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BioC 3.4: CHECK report for ChIPseqR on morelia

This page was generated on 2017-04-15 16:23:05 -0400 (Sat, 15 Apr 2017).

Package 197/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.28.0
Peter Humburg
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ChIPseqR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ChIPseqR
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPseqR_1.28.0.tar.gz
StartedAt: 2017-04-14 23:49:35 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:54:10 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 274.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPseqR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPseqR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ChIPseqR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.28.0’
* 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-3.4-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 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 ... 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
BindScore          15.693  0.249  15.955
RLEBindScore-class 15.192  0.232  15.438
callBindingSites   15.100  0.322  15.443
simpleNucCall      14.350  0.288  14.651
alignFeature        8.201  1.233   9.451
* 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
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.


ChIPseqR.Rcheck/00install.out:

* installing *source* package ‘ChIPseqR’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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 /Users/biocbuild/bbs-3.4-bioc/meat/ChIPseqR.Rcheck/ChIPseqR/libs
** R
** inst
** preparing 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’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
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’
* DONE (ChIPseqR)

ChIPseqR.Rcheck/ChIPseqR-Ex.timings:

nameusersystemelapsed
BindScore15.693 0.24915.955
ChIPseqR-package0.0010.0000.001
RLEBindScore-class15.192 0.23215.438
RLEReadCounts-class0.0240.0000.025
ReadCounts0.0300.0000.031
alignFeature8.2011.2339.451
callBindingSites15.100 0.32215.443
pos2gff0.0070.0000.008
simpleNucCall14.350 0.28814.651
strandPileup0.010.000.01
windowCounts0.1320.0000.132