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BioC experimental data: CHECK report for pd.atdschip.tiling on windows1.bioconductor.org

This page was generated on 2015-10-24 18:52:50 -0400 (Sat, 24 Oct 2015).

Package 185/257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pd.atdschip.tiling 0.8.0
Kristof De Beuf
Snapshot Date: 2015-10-24 12:50:03 -0400 (Sat, 24 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_2/experiment/pkgs/pd.atdschip.tiling
Last Changed Rev: 3460 / Revision: 3473
Last Changed Date: 2015-10-13 16:14:23 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: pd.atdschip.tiling
Version: 0.8.0
Command: rm -rf pd.atdschip.tiling.buildbin-libdir pd.atdschip.tiling.Rcheck && mkdir pd.atdschip.tiling.buildbin-libdir pd.atdschip.tiling.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pd.atdschip.tiling.buildbin-libdir pd.atdschip.tiling_0.8.0.tar.gz >pd.atdschip.tiling.Rcheck\00install.out 2>&1 && cp pd.atdschip.tiling.Rcheck\00install.out pd.atdschip.tiling-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=pd.atdschip.tiling.buildbin-libdir --install="check:pd.atdschip.tiling-install.out" --force-multiarch --no-vignettes --timings pd.atdschip.tiling_0.8.0.tar.gz
StartedAt: 2015-10-24 15:21:25 -0400 (Sat, 24 Oct 2015)
EndedAt: 2015-10-24 15:26:39 -0400 (Sat, 24 Oct 2015)
EllapsedTime: 314.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: pd.atdschip.tiling.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   rm -rf pd.atdschip.tiling.buildbin-libdir pd.atdschip.tiling.Rcheck && mkdir pd.atdschip.tiling.buildbin-libdir pd.atdschip.tiling.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pd.atdschip.tiling.buildbin-libdir pd.atdschip.tiling_0.8.0.tar.gz >pd.atdschip.tiling.Rcheck\00install.out 2>&1 && cp pd.atdschip.tiling.Rcheck\00install.out pd.atdschip.tiling-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=pd.atdschip.tiling.buildbin-libdir --install="check:pd.atdschip.tiling-install.out" --force-multiarch --no-vignettes --timings pd.atdschip.tiling_0.8.0.tar.gz
###
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##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-data-experiment/meat/pd.atdschip.tiling.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 'pd.atdschip.tiling/DESCRIPTION' ... OK
* this is package 'pd.atdschip.tiling' version '0.8.0'
* 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 'pd.atdschip.tiling' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 256.4Mb
  sub-directories of 1Mb or more:
    data      43.3Mb
    extdata  213.0Mb
* checking package 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 ... WARNING
---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'pd.atdschip.tiling', details:
  call: NULL
  error: Expired SQLiteResult 
* 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 ... WARNING
---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'pd.atdschip.tiling', details:
  call: NULL
  error: Expired SQLiteResult 
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'RSQLite' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'IRanges'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'methods' 'oligo' 'oligoClasses'
  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
File 'pd.atdschip.tiling/R/all.R':
  .onLoad calls:
    require(RSQLite, quietly = TRUE)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
  inst/UnitTests/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
probeSequences 5.61   0.21    5.82
** running examples for arch 'x64' ... [10s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
probeSequences 5.03    0.2    5.24
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  'C:/biocbld/bbs-3.2-data-experiment/meat/pd.atdschip.tiling.Rcheck/00check.log'
for details.


pd.atdschip.tiling.Rcheck/00install.out:


install for i386

* installing *source* package 'pd.atdschip.tiling' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'pd.atdschip.tiling' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pd.atdschip.tiling' as pd.atdschip.tiling_0.8.0.zip
* DONE (pd.atdschip.tiling)

pd.atdschip.tiling.Rcheck/examples_i386/pd.atdschip.tiling-Ex.timings:

nameusersystemelapsed
probeSequences5.610.215.82

pd.atdschip.tiling.Rcheck/examples_x64/pd.atdschip.tiling-Ex.timings:

nameusersystemelapsed
probeSequences5.030.205.24