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BioC 3.5: CHECK report for KEGGlincs on tokay2

This page was generated on 2017-08-16 13:26:17 -0400 (Wed, 16 Aug 2017).

Package 702/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGlincs 1.2.0
Shana White , Mario Medvedovic
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/KEGGlincs
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: KEGGlincs
Version: 1.2.0
Command: rm -rf KEGGlincs.buildbin-libdir KEGGlincs.Rcheck && mkdir KEGGlincs.buildbin-libdir KEGGlincs.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGlincs.buildbin-libdir KEGGlincs_1.2.0.tar.gz >KEGGlincs.Rcheck\00install.out 2>&1 && cp KEGGlincs.Rcheck\00install.out KEGGlincs-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=KEGGlincs.buildbin-libdir --install="check:KEGGlincs-install.out" --force-multiarch --no-vignettes --timings KEGGlincs_1.2.0.tar.gz
StartedAt: 2017-08-16 00:47:28 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:53:23 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 354.8 seconds
RetCode: 0
Status:  OK  
CheckDir: KEGGlincs.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf KEGGlincs.buildbin-libdir KEGGlincs.Rcheck && mkdir KEGGlincs.buildbin-libdir KEGGlincs.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGlincs.buildbin-libdir KEGGlincs_1.2.0.tar.gz >KEGGlincs.Rcheck\00install.out 2>&1 && cp KEGGlincs.Rcheck\00install.out KEGGlincs-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=KEGGlincs.buildbin-libdir --install="check:KEGGlincs-install.out" --force-multiarch --no-vignettes --timings KEGGlincs_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/KEGGlincs.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KEGGlincs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGlincs' version '1.2.0'
* 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 'KEGGlincs' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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 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
overlap_info            16.64   0.97   17.93
add_edge_data           15.22   1.03   17.27
add_KEGG_drugs          10.20   0.27   16.19
refine_mappings          9.27   0.33    9.92
path_genes_by_cell_type  8.59   0.20    9.07
edge_mapping_info        8.42   0.32    9.02
get_graph_object         7.88   0.21    8.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
add_edge_data           15.76   0.52   16.54
overlap_info            13.70   0.59   14.57
add_KEGG_drugs          11.79   0.30   19.22
edge_mapping_info        8.92   0.25    9.42
path_genes_by_cell_type  8.38   0.30    8.94
refine_mappings          7.53   0.27    8.06
get_graph_object         5.01   0.06    5.32
* 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: OK

KEGGlincs.Rcheck/00install.out:


install for i386

* installing *source* package 'KEGGlincs' ...
** R
** 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 'KEGGlincs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGlincs' as KEGGlincs_1.2.0.zip
* DONE (KEGGlincs)

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

nameusersystemelapsed
KEGG_lincs000
add_KEGG_drugs10.20 0.2716.19
add_edge_data15.22 1.0317.27
cyto_vis0.490.020.76
edge_mapping_info8.420.329.02
expand_KEGG_edges0.340.000.62
expand_KEGG_mappings0.270.000.53
generate_mappings000
get_KGML0.260.031.13
get_drug_table0.410.001.87
get_fisher_info000
get_graph_object7.880.218.39
node_mapping_info0.280.000.57
overlap_info16.64 0.9717.93
path_genes_by_cell_type8.590.209.07
refine_mappings9.270.339.92

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

nameusersystemelapsed
KEGG_lincs000
add_KEGG_drugs11.79 0.3019.22
add_edge_data15.76 0.5216.54
cyto_vis0.550.000.81
edge_mapping_info8.920.259.42
expand_KEGG_edges0.710.031.03
expand_KEGG_mappings0.280.000.54
generate_mappings0.020.000.02
get_KGML0.310.001.14
get_drug_table0.330.001.25
get_fisher_info0.020.000.02
get_graph_object5.010.065.32
node_mapping_info0.300.000.57
overlap_info13.70 0.5914.57
path_genes_by_cell_type8.380.308.94
refine_mappings7.530.278.06