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 3.6: CHECK report for bumphunter on tokay1

This page was generated on 2017-08-16 13:31:01 -0400 (Wed, 16 Aug 2017).

Package 161/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bumphunter 1.17.2
Rafael A. Irizarry
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter
Last Changed Rev: 129749 / Revision: 131943
Last Changed Date: 2017-05-19 09:43:40 -0400 (Fri, 19 May 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bumphunter
Version: 1.17.2
Command: rm -rf bumphunter.buildbin-libdir bumphunter.Rcheck && mkdir bumphunter.buildbin-libdir bumphunter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bumphunter.buildbin-libdir bumphunter_1.17.2.tar.gz >bumphunter.Rcheck\00install.out 2>&1 && cp bumphunter.Rcheck\00install.out bumphunter-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=bumphunter.buildbin-libdir --install="check:bumphunter-install.out" --force-multiarch --no-vignettes --timings bumphunter_1.17.2.tar.gz
StartedAt: 2017-08-15 22:08:26 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:25:16 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 1009.3 seconds
RetCode: 0
Status:  OK  
CheckDir: bumphunter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf bumphunter.buildbin-libdir bumphunter.Rcheck && mkdir bumphunter.buildbin-libdir bumphunter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bumphunter.buildbin-libdir bumphunter_1.17.2.tar.gz >bumphunter.Rcheck\00install.out 2>&1 && cp bumphunter.Rcheck\00install.out bumphunter-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=bumphunter.buildbin-libdir --install="check:bumphunter-install.out" --force-multiarch --no-vignettes --timings bumphunter_1.17.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/bumphunter.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 'bumphunter/DESCRIPTION' ... OK
* this is package 'bumphunter' version '1.17.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges' 'foreach'
  'iterators' 'parallel' 'locfit'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'bumphunter' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 object imported by a ':::' call: 'doParallel:::.options'
  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
bumphunterEngine: no visible binding for global variable 'bootstraps'
Undefined global functions or variables:
  bootstraps
* 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
Examples with CPU or elapsed time > 5s
           user system elapsed
bumphunter 0.75   0.03   11.50
smoother   0.09   0.01   11.49
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
bumphunter 0.64      0   11.92
smoother   0.06      0   13.77
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
  Running 'test-all.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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/bumphunter.Rcheck/00check.log'
for details.


bumphunter.Rcheck/00install.out:


install for i386

* installing *source* package 'bumphunter' ...
** 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 'bumphunter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bumphunter' as bumphunter_1.17.2.zip
* DONE (bumphunter)

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

nameusersystemelapsed
annotateNearest1.360.001.36
annotateTranscripts000
bumphunter 0.75 0.0311.50
clusterMaker0.030.000.03
dummyData0.010.000.02
getSegments0.050.000.12
locfitByCluster0.270.000.27
loessByCluster0.180.000.19
matchGenes000
regionFinder0.080.000.08
runmedByCluster0.020.000.01
smoother 0.09 0.0111.49

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

nameusersystemelapsed
annotateNearest1.540.001.55
annotateTranscripts000
bumphunter 0.64 0.0011.92
clusterMaker0.020.000.02
dummyData0.030.000.03
getSegments0.040.000.77
locfitByCluster0.300.000.29
loessByCluster0.200.020.22
matchGenes000
regionFinder0.080.000.08
runmedByCluster000
smoother 0.06 0.0013.77