Maren Sitte
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/pwOmics |
| Branch: RELEASE_3_6 |
| Last Commit: d297dc2 |
| Last Changed Date: 2017-12-13 11:21:44 -0400 (Wed, 13 Dec 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:18 -0400 (Thu, 12 Apr 2018).
| Package 1093/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pwOmics 1.10.1 Maren Sitte
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: pwOmics |
| Version: 1.10.1 |
| Command: rm -rf pwOmics.buildbin-libdir pwOmics.Rcheck && mkdir pwOmics.buildbin-libdir pwOmics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pwOmics.buildbin-libdir pwOmics_1.10.1.tar.gz >pwOmics.Rcheck\00install.out 2>&1 && cp pwOmics.Rcheck\00install.out pwOmics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=pwOmics.buildbin-libdir --install="check:pwOmics-install.out" --force-multiarch --no-vignettes --timings pwOmics_1.10.1.tar.gz |
| StartedAt: 2018-04-12 02:21:24 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:31:00 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 575.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pwOmics.Rcheck |
| Warnings: 0 |
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### Running command:
###
### rm -rf pwOmics.buildbin-libdir pwOmics.Rcheck && mkdir pwOmics.buildbin-libdir pwOmics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pwOmics.buildbin-libdir pwOmics_1.10.1.tar.gz >pwOmics.Rcheck\00install.out 2>&1 && cp pwOmics.Rcheck\00install.out pwOmics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=pwOmics.buildbin-libdir --install="check:pwOmics-install.out" --force-multiarch --no-vignettes --timings pwOmics_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/pwOmics.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pwOmics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pwOmics' version '1.10.1'
* 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 'pwOmics' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Namespaces in Imports field not imported from:
'grDevices' 'stats' 'utils'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SteinerTree_cons: no visible global function definition for 'na.omit'
clusterTimeProfiles: no visible global function definition for
'na.omit'
consDynamicNet: no visible global function definition for 'ts'
findSignalingAxes: no visible global function definition for 'na.omit'
findxneighborsoverlap: no visible global function definition for
'na.omit'
generate_DSSignalingBase: no visible global function definition for
'write.csv'
getAliasfromSTRINGIDs: no visible global function definition for
'na.omit'
getConsensusSTRINGIDs: no visible global function definition for
'na.omit'
getFCsplines: no visible global function definition for 'smooth.spline'
getGenesIntersection: no visible global function definition for
'na.omit'
getOmicsDataset: no visible global function definition for 'write.csv'
getProteinIntersection: no visible global function definition for
'na.omit'
getTFIntersection: no visible global function definition for 'na.omit'
identifyPWTFTGs: no visible binding for global variable 'upreg'
identifyPWTFTGs: no visible binding for global variable 'phosphoeffect'
identifyRsofTFs: no visible global function definition for 'na.omit'
infoConsensusGraph: no visible global function definition for 'from'
plotConsDynNet: no visible global function definition for 'pdf'
plotConsDynNet: no visible global function definition for 'qnorm'
plotConsDynNet: no visible global function definition for 'dev.off'
plotConsensusGraph: no visible global function definition for 'pdf'
plotConsensusGraph: no visible global function definition for 'dev.off'
plotConsensusProfiles: no visible global function definition for 'pdf'
plotConsensusProfiles: no visible global function definition for
'dev.off'
plotTimeProfileClusters: no visible global function definition for
'pdf'
plotTimeProfileClusters: no visible global function definition for
'rainbow'
plotTimeProfileClusters: no visible global function definition for
'dev.off'
predictFCvals: no visible global function definition for 'predict'
readPhosphodata: no visible global function definition for 'read.delim'
readTFtargets: no visible global function definition for 'read.delim'
selectPWsofTFs: no visible global function definition for 'na.omit'
staticConsensusNet: no visible global function definition for 'na.omit'
temp_correlations: no visible global function definition for 'read.csv'
temp_correlations: no visible global function definition for 'pdf'
temp_correlations: no visible global function definition for
'colorRampPalette'
temp_correlations: no visible global function definition for 'dev.off'
Undefined global functions or variables:
colorRampPalette dev.off from na.omit pdf phosphoeffect predict qnorm
rainbow read.csv read.delim smooth.spline ts upreg write.csv
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
"rainbow")
importFrom("stats", "na.omit", "predict", "qnorm", "smooth.spline",
"ts")
importFrom("utils", "read.csv", "read.delim", "write.csv")
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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
temp_correlations 173.32 0.39 174.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
temp_correlations 221.48 0.34 222.08
* 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 PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/pwOmics.Rcheck/00check.log'
for details.
pwOmics.Rcheck/00install.out
install for i386
* installing *source* package 'pwOmics' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'pwOmics'
finding HTML links ... done
OmicsExampleData html
PWidentallprots html
PWidentallprotssub html
PWidenttps html
SteinerTree_cons html
TFidentallgenes html
TFidenttps html
addFeedbackLoops html
clusterTimeProfiles html
consDynamicNet html
createBiopaxnew html
createIntIDs html
findSignalingAxes html
findxneighborsoverlap html
findxnextneighbors html
genGenelists html
genGenelistssub html
genIntIDs html
generate_DSSignalingBase html
genfullConsensusGraph html
getAlias_Ensemble html
getAliasfromSTRINGIDs html
getBiopaxModel html
getConsensusSTRINGIDs html
getDS_PWs html
getDS_TFs html
getDS_TGs html
getFCsplines html
getGenesIntersection html
getOmicsDataset html
getOmicsTimepoints html
getOmicsallGeneIDs html
getOmicsallProteinIDs html
getProteinIntersection html
getSTRING_graph html
getTFIntersection html
getUS_PWs html
getUS_TFs html
getUS_regulators html
get_matching_transcripts html
getbipartitegraphInfo html
gettpIntersection html
identPWsofTFs html
identRegulators html
identTFTGsinPWs html
identTFs html
identifyPR html
identifyPWTFTGs html
identifyPWs html
identifyRsofTFs html
identifyTFs html
infoConsensusGraph html
loadGenelists html
loadPWs html
plotConsDynNet html
plotConsensusGraph html
plotConsensusProfiles html
plotTimeProfileClusters html
predictFCvals html
preparePWinfo html
print.OmicsData html
pwIntOmics-package html
readOmics html
readPWdata html
readPhosphodata html
readTFdata html
readTFtargets html
selectPWsofTFs html
staticConsensusNet html
temp_correlations html
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'pwOmics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pwOmics' as pwOmics_1.10.1.zip
* DONE (pwOmics)
In R CMD INSTALL
In R CMD INSTALL
|
pwOmics.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("pwOmics")
RUNIT TEST PROTOCOL -- Thu Apr 12 02:30:48 2018
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
pwOmics RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
3.93 0.18 4.26
|
pwOmics.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("pwOmics")
RUNIT TEST PROTOCOL -- Thu Apr 12 02:30:53 2018
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
pwOmics RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
4.54 0.12 4.84
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pwOmics.Rcheck/examples_i386/pwOmics-Ex.timings
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pwOmics.Rcheck/examples_x64/pwOmics-Ex.timings
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