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BioC 3.0: CHECK report for ChIPseqR on perceval

This page was generated on 2015-04-10 09:54:44 -0700 (Fri, 10 Apr 2015).

Package 151/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChIPseqR 1.20.0
Peter Humburg
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ChIPseqR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: ChIPseqR
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPseqR_1.20.0.tar.gz
StartedAt: 2015-04-09 23:48:53 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:56:50 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 477.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ChIPseqR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPseqR_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ChIPseqR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.20.0’
* 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 ... [37s/39s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘graphics::image’ when loading ‘ChIPseqR’
See ‘/Users/biocbuild/bbs-3.0-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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): argument "textVersion" is missing, with no default
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.twoWayTest’
* 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 ... [112s/113s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
alignFeature       26.691  2.701  29.398
BindScore          22.757  0.382  23.657
callBindingSites   13.672  0.409  14.082
RLEBindScore-class 13.426  0.429  13.905
simpleNucCall      13.068  0.503  13.579
* 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

WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ChIPseqR.Rcheck/00check.log’
for details.

ChIPseqR.Rcheck/00install.out:

* installing *source* package ‘ChIPseqR’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c startScore.c -o startScore.o
startScore.c: In function ‘_ratioStat_pois’:
startScore.c:66: warning: unused variable ‘tmp_stat’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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-3.0-bioc/meat/ChIPseqR.Rcheck/ChIPseqR/libs
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::image’ when loading ‘ChIPseqR’
No methods found in "IRanges" for requests: sapply
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::image’ when loading ‘ChIPseqR’
No methods found in "IRanges" for requests: sapply
* DONE (ChIPseqR)

ChIPseqR.Rcheck/ChIPseqR-Ex.timings:

nameusersystemelapsed
BindScore22.757 0.38223.657
ChIPseqR-package0.0000.0000.001
RLEBindScore-class13.426 0.42913.905
RLEReadCounts-class0.030.000.03
ReadCounts0.0470.0000.048
alignFeature26.691 2.70129.398
callBindingSites13.672 0.40914.082
pos2gff0.0070.0000.008
simpleNucCall13.068 0.50313.579
strandPileup0.0120.0000.013
windowCounts0.0660.0010.066