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BioC 3.4: CHECK report for derfinder on tokay1

This page was generated on 2017-04-15 16:19:12 -0400 (Sat, 15 Apr 2017).

Package 315/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.8.5
Leonardo Collado-Torres
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/derfinder
Last Changed Rev: 127599 / Revision: 128728
Last Changed Date: 2017-03-21 18:10:48 -0400 (Tue, 21 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: derfinder
Version: 1.8.5
Command: rm -rf derfinder.buildbin-libdir derfinder.Rcheck && mkdir derfinder.buildbin-libdir derfinder.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=derfinder.buildbin-libdir derfinder_1.8.5.tar.gz >derfinder.Rcheck\00install.out 2>&1 && cp derfinder.Rcheck\00install.out derfinder-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=derfinder.buildbin-libdir --install="check:derfinder-install.out" --force-multiarch --no-vignettes --timings derfinder_1.8.5.tar.gz
StartedAt: 2017-04-14 21:54:09 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:05:40 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 690.8 seconds
RetCode: 0
Status:  OK  
CheckDir: derfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf derfinder.buildbin-libdir derfinder.Rcheck && mkdir derfinder.buildbin-libdir derfinder.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=derfinder.buildbin-libdir derfinder_1.8.5.tar.gz >derfinder.Rcheck\00install.out 2>&1 && cp derfinder.Rcheck\00install.out derfinder-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=derfinder.buildbin-libdir --install="check:derfinder-install.out" --force-multiarch --no-vignettes --timings derfinder_1.8.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/derfinder.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'derfinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'derfinder' version '1.8.5'
* 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 'derfinder' 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
Unexported objects imported by ':::' calls:
  'GenomeInfoDb:::.guessSpeciesStyle'
  'GenomeInfoDb:::.supportedSeqnameMappings'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.smootherFstats'
* 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 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: 'RefManageR'
* 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-3.4-bioc/meat/derfinder.Rcheck/00check.log'
for details.


derfinder.Rcheck/00install.out:


install for i386

* installing *source* package 'derfinder' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'derfinder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'derfinder' as derfinder_1.8.5.zip
* DONE (derfinder)

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

nameusersystemelapsed
analyzeChr0.470.020.49
annotateRegions0.280.010.30
calculatePvalues0.350.000.34
calculateStats0.090.020.11
coerceGR0.050.000.05
collapseFullCoverage0.010.000.01
coverageToExon2.070.552.61
createBw0.110.000.11
createBwSample0.030.000.03
define_cluster0.010.000.02
derfinder-deprecated000
extendedMapSeqlevels0.070.030.09
filterData0.120.010.14
findRegions0.230.080.31
fullCoverage0.210.000.21
getRegionCoverage0.200.000.22
getTotalMapped0.020.000.01
loadCoverage0.120.000.13
makeGenomicState2.550.052.62
makeModels0.010.000.02
mergeResults0.250.030.28
preprocessCoverage0.110.000.11
railMatrix000
rawFiles0.020.000.01
regionMatrix0.280.030.32
sampleDepth0.030.000.03

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

nameusersystemelapsed
analyzeChr0.60.00.7
annotateRegions0.340.010.36
calculatePvalues0.380.030.41
calculateStats0.140.000.14
coerceGR0.060.000.06
collapseFullCoverage000
coverageToExon2.750.283.03
createBw0.130.000.13
createBwSample0.040.000.05
define_cluster000
derfinder-deprecated0.020.000.01
extendedMapSeqlevels0.080.020.09
filterData0.140.000.15
findRegions0.250.030.28
fullCoverage0.230.010.25
getRegionCoverage0.30.00.3
getTotalMapped000
loadCoverage0.160.020.18
makeGenomicState3.440.033.47
makeModels0.030.000.03
mergeResults0.310.030.34
preprocessCoverage0.140.000.14
railMatrix000
rawFiles000
regionMatrix0.380.000.38
sampleDepth0.030.000.03