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BioC 3.1: CHECK report for SLGI on moscato2

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

Package 916/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.28.0
Nolwenn Le Meur
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/SLGI
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: SLGI
Version: 1.28.0
Command: rm -rf SLGI.buildbin-libdir SLGI.Rcheck && mkdir SLGI.buildbin-libdir SLGI.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SLGI.buildbin-libdir SLGI_1.28.0.tar.gz >SLGI.Rcheck\00install.out 2>&1 && cp SLGI.Rcheck\00install.out SLGI-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=SLGI.buildbin-libdir --install="check:SLGI-install.out" --force-multiarch --no-vignettes --timings SLGI_1.28.0.tar.gz
StartedAt: 2015-10-09 06:20:35 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:27:37 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 421.9 seconds
RetCode: 0
Status:  OK  
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SLGI.buildbin-libdir SLGI.Rcheck && mkdir SLGI.buildbin-libdir SLGI.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SLGI.buildbin-libdir SLGI_1.28.0.tar.gz >SLGI.Rcheck\00install.out 2>&1 && cp SLGI.Rcheck\00install.out SLGI-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=SLGI.buildbin-libdir --install="check:SLGI-install.out" --force-multiarch --no-vignettes --timings SLGI_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/SLGI.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 'SLGI/DESCRIPTION' ... OK
* this is package 'SLGI' version '1.28.0'
* 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
Malformed Description field: should contain one or more complete sentences.
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 ... NOTE
'library' or 'require' call to 'GO.db' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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' ... [129s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
iSummary        24.26   0.22   24.47
siResult-class  14.34   1.99   16.33
compare         13.64   2.29   15.92
plot            15.52   0.00   15.53
modelSLGI       14.22   0.17   14.40
topInteraction   7.95   1.66    9.61
normInteraction  6.21   0.43    6.64
twoWayTable      5.03   0.04    5.07
** running examples for arch 'x64' ... [118s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
iSummary       24.12   0.97   25.09
compare        14.98   1.14   16.11
plot           12.30   0.00   12.29
siResult-class 11.23   0.40   11.64
modelSLGI      11.39   0.00   11.39
topInteraction  7.10   0.84    7.94
twoWayTable     7.42   0.11    7.54
* 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/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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot

install for x64

* installing *source* package 'SLGI' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
No methods found in "BiocGenerics" for requests: plot
* MD5 sums
packaged installation of 'SLGI' as SLGI_1.28.0.zip
* DONE (SLGI)

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

nameusersystemelapsed
Atong0.010.000.01
AtongFnDomain4.600.034.64
AtongPair0.600.000.59
SDL0.010.000.02
SGA0.020.000.01
SGD.SL0.250.000.25
TFmat0.120.000.13
byComplex0.520.020.53
comemberIn0.760.020.78
compare13.64 2.2915.92
congruence000
createSquareMatrix0.200.030.24
domainDist4.230.064.29
essglist0.020.000.02
getInteraction0.010.000.01
getSharedDomains0.030.000.04
getSharedInteraction0.020.000.01
getTestedPairs0.020.000.02
getUniquePairs0.030.000.03
gi20050.090.000.09
gi20070.200.020.22
gi2Interactome000
hyperG0.020.000.02
iSummary24.26 0.2224.47
modelSLGI14.22 0.1714.40
normInteraction6.210.436.64
plot15.52 0.0015.53
seqMatcherAlign000
sharedBy3.100.043.13
sharedInt0.020.000.02
siResult-class14.34 1.9916.33
test2Interact000
topInteraction7.951.669.61
twoWayTable5.030.045.07
withinComplex1.150.031.19

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

nameusersystemelapsed
Atong000
AtongFnDomain4.760.024.77
AtongPair0.090.000.09
SDL0.010.000.02
SGA0.020.000.01
SGD.SL0.200.000.21
TFmat0.110.000.11
byComplex0.620.030.65
comemberIn0.490.080.56
compare14.98 1.1416.11
congruence000
createSquareMatrix0.420.000.43
domainDist2.870.072.94
essglist000
getInteraction0.010.000.02
getSharedDomains0.020.000.01
getSharedInteraction000
getTestedPairs0.010.000.02
getUniquePairs0.020.000.01
gi20050.060.000.06
gi20070.140.000.14
gi2Interactome000
hyperG000
iSummary24.12 0.9725.09
modelSLGI11.39 0.0011.39
normInteraction4.890.044.95
plot12.30 0.0012.29
seqMatcherAlign000
sharedBy3.490.073.56
sharedInt0.020.000.01
siResult-class11.23 0.4011.64
test2Interact000
topInteraction7.100.847.94
twoWayTable7.420.117.54
withinComplex1.640.001.63