK
* this is package ‘chipseq’ version ‘1.49.0’
* 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 ‘chipseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘IRanges’ ‘GenomicRanges’ ‘ShortRead’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.genomicContext: no visible global function definition for
  ‘transcripts’
.genomicContext: no visible global function definition for ‘cdsBy’
.genomicContext: no visible global function definition for
  ‘threeUTRsByTranscript’
.genomicContext: no visible global function definition for
  ‘fiveUTRsByTranscript’
.genomicContext: no visible global function definition for
  ‘intronsByTranscript’
.nearestTss: no visible global function definition for ‘transcripts’
.nearestTss: no visible global function definition for ‘seqlevels<-’
.nearestTss: no visible global function definition for ‘seqlevels’
applyPosByChrAndStrand: no visible global function definition for
  ‘seqnames’
correlation.estimate: no visible binding for global variable ‘mu’
correlation.estimate: no visible binding for global variable ‘corr’
correlationProfile : <anonymous>: no visible global function definition
  for ‘subseq’
coverage.estimate: no visible binding for global variable ‘mu’
coverage.estimate: no visible binding for global variable ‘covered’
islandDepthPlot: no visible binding for global variable ‘depth’
islandDepthPlot : <anonymous>: no visible global function definition
  for ‘panel.lines’
islandDepthPlot : <anonymous>: no visible global function definition
  for ‘panel.xyplot’
laneSubsample: no visible global function definition for ‘seqnames’
laneSubsample: no visible global function definition for ‘GRangesList’
subsetSummary: no visible global function definition for ‘seqlengths’
subsetSummary: no visible global function definition for ‘GRanges’
subsetSummary: no visible global function definition for ‘seqnames’
subsetSummary: no visible global function definition for ‘seqlengths<-’
diffPeakSummary,RleViewsList-RleViewsList: no visible global function
  definition for ‘GRanges’
estimate.mean.fraglen,GRanges: no visible global function definition
  for ‘seqnames’
peakSummary,RleViewsList: no visible global function definition for
  ‘GRanges’
Undefined global functions or variables:
  GRanges GRangesList cdsBy corr covered depth fiveUTRsByTranscript
  intronsByTranscript mu panel.lines panel.xyplot seqlengths
  seqlengths<- seqlevels seqlevels<- seqnames subseq
  threeUTRsByTranscript transcripts
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'densityCorr' and siglist 'GenomicRanges'
  generic 'densityCorr' and siglist 'list'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'estimate.mean.fraglen':
densityCorr
  Code: function(x, ...)
  Docs: function(x, shift = seq(0, 500, 5), center = FALSE, width =
                 seqLen * 2L, seqLen = 100L, maxDist = 500L, ...)
  Argument names in docs not in code:
    shift center width seqLen maxDist
  Mismatches in argument names:
    Position: 2 Code: ... Docs: shift

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘BSgenome.Mmusculus.UCSC.mm9’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
diffPeakSummary       8.130  0.226  10.985
estimate.mean.fraglen 4.633  0.154   6.297
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/chipseq.Rcheck/00check.log’
for details.



Installation output

chipseq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL chipseq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘chipseq’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include    -fPIC  -Wall -g -O2  -c rlesumprod.c -o rlesumprod.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o chipseq.so rlesumprod.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-chipseq/00new/chipseq/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chipseq)

Tests output


Example timings

chipseq.Rcheck/chipseq-Ex.timings

nameusersystemelapsed
chipseqFilter0.8490.3641.599
coverageplot0.1830.0050.255
cstest0.3510.0180.502
diffPeakSummary 8.130 0.22610.985
estimate.mean.fraglen4.6330.1546.297
islandDepthPlot1.4190.0661.940
laneSubsample0.7330.0290.993
peakCutoff2.2920.0753.097