BioC 3.5: CHECK report for sevenbridges on tokay2

Package: sevenbridges

Version: 1.6.0

Command: rm -rf sevenbridges.buildbin-libdir sevenbridges.Rcheck && mkdir sevenbridges.buildbin-libdir sevenbridges.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sevenbridges.buildbin-libdir sevenbridges_1.6.0.tar.gz >sevenbridges.Rcheck\00install.out 2>&1 && cp sevenbridges.Rcheck\00install.out sevenbridges-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=sevenbridges.buildbin-libdir --install="check:sevenbridges-install.out" --force-multiarch --no-vignettes --timings sevenbridges_1.6.0.tar.gz

StartedAt: 2017-08-16 02:50:49 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:57:02 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 372.5 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sevenbridges.buildbin-libdir sevenbridges_1.6.0.tar.gz >sevenbridges.Rcheck\00install.out 2>&1 && cp sevenbridges.Rcheck\00install.out sevenbridges-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=sevenbridges.buildbin-libdir --install="check:sevenbridges-install.out" --force-multiarch --no-vignettes --timings sevenbridges_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/sevenbridges.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 'sevenbridges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sevenbridges' version '1.6.0'
* 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 '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        53.11   0.09   53.21
Tool-class  13.97   0.00   13.97
link_what    9.22   0.00    9.22
link         9.07   0.00    9.06
convert_app  6.30   0.01    6.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
Flow        81.05   0.05   81.11
Tool-class  14.89   0.00   14.89
link        10.75   0.00   10.75
convert_app  9.88   0.00    9.87
link_what    9.67   0.00    9.67
* 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_1.6.0.zip
* DONE (sevenbridges)

name	user	system	elapsed
App-class	0	0	0
Auth-class	0.01	0.00	0.02
Binding	0.05	0.00	0.05
CCBList	0.02	0.00	0.01
CWL	0	0	0
CommandInputParameter-class	0.03	0.00	0.03
CommandInputSchema-class	0.04	0.00	0.05
CommandLineBinding-class	0	0	0
CommandLineTool	0.02	0.00	0.01
CommandOutputBinding-class	0.01	0.00	0.02
CommandOutputParameter-class	0.02	0.00	0.01
CommandOutputSchema-class	0.04	0.00	0.05
DSCList	0.03	0.00	0.03
Enum	0.05	0.00	0.05
Expression-class	0	0	0
ExpressionTool-class	0.01	0.00	0.02
File-class	0.11	0.00	0.11
Files-class	0.02	0.00	0.01
Flow	53.11	0.09	53.21
Folders-class	0.06	0.00	0.06
Metadata	0.14	0.00	0.14
Parameter	0.05	0.00	0.05
Process	0.08	0.00	0.08
ProcessRequirement	0.06	0.00	0.06
Schema	0.01	0.00	0.01
TaskHook	0	0	0
Tool-class	13.97	0.00	13.97
ToolUI	0	0	0
Workflow	0.03	0.00	0.03
WorkflowStep	0.01	0.00	0.01
addIdNum	0	0	0
api	0	0	0
as-methods	0.10	0.02	0.11
batch	0	0	0
cli_list_projects	0	0	0
cli_list_tags	0	0	0
cli_upload	0	0	0
convert_app	6.30	0.01	6.32
cwl-utils	0.29	0.02	0.31
delete-methods	0	0	0
download-methods	0	0	0
get_token	0	0	0
get_uploader	0	0	0
input_output_matrix	0.31	0.00	0.31
link	9.07	0.00	9.06
link_what	9.22	0.00	9.22
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

name	user	system	elapsed
App-class	0	0	0
Auth-class	0.02	0.00	0.02
Binding	0.05	0.03	0.10
CCBList	0.00	0.01	0.01
CWL	0	0	0
CommandInputParameter-class	0.06	0.00	0.07
CommandInputSchema-class	0.10	0.00	0.09
CommandLineBinding-class	0.01	0.00	0.02
CommandLineTool	0.03	0.00	0.03
CommandOutputBinding-class	0.02	0.00	0.01
CommandOutputParameter-class	0.01	0.00	0.02
CommandOutputSchema-class	0.05	0.00	0.05
DSCList	0.03	0.00	0.03
Enum	0.07	0.00	0.06
Expression-class	0.01	0.00	0.01
ExpressionTool-class	0.03	0.00	0.04
File-class	0.14	0.00	0.14
Files-class	0.01	0.00	0.02
Flow	81.05	0.05	81.11
Folders-class	0.03	0.00	0.03
Metadata	0.17	0.00	0.18
Parameter	0.03	0.00	0.03
Process	0.05	0.00	0.04
ProcessRequirement	0.05	0.00	0.05
Schema	0.02	0.00	0.01
TaskHook	0	0	0
Tool-class	14.89	0.00	14.89
ToolUI	0	0	0
Workflow	0.06	0.00	0.07
WorkflowStep	0	0	0
addIdNum	0.01	0.00	0.01
api	0	0	0
as-methods	0.18	0.00	0.17
batch	0	0	0
cli_list_projects	0	0	0
cli_list_tags	0	0	0
cli_upload	0	0	0
convert_app	9.88	0.00	9.87
cwl-utils	0.34	0.00	0.35
delete-methods	0	0	0
download-methods	0	0	0
get_token	0	0	0
get_uploader	0	0	0
input_output_matrix	0.39	0.00	0.39
link	10.75	0.00	10.75
link_what	9.67	0.00	9.67
project_details	0	0	0
project_members	0	0	0
requirements	0.07	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	0.01	0.00	0.02
tag-methods	0	0	0
test_tool_bunny	0.00	0.02	0.01
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