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BioC 3.2: CHECK report for derfinder on windows1.bioconductor.org

This page was generated on 2015-10-27 17:31:38 -0400 (Tue, 27 Oct 2015).

Package 265/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
derfinder 1.4.0
Leonardo Collado-Torres
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/derfinder
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: derfinder
Version: 1.4.0
Command: rm -rf derfinder.buildbin-libdir derfinder.Rcheck && mkdir derfinder.buildbin-libdir derfinder.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=derfinder.buildbin-libdir derfinder_1.4.0.tar.gz >derfinder.Rcheck\00install.out 2>&1 && cp derfinder.Rcheck\00install.out derfinder-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=derfinder.buildbin-libdir --install="check:derfinder-install.out" --force-multiarch --no-vignettes --timings derfinder_1.4.0.tar.gz
StartedAt: 2015-10-27 01:12:05 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:17:23 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 317.1 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:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=derfinder.buildbin-libdir derfinder_1.4.0.tar.gz >derfinder.Rcheck\00install.out 2>&1 && cp derfinder.Rcheck\00install.out derfinder-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=derfinder.buildbin-libdir --install="check:derfinder-install.out" --force-multiarch --no-vignettes --timings derfinder_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/derfinder.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.4.0'
* 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 '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
'library' or 'require' call to 'TxDb.Hsapiens.UCSC.hg19.knownGene' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'GenomeInfoDb:::.guessSpeciesStyle'
  'GenomeInfoDb:::.supportedSeqnameMappings'
  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 ... 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... [19s] OK
** running examples for arch 'x64' ... [24s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [0s]
 [1s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [0s]
 [0s] 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:/biocbld/bbs-3.2-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_1.4.0.zip
* DONE (derfinder)

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

nameusersystemelapsed
advancedArg0.020.000.01
analyzeChr0.530.000.54
annotateRegions0.340.000.34
calculatePvalues0.630.000.62
calculateStats0.50.00.5
coerceGR0.090.000.10
collapseFullCoverage000
coverageToExon2.210.222.47
createBw0.20.00.2
createBwSample0.080.000.08
extendedMapSeqlevels0.070.050.12
filterData0.20.00.2
findRegions0.140.000.14
fullCoverage0.250.010.27
getRegionCoverage0.470.000.47
loadCoverage0.210.000.20
makeGenomicState2.890.072.95
makeModels0.010.000.02
mergeResults0.300.060.36
preprocessCoverage0.080.000.08
rawFiles0.010.000.01
regionMatrix0.440.030.47
sampleDepth0.030.000.03

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

nameusersystemelapsed
advancedArg000
analyzeChr0.680.000.67
annotateRegions0.400.030.43
calculatePvalues101
calculateStats0.390.000.40
coerceGR0.080.000.09
collapseFullCoverage000
coverageToExon3.640.153.80
createBw0.220.020.24
createBwSample0.150.000.15
extendedMapSeqlevels0.110.020.13
filterData0.220.010.23
findRegions0.170.000.17
fullCoverage0.260.000.26
getRegionCoverage0.410.020.43
loadCoverage0.230.030.26
makeGenomicState3.690.033.72
makeModels0.010.010.03
mergeResults0.390.020.40
preprocessCoverage0.10.00.1
rawFiles000
regionMatrix0.40.00.4
sampleDepth0.020.000.02