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BioC 3.4: CHECK report for bsseq on moscato1

This page was generated on 2016-09-21 03:44:16 -0700 (Wed, 21 Sep 2016).

Package 141/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.9.2
Kasper Daniel Hansen
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: bsseq
Version: 1.9.2
Command: rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.9.2.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.9.2.tar.gz
StartedAt: 2016-09-20 04:56:20 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:02:13 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 352.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: bsseq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.9.2.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/bsseq.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bsseq/DESCRIPTION' ... OK
* this is package 'bsseq' version '1.9.2'
* 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 'bsseq' 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 ... OK
* 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'BSseqStat,ANY,ANY,ANY'
  generic '[' and siglist 'BSseqTstat,ANY,ANY,ANY'
  generic '[' and siglist 'hasGRanges,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
BSmooth.tstat 7.19    0.5    9.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
BSmooth.tstat 6.54   0.52    7.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 WARNING
See
  'D:/biocbld/bbs-3.4-bioc/meat/bsseq.Rcheck/00check.log'
for details.


bsseq.Rcheck/00install.out:


install for i386

* installing *source* package 'bsseq' ...
** 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 'bsseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bsseq' as bsseq_1.9.2.zip
* DONE (bsseq)

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

nameusersystemelapsed
BS.chr221.410.061.46
BSmooth000
BSmooth.fstat000
BSmooth.tstat7.190.509.72
BSseq-class0.140.000.14
BSseq0.110.000.11
computeStat000
data.frame2GRanges0.020.000.01
dmrFinder2.150.192.83
fisherTests0.070.000.06
getCoverage0.760.030.80
getMeth1.950.342.29
getStats0.470.020.48
goodnessOfFit2.540.103.12
hasGRanges-class000
read.bismark0.150.000.94
read.umtab000
smoothSds0.020.000.01

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

nameusersystemelapsed
BS.chr221.450.031.49
BSmooth000
BSmooth.fstat000
BSmooth.tstat6.540.527.05
BSseq-class0.180.000.18
BSseq0.140.000.14
computeStat000
data.frame2GRanges0.040.000.04
dmrFinder1.980.112.09
fisherTests0.090.000.09
getCoverage0.730.040.78
getMeth1.890.382.26
getStats0.420.070.50
goodnessOfFit2.480.242.72
hasGRanges-class000
read.bismark0.240.011.48
read.umtab000
smoothSds000