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BioC 3.4: CHECK report for ProCoNA on tokay1

This page was generated on 2017-04-15 16:18:12 -0400 (Sat, 15 Apr 2017).

Package 950/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ProCoNA 1.12.0
David L Gibbs
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ProCoNA
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  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: ProCoNA
Version: 1.12.0
Command: rm -rf ProCoNA.buildbin-libdir ProCoNA.Rcheck && mkdir ProCoNA.buildbin-libdir ProCoNA.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.12.0.tar.gz >ProCoNA.Rcheck\00install.out 2>&1 && cp ProCoNA.Rcheck\00install.out ProCoNA-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.12.0.tar.gz
StartedAt: 2017-04-15 00:10:36 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:16:01 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 325.2 seconds
RetCode: 0
Status:  OK  
CheckDir: ProCoNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ProCoNA.buildbin-libdir ProCoNA.Rcheck && mkdir ProCoNA.buildbin-libdir ProCoNA.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.12.0.tar.gz >ProCoNA.Rcheck\00install.out 2>&1 && cp ProCoNA.Rcheck\00install.out ProCoNA-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ProCoNA.buildbin-libdir --install="check:ProCoNA-install.out" --force-multiarch --no-vignettes --timings ProCoNA_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/ProCoNA.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ProCoNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ProCoNA' version '1.12.0'
* 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 'ProCoNA' 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.
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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bootstrapProconaNetwork: no visible global function definition for
  'as.dist'
bootstrapProconaNetwork: no visible global function definition for
  'cutreeDynamic'
buildProconaNetwork: no visible global function definition for
  'as.dist'
buildProconaNetwork: no visible global function definition for
  'cutreeDynamic'
MMvsPSallModules,proconaNet-matrix-numeric-character: no visible global
  function definition for 'pdf'
MMvsPSallModules,proconaNet-matrix-numeric-character: no visible global
  function definition for 'dev.off'
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for 'par'
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for 'pdf'
correlationWithPhenotypesHeatMap,proconaNet-matrix-numeric-character-character-numeric:
  no visible global function definition for 'dev.off'
getFisherMatrix,character-character-numeric-numeric: no visible global
  function definition for 'fisher.test'
peptideConnectivityTest,proconaNet-data.frame-character-character-numeric:
  no visible global function definition for 't.test'
peptideCorrelationTest,matrix-data.frame-character-character: no
  visible global function definition for 't.test'
Undefined global functions or variables:
  as.dist cutreeDynamic dev.off fisher.test par pdf t.test
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "as.dist", "fisher.test", "t.test")
to your NAMESPACE file.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork 5.28   0.11    5.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapProconaNetwork 7.36   0.07    7.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/ProCoNA.Rcheck/00check.log'
for details.


ProCoNA.Rcheck/00install.out:


install for i386

* installing *source* package 'ProCoNA' ...
** R
** data
** inst
** preparing package for lazy loading
==========================================================================
*
*  Package WGCNA 1.51 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=20
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=20
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
==========================================================================
*
*  Package WGCNA 1.51 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=20
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=20
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================



install for x64

* installing *source* package 'ProCoNA' ...
** testing if installed package can be loaded
==========================================================================
*
*  Package WGCNA 1.51 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=20
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=20
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


* MD5 sums
packaged installation of 'ProCoNA' as ProCoNA_1.12.0.zip
* DONE (ProCoNA)

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

nameusersystemelapsed
MMvsPS0.320.000.32
MMvsPSallModules000
accessors0.230.030.26
bootstrapProconaNetwork5.280.115.39
buildProconaNetwork3.020.063.08
compareNetworksWithFishersExactTest000
compareNetworksWithFishersExactTestProcona0.010.000.02
corBootstrap0.970.000.96
correlationWithPhenotypesHeatMap3.250.073.32
getFisherMatrix0.690.010.70
goStatTest000
hclust000
moduleMemberCorrelations0.260.000.27
modulePhenotypeCorrelations0.240.020.25
peptideConnectivityTest0.720.140.85
peptideCorrelationTest3.400.033.44
plotNet0.220.040.25
ppiPermTest0.300.000.29
printNet000
subsetPeptideData0.320.040.36
toPermTest0.500.020.52
utri000

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

nameusersystemelapsed
MMvsPS0.220.050.27
MMvsPSallModules0.020.000.02
accessors0.220.000.21
bootstrapProconaNetwork7.360.077.44
buildProconaNetwork4.150.074.22
compareNetworksWithFishersExactTest000
compareNetworksWithFishersExactTestProcona000
corBootstrap1.320.001.31
correlationWithPhenotypesHeatMap4.170.084.25
getFisherMatrix0.260.020.28
goStatTest000
hclust0.020.000.02
moduleMemberCorrelations0.200.010.21
modulePhenotypeCorrelations0.280.000.29
peptideConnectivityTest1.320.031.34
peptideCorrelationTest4.480.024.50
plotNet0.220.010.23
ppiPermTest0.280.000.29
printNet000
subsetPeptideData0.280.050.32
toPermTest0.420.020.44
utri000