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 3.1: CHECK report for SRAdb on moscato2

This page was generated on 2015-10-09 09:28:49 -0700 (Fri, 09 Oct 2015).

Package 943/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SRAdb 1.26.0
Jack Zhu
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/SRAdb
Last Changed Rev: 108240 / Revision: 109384
Last Changed Date: 2015-09-07 06:14:54 -0700 (Mon, 07 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SRAdb
Version: 1.26.0
Command: rm -rf SRAdb.buildbin-libdir SRAdb.Rcheck && mkdir SRAdb.buildbin-libdir SRAdb.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SRAdb.buildbin-libdir SRAdb_1.26.0.tar.gz >SRAdb.Rcheck\00install.out 2>&1 && cp SRAdb.Rcheck\00install.out SRAdb-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=SRAdb.buildbin-libdir --install="check:SRAdb-install.out" --force-multiarch --no-vignettes --timings SRAdb_1.26.0.tar.gz
StartedAt: 2015-10-09 06:32:14 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:33:23 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 68.9 seconds
RetCode: 0
Status:  OK  
CheckDir: SRAdb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SRAdb.buildbin-libdir SRAdb.Rcheck && mkdir SRAdb.buildbin-libdir SRAdb.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SRAdb.buildbin-libdir SRAdb_1.26.0.tar.gz >SRAdb.Rcheck\00install.out 2>&1 && cp SRAdb.Rcheck\00install.out SRAdb-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=SRAdb.buildbin-libdir --install="check:SRAdb-install.out" --force-multiarch --no-vignettes --timings SRAdb_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/SRAdb.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SRAdb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SRAdb' version '1.26.0'
* 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 'SRAdb' 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 ... NOTE
The following files look like leftovers:
  'SRAdb/SRAdb-package.Rd'
Please remove them from your package.
* 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 'RCurl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RSQLite' 'graph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colDescriptions: no visible global function definition for 'dbGetQuery'
entityGraph : <anonymous>: no visible global function definition for
  'addEdge'
getFASTQinfo: no visible global function definition for 'dbGetQuery'
getSRA: no visible global function definition for 'dbGetQuery'
getSRAdbFile: no visible global function definition for 'dbConnect'
getSRAdbFile: no visible global function definition for 'SQLite'
getSRAdbFile: no visible global function definition for 'dbGetQuery'
getSRAdbFile: no visible global function definition for 'dbDisconnect'
sraConvert: no visible global function definition for 'dbGetQuery'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] 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: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/SRAdb.Rcheck/00check.log'
for details.


SRAdb.Rcheck/00install.out:


install for i386

* installing *source* package 'SRAdb' ...
** R
** 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 'SRAdb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SRAdb' as SRAdb_1.26.0.zip
* DONE (SRAdb)

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

nameusersystemelapsed
IGVclear000
IGVcollapse000
IGVgenome000
IGVgoto000
IGVload000
IGVsession0.000.000.02
IGVsnapshot000
IGVsocket000
IGVsort000
SRAdb-package0.030.000.04
ascpR000
ascpSRA000
colDescriptions000
entityGraph000
getFASTQfile000
getFASTQinfo000
getSRA000
getSRAdbFile000
getSRAfile0.020.000.01
getSRAinfo000
listSRAfile000
sraConvert000
sraGraph0.010.000.02
startIGV000

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

nameusersystemelapsed
IGVclear000
IGVcollapse000
IGVgenome000
IGVgoto000
IGVload0.020.000.02
IGVsession0.010.000.01
IGVsnapshot000
IGVsocket000
IGVsort000
SRAdb-package0.020.000.02
ascpR000
ascpSRA000
colDescriptions000
entityGraph000
getFASTQfile000
getFASTQinfo000
getSRA000
getSRAdbFile000
getSRAfile000
getSRAinfo000
listSRAfile000
sraConvert000
sraGraph000
startIGV000