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BioC 3.0: CHECK report for HiTC on moscato1

This page was generated on 2015-04-10 09:47:55 -0700 (Fri, 10 Apr 2015).

Package 428/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiTC 1.10.0
Nicolas Servant
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/HiTC
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  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: HiTC
Version: 1.10.0
Command: rm -rf HiTC.buildbin-libdir HiTC.Rcheck && mkdir HiTC.buildbin-libdir HiTC.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.10.0.tar.gz >HiTC.Rcheck\00install.out 2>&1 && cp HiTC.Rcheck\00install.out HiTC-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.10.0.tar.gz
StartedAt: 2015-04-10 02:12:27 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:20:04 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 457.4 seconds
RetCode: 0
Status:  OK  
CheckDir: HiTC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HiTC.buildbin-libdir HiTC.Rcheck && mkdir HiTC.buildbin-libdir HiTC.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiTC.buildbin-libdir HiTC_1.10.0.tar.gz >HiTC.Rcheck\00install.out 2>&1 && cp HiTC.Rcheck\00install.out HiTC-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=HiTC.buildbin-libdir --install="check:HiTC-install.out" --force-multiarch --no-vignettes --timings HiTC_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/HiTC.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiTC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiTC' version '1.10.0'
* 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 whether package 'HiTC' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
HTCexp: no visible global function definition for 'seqlevels'
HTClist : <anonymous>: no visible global function definition for
  'seqlevels'
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'
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<-'
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'
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'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [47s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mapC         7.43   0.28    7.71
CQC          7.43   0.18    7.67
HTCexp-class 5.58   0.07    5.66
** running examples for arch 'x64' ... [54s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mapC         10.33   0.15   11.15
CQC           7.31   0.13    7.52
HTCexp-class  4.92   0.11    5.76
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-bioc/meat/HiTC.Rcheck/00check.log'
for details.

HiTC.Rcheck/00install.out:


install for i386

* installing *source* package 'HiTC' ...
** R
** data
** inst
** preparing package for lazy loading
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

install for x64

* installing *source* package 'HiTC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiTC' as HiTC_1.10.0.zip
* DONE (HiTC)

HiTC.Rcheck/examples_i386/HiTC-Ex.timings:

nameusersystemelapsed
CQC7.430.187.67
HTCexp-class5.580.075.66
HTClist-class2.230.002.24
Nora_5C0.220.000.21
binningC2.710.052.76
discretize000
export.my5C000
exportC000
extractRegion0.450.000.45
getAnnotatedRestrictionSites000
getExpectedCounts3.390.083.47
getRestrictionFragmentsPerChromosome000
import.my5C0.20.00.2
importC0.020.000.01
intervalsDist0.560.010.58
mapC7.430.287.71
normICE000
normLGF000
pca.hic1.130.021.15
removeIntervals0.270.020.28
setGenomicFeatures000
setIntervalScale1.590.031.63

HiTC.Rcheck/examples_x64/HiTC-Ex.timings:

nameusersystemelapsed
CQC7.310.137.52
HTCexp-class4.920.115.76
HTClist-class2.280.012.29
Nora_5C0.190.000.19
binningC2.590.032.62
discretize000
export.my5C000
exportC000
extractRegion0.470.020.49
getAnnotatedRestrictionSites000
getExpectedCounts3.960.033.99
getRestrictionFragmentsPerChromosome000
import.my5C0.170.010.18
importC000
intervalsDist0.650.040.69
mapC10.33 0.1511.15
normICE000
normLGF000
pca.hic1.260.021.98
removeIntervals0.220.040.27
setGenomicFeatures000
setIntervalScale1.750.021.76