HiTC 1.12.0
Nicolas Servant
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/HiTC | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HiTC_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/HiTC.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.12.0’
* 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 ‘HiTC’ can be installed ... [26s/26s] 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
binningC: no visible global function definition for ‘seqlevels’
export.my5C : <anonymous>: no visible global function definition for
‘seqlevels’
exportC : <anonymous>: no visible global function definition for
‘seqlevels’
getAnnotatedRestrictionSites: no visible global function definition for
‘seqlevels’
getAnnotatedRestrictionSites: no visible global function definition for
‘mclapply’
getBlocsIndex: no visible global function definition for ‘Rle’
getExpectedCounts: no visible global function definition for ‘mclapply’
getRestrictionFragmentsPerChromosome: no visible global function
definition for ‘seqlevels’
getRestrictionFragmentsPerChromosome: no visible global function
definition for ‘mclapply’
getRestrictionFragmentsPerChromosome : <anonymous>: no visible global
function definition for ‘seqlengths’
HTCexp: no visible global function definition for ‘seqlevels’
HTClist : <anonymous>: no visible global function definition for
‘seqlevels’
import.my5C: no visible global function definition for ‘seqlevels’
normLGF: no visible global function definition for ‘seqlevels’
normLGF: no visible global function definition for ‘glm.nb’
setEnvDisplay: no visible global function definition for ‘seqlevels’
setGenomicFeatures: no visible global function definition for
‘seqlevels’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts: no visible global function definition for
‘sortSeqlevels’
splitCombinedContacts: no visible global function definition for
‘seqlevels’
splitCombinedContacts: no visible global function definition for
‘mclapply’
splitCombinedContacts : <anonymous>: no visible global function
definition for ‘seqlevels<-’
detail,HTCexp : .local: no visible global function definition for
‘seqlevels’
forcePairwise,HTClist: no visible global function definition for
‘seqlevels’
forcePairwise,HTClist: no visible global function definition for
‘mclapply’
forceSymmetric,HTClist-character: no visible global function definition
for ‘sortSeqlevels’
forceSymmetric,HTClist-character: no visible global function definition
for ‘seqlevels’
getCombinedContacts,HTClist: no visible global function definition for
‘seqlevels’
isBinned,HTCexp: no visible global function definition for
‘countMatches’
isComplete,HTClist: no visible global function definition for
‘seqlevels’
isIntraChrom,HTCexp: no visible global function definition for
‘seqlevels’
isPairwise,HTClist: no visible global function definition for
‘seqlevels’
isSymmetric,HTCexp : .local: no visible global function definition for
‘seqlevels’
mapC,HTCexp-HTCexp : .local: no visible global function definition for
‘seqlevels’
mapC,HTClist-ANY : .local: no visible global function definition for
‘seqlevels’
seqlevels,HTCexp: no visible global function definition for ‘seqlevels’
seqlevels,HTClist: no visible binding for global variable ‘seqlevels’
show,HTCexp: no visible global function definition for ‘seqlevels’
sortSeqlevels,HTClist : .local: no visible global function definition
for ‘seqlevels’
sortSeqlevels,HTClist : .local: no visible global function definition
for ‘sortSeqlevels’
summary,HTCexp : .local: no visible global function definition for
‘seqlevels’
* checking Rd files ... NOTE
prepare_Rd: directionalityIndex.Rd:25: Dropping empty section \examples
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/52s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mapC 10.046 0.494 10.583
CQC 6.287 0.310 7.043
HTCexp-class 5.477 0.212 5.812
* 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-3.1-bioc/meat/HiTC.Rcheck/00check.log’
for details.
* installing *source* package ‘HiTC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘isSymmetric’ from package ‘base’ in package ‘HiTC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (HiTC)