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BioC 3.4: CHECK report for easyRNASeq on moscato1

This page was generated on 2016-09-21 03:44:00 -0700 (Wed, 21 Sep 2016).

Package 347/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
easyRNASeq 2.9.2
Nicolas Delhomme
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/easyRNASeq
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  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: easyRNASeq
Version: 2.9.2
Command: rm -rf easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && mkdir easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=easyRNASeq.buildbin-libdir easyRNASeq_2.9.2.tar.gz >easyRNASeq.Rcheck\00install.out 2>&1 && cp easyRNASeq.Rcheck\00install.out easyRNASeq-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=easyRNASeq.buildbin-libdir --install="check:easyRNASeq-install.out" --force-multiarch --no-vignettes --timings easyRNASeq_2.9.2.tar.gz
StartedAt: 2016-09-20 07:32:57 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:40:13 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 436.6 seconds
RetCode: 0
Status:  OK  
CheckDir: easyRNASeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && mkdir easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=easyRNASeq.buildbin-libdir easyRNASeq_2.9.2.tar.gz >easyRNASeq.Rcheck\00install.out 2>&1 && cp easyRNASeq.Rcheck\00install.out easyRNASeq-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=easyRNASeq.buildbin-libdir --install="check:easyRNASeq-install.out" --force-multiarch --no-vignettes --timings easyRNASeq_2.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/easyRNASeq.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 'easyRNASeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'easyRNASeq' version '2.9.2'
* 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 'easyRNASeq' 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.convertToUCSC'
* 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 '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 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/easyRNASeq.Rcheck/00check.log'
for details.


easyRNASeq.Rcheck/00install.out:


install for i386

* installing *source* package 'easyRNASeq' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "S4Vectors" for requests: ifelse
Creating a generic function for 'basename' from package 'base' in package 'easyRNASeq'
Creating a generic function for 'file.exists' from package 'base' in package 'easyRNASeq'
Creating a generic function for 'print' from package 'base' in package 'easyRNASeq'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "S4Vectors" for requests: ifelse

install for x64

* installing *source* package 'easyRNASeq' ...
** testing if installed package can be loaded
No methods found in "S4Vectors" for requests: ifelse
* MD5 sums
packaged installation of 'easyRNASeq' as easyRNASeq_2.9.2.zip
* DONE (easyRNASeq)

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

nameusersystemelapsed
DESeq-methods000
GenomicRanges-methods0.170.040.21
IRanges-methods000
Rsamtools-methods0.060.001.15
ShortRead-methods000
easyRNASeq-AnnotParam-accessors000
easyRNASeq-AnnotParam-class000
easyRNASeq-AnnotParam000
easyRNASeq-BamFileList0.140.000.23
easyRNASeq-BamParam-accessors000
easyRNASeq-BamParam-class000
easyRNASeq-BamParam0.010.000.02
easyRNASeq-RnaSeqParam-accessors000
easyRNASeq-RnaSeqParam-class000
easyRNASeq-RnaSeqParam000
easyRNASeq-accessors000
easyRNASeq-annotation-methods000
easyRNASeq-class000
easyRNASeq-correction-methods000
easyRNASeq-coverage-methods000
easyRNASeq-easyRNASeq000
easyRNASeq-island-methods000
easyRNASeq-package000
easyRNASeq-simpleRNASeq000
easyRNASeq-summarization-methods000
easyRNASeq-synthetic-transcripts000
edgeR-methods000
genomeIntervals-methods000
parallel-methods000

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

nameusersystemelapsed
DESeq-methods000
GenomicRanges-methods0.230.000.24
IRanges-methods000
Rsamtools-methods0.060.000.07
ShortRead-methods000
easyRNASeq-AnnotParam-accessors000
easyRNASeq-AnnotParam-class000
easyRNASeq-AnnotParam000
easyRNASeq-BamFileList0.140.000.14
easyRNASeq-BamParam-accessors000
easyRNASeq-BamParam-class000
easyRNASeq-BamParam0.010.000.02
easyRNASeq-RnaSeqParam-accessors000
easyRNASeq-RnaSeqParam-class000
easyRNASeq-RnaSeqParam0.020.000.01
easyRNASeq-accessors000
easyRNASeq-annotation-methods000
easyRNASeq-class000
easyRNASeq-correction-methods000
easyRNASeq-coverage-methods000
easyRNASeq-easyRNASeq0.010.000.02
easyRNASeq-island-methods000
easyRNASeq-package000
easyRNASeq-simpleRNASeq000
easyRNASeq-summarization-methods000
easyRNASeq-synthetic-transcripts000
edgeR-methods000
genomeIntervals-methods000
parallel-methods0.020.000.01