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BioC experimental data: CHECK report for ChAMPdata on moscato1

This page was generated on 2015-08-22 17:44:24 -0700 (Sat, 22 Aug 2015).

Package 38/246HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMPdata 1.7.0
Tiffany Morris
Snapshot Date: 2015-08-22 06:15:25 -0700 (Sat, 22 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ChAMPdata
Last Changed Rev: 3281 / Revision: 3391
Last Changed Date: 2015-04-16 13:20:43 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: ChAMPdata
Version: 1.7.0
Command: rm -rf ChAMPdata.buildbin-libdir ChAMPdata.Rcheck && mkdir ChAMPdata.buildbin-libdir ChAMPdata.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChAMPdata.buildbin-libdir ChAMPdata_1.7.0.tar.gz >ChAMPdata.Rcheck\00install.out 2>&1 && cp ChAMPdata.Rcheck\00install.out ChAMPdata-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ChAMPdata.buildbin-libdir --install="check:ChAMPdata-install.out" --force-multiarch --no-vignettes --timings ChAMPdata_1.7.0.tar.gz
StartedAt: 2015-08-22 10:31:58 -0700 (Sat, 22 Aug 2015)
EndedAt: 2015-08-22 10:41:52 -0700 (Sat, 22 Aug 2015)
EllapsedTime: 594.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ChAMPdata.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ChAMPdata.buildbin-libdir ChAMPdata.Rcheck && mkdir ChAMPdata.buildbin-libdir ChAMPdata.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ChAMPdata.buildbin-libdir ChAMPdata_1.7.0.tar.gz >ChAMPdata.Rcheck\00install.out 2>&1 && cp ChAMPdata.Rcheck\00install.out ChAMPdata-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=ChAMPdata.buildbin-libdir --install="check:ChAMPdata-install.out" --force-multiarch --no-vignettes --timings ChAMPdata_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-data-experiment/meat/ChAMPdata.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 'ChAMPdata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChAMPdata' version '1.7.0'
* 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 'ChAMPdata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 245.6Mb
  sub-directories of 1Mb or more:
    data     122.0Mb
    extdata  123.6Mb
* 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
* 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 Rd files ... NOTE
prepare_Rd: bloodCtl.Rd:162-164: Dropping empty section \details
prepare_Rd: bloodCtl.Rd:165-167: Dropping empty section \source
prepare_Rd: bloodCtl.Rd:168-170: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'multi.hit' 'snp.hit'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Data codoc mismatches from documentation object 'probe.features':
Variables in data frame 'probe.features'
  Code: CHR MAPINFO arm cgi conserved_tfbs distancetoGene feat.cgi
        feature gene
  Docs: CHR MAPINFO arm cgi feat.cgi feature feature.1 feature.2
        feature.3 feature.4 gene.1 gene.2 gene.3 gene.4

* 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 examples ...
** running examples for arch 'i386' ... [62s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ChAMPdata-package 35.94   0.39   36.39
testDataSet       21.76   0.27   22.03
** running examples for arch 'x64' ... [63s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
ChAMPdata-package 39.76   0.40    40.2
testDataSet       18.33   0.27    18.6
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-data-experiment/meat/ChAMPdata.Rcheck/00check.log'
for details.


ChAMPdata.Rcheck/00install.out:


install for i386

* installing *source* package 'ChAMPdata' ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'ChAMPdata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChAMPdata' as ChAMPdata_1.7.0.zip
* DONE (ChAMPdata)

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

nameusersystemelapsed
ChAMPdata-package35.94 0.3936.39
bloodCtl000
probe.features1.780.001.78
probeInfoALL.lv1.270.031.29
testDataSet21.76 0.2722.03

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

nameusersystemelapsed
ChAMPdata-package39.76 0.4040.20
bloodCtl000
probe.features2.190.072.24
probeInfoALL.lv0.920.010.93
testDataSet18.33 0.2718.60