StarBioTrek 1.0.3
Claudia Cava
| 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/StarBioTrek | | Last Changed Rev: 126629 / Revision: 128728 | | Last Changed Date: 2017-02-09 04:51:48 -0500 (Thu, 09 Feb 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf StarBioTrek.buildbin-libdir StarBioTrek.Rcheck && mkdir StarBioTrek.buildbin-libdir StarBioTrek.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=StarBioTrek.buildbin-libdir StarBioTrek_1.0.3.tar.gz >StarBioTrek.Rcheck\00install.out 2>&1 && cp StarBioTrek.Rcheck\00install.out StarBioTrek-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=StarBioTrek.buildbin-libdir --install="check:StarBioTrek-install.out" --force-multiarch --no-vignettes --timings StarBioTrek_1.0.3.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/StarBioTrek.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 'StarBioTrek/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'StarBioTrek' version '1.0.3'
* 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 'StarBioTrek' can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.8Mb
sub-directories of 1Mb or more:
data 8.8Mb
doc 1.8Mb
* checking package directory ... OK
* checking 'build' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GE_matrix: no visible binding for global variable 'path'
getKEGGdata: no visible binding for global variable 'Carbohydrate'
getKEGGdata: no visible binding for global variable 'Energy'
getKEGGdata: no visible binding for global variable 'Lipid'
getKEGGdata: no visible binding for global variable 'Aminoacid'
getKEGGdata: no visible binding for global variable 'Glybio_met'
getKEGGdata: no visible binding for global variable 'Cofa_vita_met'
getKEGGdata: no visible binding for global variable 'Transcription'
getKEGGdata: no visible binding for global variable 'Translation'
getKEGGdata: no visible binding for global variable
'Folding_sorting_and_degradation'
getKEGGdata: no visible binding for global variable
'Replication_and_repair'
getKEGGdata: no visible binding for global variable
'Signal_transduction'
getKEGGdata: no visible binding for global variable
'Signaling_molecules_and_interaction'
getKEGGdata: no visible binding for global variable
'Transport_and_catabolism'
getKEGGdata: no visible binding for global variable
'Cell_growth_and_death'
getKEGGdata: no visible binding for global variable
'Cellular_community'
getKEGGdata: no visible binding for global variable 'Immune_system'
getKEGGdata: no visible binding for global variable 'Endocrine_system'
getKEGGdata: no visible binding for global variable
'Circulatory_system'
getKEGGdata: no visible binding for global variable 'Digestive_system'
getKEGGdata: no visible binding for global variable 'Excretory_system'
getKEGGdata: no visible binding for global variable 'Nervous_system'
getKEGGdata: no visible binding for global variable 'Sensory_system'
matrix_plot: no visible binding for global variable 'path'
plotting_cross_talk: no visible binding for global variable 'path'
svm_classification: no visible binding for global variable 'Target'
Undefined global functions or variables:
Aminoacid Carbohydrate Cell_growth_and_death Cellular_community
Circulatory_system Cofa_vita_met Digestive_system Endocrine_system
Energy Excretory_system Folding_sorting_and_degradation Glybio_met
Immune_system Lipid Nervous_system Replication_and_repair
Sensory_system Signal_transduction
Signaling_molecules_and_interaction Target Transcription Translation
Transport_and_catabolism path
* 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
getNETdata 12.39 2.29 15.30
list_path_net 10.42 0.32 10.75
getKEGGdata 3.79 0.07 6.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getNETdata 9.12 2.44 12.16
list_path_net 10.91 0.23 11.14
getKEGGdata 6.67 0.14 9.20
path_net 6.36 0.22 6.58
* 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/StarBioTrek.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'StarBioTrek' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'StarBioTrek' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'StarBioTrek' as StarBioTrek_1.0.3.zip
* DONE (StarBioTrek)