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 BiGGR on moscato2

This page was generated on 2015-10-09 09:30:38 -0700 (Fri, 09 Oct 2015).

Package 86/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiGGR 1.4.0
Anand K. Gavai , Hannes Hettling
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/BiGGR
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  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: BiGGR
Version: 1.4.0
Command: rm -rf BiGGR.buildbin-libdir BiGGR.Rcheck && mkdir BiGGR.buildbin-libdir BiGGR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiGGR.buildbin-libdir BiGGR_1.4.0.tar.gz >BiGGR.Rcheck\00install.out 2>&1 && cp BiGGR.Rcheck\00install.out BiGGR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=BiGGR.buildbin-libdir --install="check:BiGGR-install.out" --force-multiarch --no-vignettes --timings BiGGR_1.4.0.tar.gz
StartedAt: 2015-10-08 23:38:00 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:49:53 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 713.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BiGGR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BiGGR.buildbin-libdir BiGGR.Rcheck && mkdir BiGGR.buildbin-libdir BiGGR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiGGR.buildbin-libdir BiGGR_1.4.0.tar.gz >BiGGR.Rcheck\00install.out 2>&1 && cp BiGGR.Rcheck\00install.out BiGGR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=BiGGR.buildbin-libdir --install="check:BiGGR-install.out" --force-multiarch --no-vignettes --timings BiGGR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/BiGGR.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 'BiGGR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiGGR' version '1.4.0'
* 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 'BiGGR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'stringr'
  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
gprMapping: no visible global function definition for 'str_detect'
sampleFluxEnsemble: no visible global function definition for 'Xsample'
sampleFluxEnsemble: no visible global function definition for 'xsample'
sbml2hyperdraw: no visible global function definition for 'graphLayout'
sbml2hyperdraw: no visible global function definition for
  'nodeDataDefaults<-'
sbml2hyperdraw: no visible global function definition for
  'edgeDataDefaults<-'
sbml2hyperdraw: no visible global function definition for
  'graphDataDefaults<-'
sbml2hyperdraw : <anonymous>: no visible global function definition for
  'edgeData<-'
* 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' ... [294s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
gprMapping            213.24   0.00  213.30
gprMappingAvg          20.39   0.05   20.45
buildSBMLFromGenes      9.61   0.09    9.70
buildSBMLFromPathways   5.82   0.05    5.91
BiGGR-package           4.57   0.13    5.01
** running examples for arch 'x64' ... [278s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
gprMapping            204.15   0.02  204.19
gprMappingAvg          22.23   0.04   22.29
buildSBMLFromGenes      7.94   0.21    8.14
buildSBMLFromPathways   5.65   0.01    5.66
* 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/BiGGR.Rcheck/00check.log'
for details.


BiGGR.Rcheck/00install.out:


install for i386

* installing *source* package 'BiGGR' ...
** R
** data
** 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 'BiGGR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiGGR' as BiGGR_1.4.0.zip
* DONE (BiGGR)

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

nameusersystemelapsed
BiGGR-package4.570.135.01
E.coli_iAF12601.640.111.74
E.coli_iJR9040.900.010.92
E.coli_textbook0.110.030.14
H.pylori_ilT3410.440.040.47
H.sapiens_Recon12.110.062.17
M.barkeri_iAF6920.400.060.46
M.tuberculosis_iNJ6610.460.050.50
P.putida_iJN7460.510.030.55
Recon23.510.063.57
S.aureus_iSB6190.640.030.67
S.cerevisiae_iND7500.870.050.92
buildSBMLFromBiGG0.270.000.27
buildSBMLFromGenes9.610.099.70
buildSBMLFromPathways5.820.055.91
buildSBMLFromReactionIDs2.340.002.34
createLIMFromBiGG0.140.000.16
createLIMFromSBML1.610.031.63
extractGeneAssociations3.530.003.53
extractPathways2.870.022.88
getPathwaysForSBML3.540.013.56
getRates0.010.000.02
gprMapping213.24 0.00213.30
gprMappingAvg20.39 0.0520.45
lying.tunell.data000
rmvSpliceVariant2.890.002.89
sampleFluxEnsemble3.440.654.11
sbml2hyperdraw3.330.003.67

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

nameusersystemelapsed
BiGGR-package3.830.033.92
E.coli_iAF12600.770.080.84
E.coli_iJR9040.50.00.5
E.coli_textbook0.040.030.08
H.pylori_ilT3410.210.040.25
H.sapiens_Recon11.650.081.73
M.barkeri_iAF6920.340.100.44
M.tuberculosis_iNJ6610.380.030.40
P.putida_iJN7460.430.030.47
Recon23.110.063.17
S.aureus_iSB6190.360.020.37
S.cerevisiae_iND7500.500.010.51
buildSBMLFromBiGG0.190.000.19
buildSBMLFromGenes7.940.218.14
buildSBMLFromPathways5.650.015.66
buildSBMLFromReactionIDs2.070.002.08
createLIMFromBiGG0.170.000.58
createLIMFromSBML1.360.031.39
extractGeneAssociations2.670.002.66
extractPathways2.530.002.53
getPathwaysForSBML3.330.003.34
getRates000
gprMapping204.15 0.02204.19
gprMappingAvg22.23 0.0422.29
lying.tunell.data0.010.000.02
rmvSpliceVariant2.700.002.69
sampleFluxEnsemble3.110.743.87
sbml2hyperdraw3.580.003.59