Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for GOTHiC on moscato1

This page was generated on 2015-04-10 09:49:52 -0700 (Fri, 10 Apr 2015).

Package 395/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOTHiC 1.2.2
Borbala Mifsud
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/GOTHiC
Last Changed Rev: 96438 / Revision: 102249
Last Changed Date: 2014-11-04 07:52:16 -0800 (Tue, 04 Nov 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: GOTHiC
Version: 1.2.2
Command: rm -rf GOTHiC.buildbin-libdir GOTHiC.Rcheck && mkdir GOTHiC.buildbin-libdir GOTHiC.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOTHiC.buildbin-libdir GOTHiC_1.2.2.tar.gz >GOTHiC.Rcheck\00install.out 2>&1 && cp GOTHiC.Rcheck\00install.out GOTHiC-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GOTHiC.buildbin-libdir --install="check:GOTHiC-install.out" --force-multiarch --no-vignettes --timings GOTHiC_1.2.2.tar.gz
StartedAt: 2015-04-10 01:51:58 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:01:01 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 542.7 seconds
RetCode: 0
Status:  OK  
CheckDir: GOTHiC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GOTHiC.buildbin-libdir GOTHiC.Rcheck && mkdir GOTHiC.buildbin-libdir GOTHiC.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOTHiC.buildbin-libdir GOTHiC_1.2.2.tar.gz >GOTHiC.Rcheck\00install.out 2>&1 && cp GOTHiC.Rcheck\00install.out GOTHiC-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=GOTHiC.buildbin-libdir --install="check:GOTHiC-install.out" --force-multiarch --no-vignettes --timings GOTHiC_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/GOTHiC.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 'GOTHiC/DESCRIPTION' ... OK
* this is package 'GOTHiC' version '1.2.2'
* 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 'GOTHiC' 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 ... NOTE
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'S4Vectors:::orderIntegerPairs'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.binInteractions: no visible binding for global variable 'chr1'
.binInteractions: no visible binding for global variable 'chr2'
.binInteractions: no visible binding for global variable 'locus1'
.binInteractions: no visible binding for global variable 'locus2'
.binomialHiC: no visible binding for global variable 'resGR'
.binomialHiC: no visible binding for global variable 'frequencies'
.binomialHiC: no visible binding for global variable 'int1'
.binomialHiC: no visible binding for global variable 'int2'
.binomialHiC: no visible global function definition for 'mclapply'
.binomialHiC: no visible binding for global variable 'pvalue'
.findOverlaps.circle: no visible global function definition for
  'IntervalTree'
.findOverlaps.parallel: no visible global function definition for
  'splitRanges'
.findOverlaps.parallel: no visible global function definition for
  'mclapply'
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for 'isCircular'
.findOverlaps.parallel : <anonymous>: no visible global function
  definition for 'seqlengths'
.getRestrictionSitesFromBSgenome: no visible global function definition
  for 'biocLite'
.getRestrictionSitesFromBSgenome: no visible global function definition
  for 'seqlengths'
.getRestrictionSitesFromBSgenome: no visible global function definition
  for 'IRanges'
GOTHiC: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
GOTHiC: no visible binding for global variable 'filtered'
GOTHiC: no visible binding for global variable 'interactingLoci'
mapReadsToRestrictionSites: no visible binding for global variable
  'resGR'
* 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' ... [85s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
GOTHiC 54.4    2.5   65.94
** running examples for arch 'x64' ... [79s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
GOTHiC    54.97   2.23   57.77
pairReads  4.32   0.93    5.26
* 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 were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/GOTHiC.Rcheck/00check.log'
for details.

GOTHiC.Rcheck/00install.out:


install for i386

* installing *source* package 'GOTHiC' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GOTHiC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOTHiC' as GOTHiC_1.2.2.zip
* DONE (GOTHiC)

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

nameusersystemelapsed
GOTHiC54.40 2.5065.94
filtered0.100.000.11
mapReadsToRestrictionSites1.460.011.46
pairReads3.680.494.17

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

nameusersystemelapsed
GOTHiC54.97 2.2357.77
filtered0.060.030.09
mapReadsToRestrictionSites1.880.081.95
pairReads4.320.935.26