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CHECK report for ChIPseqR on celaya2

This page was generated on 2020-01-16 13:32:14 -0500 (Thu, 16 Jan 2020).

Package 278/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.41.0
Peter Humburg
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/ChIPseqR
Branch: master
Last Commit: 97e9181
Last Changed Date: 2019-10-29 13:35:09 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPseqR
Version: 1.41.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPseqR_1.41.0.tar.gz
StartedAt: 2020-01-16 02:46:29 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 02:53:23 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 414.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPseqR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChIPseqR_1.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.41.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘ChIPseqR’
  Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘ChIPseqR’
  Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘ChIPseqR’
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.Rcheck/00install.out’ for details.
* 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 ... OK
* 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       13.507  3.399  16.913
BindScore           8.429  0.446   9.043
RLEBindScore-class  7.819  0.657   8.478
callBindingSites    5.895  0.663   6.566
simpleNucCall       5.803  0.573   6.391
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.



Installation output

ChIPseqR.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChIPseqR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ChIPseqR’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 -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/4.0/Resources/library/00LOCK-ChIPseqR/00new/ChIPseqR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘ChIPseqR’
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘ChIPseqR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘ChIPseqR’
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘ChIPseqR’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘BiocGenerics::image’ by ‘graphics::image’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘ChIPseqR’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘ChIPseqR’
No methods found in package ‘IRanges’ for request: ‘score’ when loading ‘ChIPseqR’
** testing if installed package keeps a record of temporary installation path
* DONE (ChIPseqR)

Tests output


Example timings

ChIPseqR.Rcheck/ChIPseqR-Ex.timings

nameusersystemelapsed
BindScore8.4290.4469.043
ChIPseqR-package0.0010.0000.001
RLEBindScore-class7.8190.6578.478
RLEReadCounts-class0.0510.0010.052
ReadCounts0.0560.0030.057
alignFeature13.507 3.39916.913
callBindingSites5.8950.6636.566
pos2gff0.0100.0010.010
simpleNucCall5.8030.5736.391
strandPileup0.0220.0010.023
windowCounts0.3770.0010.378