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BioC 3.5: CHECK report for regioneR on tokay2

This page was generated on 2017-08-16 13:24:23 -0400 (Wed, 16 Aug 2017).

Package 1096/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.8.1
Bernat Gel
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/regioneR
Last Changed Rev: 131318 / Revision: 131943
Last Changed Date: 2017-07-18 08:48:04 -0400 (Tue, 18 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: regioneR
Version: 1.8.1
Command: rm -rf regioneR.buildbin-libdir regioneR.Rcheck && mkdir regioneR.buildbin-libdir regioneR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=regioneR.buildbin-libdir regioneR_1.8.1.tar.gz >regioneR.Rcheck\00install.out 2>&1 && cp regioneR.Rcheck\00install.out regioneR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=regioneR.buildbin-libdir --install="check:regioneR-install.out" --force-multiarch --no-vignettes --timings regioneR_1.8.1.tar.gz
StartedAt: 2017-08-16 02:21:51 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:39:54 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 1083.3 seconds
RetCode: 0
Status:  OK  
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf regioneR.buildbin-libdir regioneR.Rcheck && mkdir regioneR.buildbin-libdir regioneR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=regioneR.buildbin-libdir regioneR_1.8.1.tar.gz >regioneR.Rcheck\00install.out 2>&1 && cp regioneR.Rcheck\00install.out regioneR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=regioneR.buildbin-libdir --install="check:regioneR-install.out" --force-multiarch --no-vignettes --timings regioneR_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/regioneR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'regioneR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'regioneR' version '1.8.1'
* 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 'regioneR' can be installed ... OK
* 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:
  'memoise' 'GenomicRanges' 'BSgenome' 'rtracklayer' 'parallel'
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 ... 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
commonRegions: no visible global function definition for 'hasArg'
createFunctionsList: no visible global function definition for 'hasArg'
extendRegions: no visible global function definition for 'hasArg'
joinRegions: no visible global function definition for 'hasArg'
localZScore: no visible global function definition for 'hasArg'
meanDistance: no visible global function definition for 'hasArg'
meanInRegions: no visible global function definition for 'hasArg'
mergeRegions: no visible global function definition for 'hasArg'
numOverlaps: no visible global function definition for 'hasArg'
overlapGraphicalSummary: no visible global function definition for
  'hasArg'
overlapPermTest: no visible global function definition for 'hasArg'
overlapRegions: no visible global function definition for 'hasArg'
overlapRegions: no visible global function definition for 'queryHits'
overlapRegions: no visible global function definition for 'subjectHits'
permTest: no visible global function definition for 'hasArg'
plot.localZScoreResultsList: no visible global function definition for
  'is'
plot.permTestResultsList: no visible global function definition for
  'is'
plotRegions: no visible global function definition for 'hasArg'
randomizeRegions: no visible global function definition for 'hasArg'
removeOverlapping: no visible global function definition for
  'queryHits'
removeOverlapping: no visible global function definition for
  'subjectHits'
resampleRegions: no visible global function definition for 'hasArg'
splitRegions: no visible global function definition for 'hasArg'
subtractRegions: no visible global function definition for 'hasArg'
toDataframe: no visible global function definition for 'hasArg'
toDataframe: no visible global function definition for 'is'
toGRanges: no visible global function definition for 'hasArg'
toGRanges: no visible global function definition for 'is'
toGRanges : <anonymous>: no visible global function definition for
  'read.delim'
toGRanges : <anonymous> : <anonymous>: no visible global function
  definition for 'read.csv'
uniqueRegions: no visible global function definition for 'hasArg'
Undefined global functions or variables:
  hasArg is queryHits read.csv read.delim subjectHits
Consider adding
  importFrom("methods", "hasArg", "is")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
filterChromosomes        83.65   6.12   89.78
getMask                  76.34   4.33   80.68
circularRandomizeRegions 74.88   3.99   78.86
maskFromBSGenome         68.70   3.54   72.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
filterChromosomes        64.04   6.45   70.50
circularRandomizeRegions 65.82   3.66   69.47
maskFromBSGenome         62.72   4.53   67.25
getMask                  57.84   3.11   60.96
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/regioneR.Rcheck/00check.log'
for details.


regioneR.Rcheck/00install.out:


install for i386

* installing *source* package 'regioneR' ...
** R
** 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 'regioneR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'regioneR' as regioneR_1.8.1.zip
* DONE (regioneR)

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

nameusersystemelapsed
characterToBSGenome0.640.260.90
circularRandomizeRegions74.88 3.9978.86
commonRegions0.190.010.20
createFunctionsList2.770.463.22
createRandomRegions0.060.000.06
emptyCacheRegioneR000
extendRegions0.110.000.11
filterChromosomes83.65 6.1289.78
getChromosomesByOrganism000
getGenome0.030.020.05
getGenomeAndMask1.070.201.27
getMask76.34 4.3380.68
joinRegions0.080.000.08
listChrTypes000
localZScore2.940.002.94
maskFromBSGenome68.70 3.5472.25
meanDistance0.060.000.06
meanInRegions0.130.000.13
mergeRegions0.060.000.06
numOverlaps0.090.000.09
overlapGraphicalSummary0.10.00.1
overlapPermTest0.510.000.51
overlapRegions0.030.000.03
permTest0.770.000.77
plot.localZScoreResults0.80.00.8
plot.localZScoreResultsList1.780.001.78
plot.permTestResults1.250.001.25
plot.permTestResultsList1.420.001.42
plotRegions0.020.000.01
print.permTestResults0.840.000.85
randomizeRegions0.140.000.14
recomputePermTest0.550.000.55
resampleRegions0.030.000.03
splitRegions0.040.000.04
subtractRegions0.080.020.10
toDataframe0.020.000.01
toGRanges000
uniqueRegions0.190.000.19

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

nameusersystemelapsed
characterToBSGenome0.580.260.84
circularRandomizeRegions65.82 3.6669.47
commonRegions0.300.000.29
createFunctionsList1.520.502.02
createRandomRegions0.090.000.09
emptyCacheRegioneR000
extendRegions0.160.000.16
filterChromosomes64.04 6.4570.50
getChromosomesByOrganism000
getGenome0.010.000.02
getGenomeAndMask0.030.000.03
getMask57.84 3.1160.96
joinRegions0.100.000.09
listChrTypes0.010.000.02
localZScore4.280.004.28
maskFromBSGenome62.72 4.5367.25
meanDistance0.10.00.1
meanInRegions0.180.000.18
mergeRegions0.070.000.07
numOverlaps0.120.000.12
overlapGraphicalSummary0.130.000.13
overlapPermTest0.590.000.59
overlapRegions0.050.000.05
permTest1.060.001.06
plot.localZScoreResults1.080.001.08
plot.localZScoreResultsList2.150.002.15
plot.permTestResults1.710.001.71
plot.permTestResultsList1.790.001.79
plotRegions0.040.000.03
print.permTestResults1.040.001.05
randomizeRegions0.170.000.17
recomputePermTest0.670.020.69
resampleRegions0.030.000.03
splitRegions0.050.000.04
subtractRegions0.110.000.11
toDataframe0.010.000.01
toGRanges0.020.000.02
uniqueRegions0.230.000.23