Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:46 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 ChIPseqR on machv2


To the developers/maintainers of the ChIPseqR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPseqR.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 306/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.48.0  (landing page)
Peter Humburg
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/ChIPseqR
git_branch: RELEASE_3_14
git_last_commit: c68564e
git_last_commit_date: 2021-10-26 11:54:55 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ChIPseqR
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPseqR_1.48.0.tar.gz
StartedAt: 2022-04-12 11:28:21 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 11:33:52 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 330.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ChIPseqR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPseqR_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ChIPseqR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPseqR’ version ‘1.48.0’
* 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 ‘ChIPseqR’ 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 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
.fixCounts: no visible global function definition for ‘runLength’
.fixCounts: no visible global function definition for ‘runValue’
getBindLen: no visible global function definition for ‘window’
pickPeak: no visible global function definition for ‘start’
pickPeak: no visible global function definition for ‘runLength’
pickPeak : <anonymous>: no visible global function definition for
  ‘window’
[[,BindScore-ANY-numeric: no visible global function definition for
  ‘window’
decompress,Rle: no visible global function definition for ‘runValue’
decompress,RleList : <anonymous>: no visible global function definition
  for ‘runValue’
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for ‘Rle’
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for ‘runValue’
initialize,RLEBindScore : <anonymous>: no visible global function
  definition for ‘runValue<-’
plot,RLEReadCounts-missing : <anonymous>: no visible global function
  definition for ‘window’
Undefined global functions or variables:
  Rle runLength runValue runValue<- start window
Consider adding
  importFrom("stats", "start", "window")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
alignFeature       12.620  2.620  15.250
BindScore           7.656  0.251   7.917
RLEBindScore-class  6.541  0.309   6.855
simpleNucCall       6.174  0.281   6.460
callBindingSites    6.174  0.256   6.436
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.



Installation output

ChIPseqR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPseqR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘ChIPseqR’ ...
** 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 startScore.c -o startScore.o
startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable]
        double stat, tmp_stat;
                     ^
1 warning generated.
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 ChIPseqR.so startScore.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-ChIPseqR/00new/ChIPseqR/libs
** R
** 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 (ChIPseqR)

Tests output


Example timings

ChIPseqR.Rcheck/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore7.6560.2517.917
ChIPseqR-package0.0000.0000.001
RLEBindScore-class6.5410.3096.855
RLEReadCounts-class0.0310.0010.032
ReadCounts0.0380.0010.038
alignFeature12.62 2.6215.25
callBindingSites6.1740.2566.436
pos2gff0.0080.0010.008
simpleNucCall6.1740.2816.460
strandPileup0.0160.0010.016
windowCounts0.3450.0010.346