BioC 3.4: CHECK report for ProCoNA on moscato1
This page was generated on 2016-09-21 03:45:15 -0700 (Wed, 21 Sep 2016).
ProCoNA 1.11.0
David L Gibbs
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ProCoNA | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: ProCoNA
|
| Version: 1.11.0
|
| Command: rm -rf ProCoNA.buildbin-libdir ProCoNA.Rcheck && mkdir ProCoNA.buildbin-libdir ProCoNA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.11.0.tar.gz >ProCoNA.Rcheck\00install.out 2>&1 && cp ProCoNA.Rcheck\00install.out ProCoNA-install.out && D:\biocbld\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_1.11.0.tar.gz
|
| StartedAt: 2016-09-20 14:14:21 -0700 (Tue, 20 Sep 2016)
|
| EndedAt: 2016-09-20 14:20:00 -0700 (Tue, 20 Sep 2016)
|
| EllapsedTime: 339.0 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: ProCoNA.Rcheck
|
| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf ProCoNA.buildbin-libdir ProCoNA.Rcheck && mkdir ProCoNA.buildbin-libdir ProCoNA.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ProCoNA.buildbin-libdir ProCoNA_1.11.0.tar.gz >ProCoNA.Rcheck\00install.out 2>&1 && cp ProCoNA.Rcheck\00install.out ProCoNA-install.out && D:\biocbld\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_1.11.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/ProCoNA.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.11.0'
* 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
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bootstrapProconaNetwork 5.61 0.08 5.69
* 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
'D:/biocbld/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=16
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=16
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
** 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=16
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=16
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
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=16
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=16
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.6)
than is installed on your system (0.12.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
* MD5 sums
packaged installation of 'ProCoNA' as ProCoNA_1.11.0.zip
* DONE (ProCoNA)
ProCoNA.Rcheck/examples_i386/ProCoNA-Ex.timings:
| name | user | system | elapsed
|
| MMvsPS | 0.35 | 0.02 | 0.35 |
|
| MMvsPSallModules | 0 | 0 | 0 |
|
| accessors | 0.28 | 0.01 | 0.30 |
|
| bootstrapProconaNetwork | 4.30 | 0.08 | 4.38 |
|
| buildProconaNetwork | 3.2 | 0.0 | 3.2 |
|
| compareNetworksWithFishersExactTest | 0 | 0 | 0 |
|
| compareNetworksWithFishersExactTestProcona | 0 | 0 | 0 |
|
| corBootstrap | 1.09 | 0.02 | 1.11 |
|
| correlationWithPhenotypesHeatMap | 2.20 | 0.00 | 2.79 |
|
| getFisherMatrix | 0.63 | 0.00 | 0.63 |
|
| goStatTest | 0 | 0 | 0 |
|
| hclust | 0 | 0 | 0 |
|
| moduleMemberCorrelations | 0.27 | 0.00 | 0.27 |
|
| modulePhenotypeCorrelations | 0.25 | 0.01 | 0.27 |
|
| peptideConnectivityTest | 1.00 | 0.03 | 1.03 |
|
| peptideCorrelationTest | 2.87 | 0.03 | 3.16 |
|
| plotNet | 0.28 | 0.00 | 0.28 |
|
| ppiPermTest | 0.34 | 0.00 | 0.35 |
|
| printNet | 0 | 0 | 0 |
|
| subsetPeptideData | 0.38 | 0.05 | 0.42 |
|
| toPermTest | 0.75 | 0.00 | 0.75 |
|
| utri | 0 | 0 | 0 |
|
ProCoNA.Rcheck/examples_x64/ProCoNA-Ex.timings:
| name | user | system | elapsed
|
| MMvsPS | 0.31 | 0.02 | 0.32 |
|
| MMvsPSallModules | 0 | 0 | 0 |
|
| accessors | 0.25 | 0.01 | 0.27 |
|
| bootstrapProconaNetwork | 5.61 | 0.08 | 5.69 |
|
| buildProconaNetwork | 3.19 | 0.03 | 3.22 |
|
| compareNetworksWithFishersExactTest | 0 | 0 | 0 |
|
| compareNetworksWithFishersExactTestProcona | 0 | 0 | 0 |
|
| corBootstrap | 1.09 | 0.02 | 1.10 |
|
| correlationWithPhenotypesHeatMap | 2.49 | 0.04 | 2.58 |
|
| getFisherMatrix | 0.28 | 0.00 | 0.28 |
|
| goStatTest | 0 | 0 | 0 |
|
| hclust | 0 | 0 | 0 |
|
| moduleMemberCorrelations | 0.24 | 0.02 | 0.25 |
|
| modulePhenotypeCorrelations | 0.22 | 0.00 | 0.22 |
|
| peptideConnectivityTest | 1.28 | 0.00 | 1.28 |
|
| peptideCorrelationTest | 3.43 | 0.00 | 3.43 |
|
| plotNet | 0.24 | 0.01 | 0.25 |
|
| ppiPermTest | 0.33 | 0.00 | 0.33 |
|
| printNet | 0 | 0 | 0 |
|
| subsetPeptideData | 0.34 | 0.04 | 0.38 |
|
| toPermTest | 0.45 | 0.01 | 0.46 |
|
| utri | 0 | 0 | 0 |
|