BioC 3.4: CHECK report for sevenbridges on tokay1

Package: sevenbridges

Version: 1.4.9

Command: rm -rf sevenbridges.buildbin-libdir sevenbridges.Rcheck && mkdir sevenbridges.buildbin-libdir sevenbridges.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sevenbridges.buildbin-libdir sevenbridges_1.4.9.tar.gz >sevenbridges.Rcheck\00install.out 2>&1 && cp sevenbridges.Rcheck\00install.out sevenbridges-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=sevenbridges.buildbin-libdir --install="check:sevenbridges-install.out" --force-multiarch --no-vignettes --timings sevenbridges_1.4.9.tar.gz

StartedAt: 2017-04-15 00:48:07 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:53:25 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 317.6 seconds

RetCode: 0

Status:  OK

CheckDir: sevenbridges.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf sevenbridges.buildbin-libdir sevenbridges.Rcheck && mkdir sevenbridges.buildbin-libdir sevenbridges.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sevenbridges.buildbin-libdir sevenbridges_1.4.9.tar.gz >sevenbridges.Rcheck\00install.out 2>&1 && cp sevenbridges.Rcheck\00install.out sevenbridges-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=sevenbridges.buildbin-libdir --install="check:sevenbridges-install.out" --force-multiarch --no-vignettes --timings sevenbridges_1.4.9.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/sevenbridges.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 'sevenbridges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sevenbridges' version '1.4.9'
* 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 'sevenbridges' 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
Flow        44.83   0.03   44.86
Tool-class  11.14   0.00   11.14
link_what    7.74   0.02    7.75
link         6.09   0.00    6.09
convert_app  5.34   0.00    5.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
Flow        67.57      0   67.58
Tool-class  17.84      0   17.84
link_what   12.27      0   12.27
link        11.86      0   11.86
convert_app  9.34      0    9.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: OK

install for i386

* installing *source* package 'sevenbridges' ...
** 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 'sevenbridges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sevenbridges' as sevenbridges_1.4.9.zip
* DONE (sevenbridges)

name	user	system	elapsed
App-class	0	0	0
Auth-class	0	0	0
Binding	0.01	0.00	0.01
CCBList	0	0	0
CWL	0	0	0
CommandInputParameter-class	0.02	0.00	0.02
CommandInputSchema-class	0.01	0.00	0.01
CommandLineBinding-class	0	0	0
CommandLineTool	0.01	0.00	0.01
CommandOutputBinding-class	0.1	0.0	0.1
CommandOutputParameter-class	0.01	0.00	0.01
CommandOutputSchema-class	0.02	0.00	0.02
DSCList	0.01	0.00	0.01
Enum	0.02	0.00	0.02
Expression-class	0	0	0
ExpressionTool-class	0.03	0.00	0.03
File-class	0.06	0.00	0.06
Files-class	0.02	0.00	0.02
Flow	44.83	0.03	44.86
Folders-class	0.01	0.00	0.01
Metadata	0.07	0.00	0.07
Parameter	0.03	0.00	0.03
Process	0.04	0.00	0.04
ProcessRequirement	0.05	0.00	0.05
Schema	0.02	0.00	0.02
TaskHook	0	0	0
Tool-class	11.14	0.00	11.14
ToolUI	0	0	0
Workflow	0.03	0.00	0.03
WorkflowStep	0	0	0
addIdNum	0	0	0
api	0	0	0
as-methods	0.08	0.00	0.08
batch	0	0	0
cli_list_projects	0	0	0
cli_list_tags	0	0	0
cli_upload	0	0	0
convert_app	5.34	0.00	5.34
cwl-utils	0.09	0.00	0.09
delete-methods	0	0	0
download-methods	0	0	0
get_token	0	0	0
get_uploader	0.02	0.00	0.02
input_output_matrix	0.08	0.00	0.08
link	6.09	0.00	6.09
link_what	7.74	0.02	7.75
project_details	0	0	0
project_members	0	0	0
requirements	0.06	0.00	0.06
response-methods	0	0	0
sbg_get_env	0	0	0
sbg_set_env	0	0	0
set_test_env	0	0	0
shorthand-cwl	0.03	0.00	0.04
tag-methods	0	0	0
test_tool_bunny	0	0	0
test_tool_cwlrun	0	0	0
test_tool_rabix	0	0	0
upload_complete_all	0	0	0
upload_complete_part	0	0	0
upload_delete	0	0	0
upload_info	0	0	0
upload_info_part	0	0	0
upload_init	0	0	0

name	user	system	elapsed
App-class	0	0	0
Auth-class	0.01	0.00	0.02
Binding	0.02	0.00	0.06
CCBList	0	0	0
CWL	0	0	0
CommandInputParameter-class	0.03	0.00	0.03
CommandInputSchema-class	0.02	0.00	0.02
CommandLineBinding-class	0.12	0.00	0.12
CommandLineTool	0.02	0.00	0.02
CommandOutputBinding-class	0.01	0.00	0.02
CommandOutputParameter-class	0.02	0.00	0.01
CommandOutputSchema-class	0	0	0
DSCList	0.02	0.00	0.01
Enum	0.00	0.01	0.02
Expression-class	0.02	0.00	0.01
ExpressionTool-class	0.01	0.00	0.02
File-class	0.08	0.00	0.08
Files-class	0.02	0.00	0.01
Flow	67.57	0.00	67.58
Folders-class	0	0	0
Metadata	0.1	0.0	0.1
Parameter	0.04	0.00	0.04
Process	0.07	0.00	0.06
ProcessRequirement	0.06	0.00	0.07
Schema	0.02	0.00	0.02
TaskHook	0	0	0
Tool-class	17.84	0.00	17.84
ToolUI	0	0	0
Workflow	0.04	0.00	0.03
WorkflowStep	0.01	0.00	0.02
addIdNum	0	0	0
api	0	0	0
as-methods	0.08	0.00	0.08
batch	0	0	0
cli_list_projects	0	0	0
cli_list_tags	0	0	0
cli_upload	0	0	0
convert_app	9.34	0.00	9.34
cwl-utils	0.22	0.00	0.22
delete-methods	0.02	0.00	0.02
download-methods	0	0	0
get_token	0	0	0
get_uploader	0	0	0
input_output_matrix	0.17	0.00	0.17
link	11.86	0.00	11.86
link_what	12.27	0.00	12.27
project_details	0	0	0
project_members	0	0	0
requirements	0.06	0.00	0.06
response-methods	0	0	0
sbg_get_env	0	0	0
sbg_set_env	0	0	0
set_test_env	0	0	0
shorthand-cwl	0.03	0.00	0.03
tag-methods	0	0	0
test_tool_bunny	0	0	0
test_tool_cwlrun	0	0	0
test_tool_rabix	0	0	0
upload_complete_all	0	0	0
upload_complete_part	0	0	0
upload_delete	0	0	0
upload_info	0	0	0
upload_info_part	0	0	0
upload_init	0	0	0