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BioC 2.13: CHECK report for SLGI on moscato1

This page was generated on 2014-04-05 09:49:37 -0700 (Sat, 05 Apr 2014).

Package 665/750HostnameOS / ArchBUILDCHECKBUILD BIN
SLGI 1.22.0
Nolwenn Le Meur
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/SLGI
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: SLGI
Version: 1.22.0
Command: rm -rf SLGI.buildbin-libdir && mkdir SLGI.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SLGI.buildbin-libdir SLGI_1.22.0.tar.gz >SLGI-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=SLGI.buildbin-libdir --install="check:SLGI-install.out" --force-multiarch --no-vignettes --timings SLGI_1.22.0.tar.gz && mv SLGI.buildbin-libdir/* SLGI.Rcheck/ && rmdir SLGI.buildbin-libdir
StartedAt: 2014-04-05 06:49:12 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 06:58:01 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 529.0 seconds
RetCode: 0
Status:  OK  
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/SLGI.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SLGI/DESCRIPTION' ... OK
* this is package 'SLGI' version '1.22.0'
* 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 'SLGI' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.9Mb
  sub-directories of 1Mb or more:
    data      4.2Mb
    extdata  11.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'ScISI' 'lattice' 'GO.db'
A package should be listed in only one of these fields.
* 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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'SLGI.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [160s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary        27.09   0.05   27.13
siResult-class  19.63   2.31   21.94
plot            19.26   1.49   20.75
compare         16.31   0.09   16.40
modelSLGI       15.07   1.28   16.35
topInteraction   9.46   1.04   10.50
twoWayTable      9.92   0.03    9.95
normInteraction  7.41   1.27    8.69
AtongFnDomain    6.71   0.08    6.79
** running examples for arch 'x64' ... [157s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary        33.09   0.25   33.34
plot            18.31   1.86   20.17
siResult-class  17.69   1.69   19.37
modelSLGI       13.82   1.65   15.47
compare         14.34   0.00   14.34
twoWayTable     11.26   0.14   11.40
topInteraction   8.24   1.09    9.33
normInteraction  7.07   1.86    8.96
AtongFnDomain    5.75   0.03    5.77
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/SLGI.Rcheck/00check.log'
for details.

SLGI.Rcheck/00install.out:


install for i386

* installing *source* package 'SLGI' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot

install for x64

* installing *source* package 'SLGI' ...
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot
* MD5 sums
packaged installation of 'SLGI' as SLGI_1.22.0.zip
* DONE (SLGI)

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

nameusersystemelapsed
Atong0.030.000.03
AtongFnDomain6.710.086.79
AtongPair0.080.000.08
SDL0.000.020.01
SGA0.000.010.02
SGD.SL0.170.020.18
TFmat0.110.000.11
byComplex0.690.000.69
comemberIn1.000.031.03
compare16.31 0.0916.40
congruence0.030.000.03
createSquareMatrix0.360.040.39
domainDist4.600.064.66
essglist0.130.000.13
getInteraction0.140.000.14
getSharedDomains0.390.020.41
getSharedInteraction000
getTestedPairs0.040.000.03
getUniquePairs0.030.000.04
gi20050.100.000.09
gi20070.180.000.19
gi2Interactome000
hyperG0.010.000.01
iSummary27.09 0.0527.13
modelSLGI15.07 1.2816.35
normInteraction7.411.278.69
plot19.26 1.4920.75
seqMatcherAlign0.040.000.03
sharedBy4.560.064.62
sharedInt000
siResult-class19.63 2.3121.94
test2Interact0.180.000.19
topInteraction 9.46 1.0410.50
twoWayTable9.920.039.95
withinComplex1.110.001.11

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

nameusersystemelapsed
Atong0.020.000.02
AtongFnDomain5.750.035.77
AtongPair0.330.000.32
SDL0.010.000.02
SGA0.020.000.02
SGD.SL0.120.020.14
TFmat0.100.000.09
byComplex0.360.000.36
comemberIn1.130.011.14
compare14.34 0.0014.34
congruence000
createSquareMatrix0.340.000.34
domainDist2.390.002.38
essglist0.340.000.34
getInteraction0.000.020.02
getSharedDomains0.100.010.11
getSharedInteraction0.020.000.02
getTestedPairs0.010.000.01
getUniquePairs0.030.000.03
gi20050.070.000.07
gi20070.120.020.14
gi2Interactome0.020.000.01
hyperG0.010.000.02
iSummary33.09 0.2533.34
modelSLGI13.82 1.6515.47
normInteraction7.071.868.96
plot18.31 1.8620.17
seqMatcherAlign0.030.000.03
sharedBy3.810.073.89
sharedInt0.490.000.49
siResult-class17.69 1.6919.37
test2Interact0.030.000.03
topInteraction8.241.099.33
twoWayTable11.26 0.1411.40
withinComplex1.690.031.72