BioC 3.2: CHECK report for AnalysisPageServer on perceval

Package: AnalysisPageServer

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnalysisPageServer_1.4.0.tar.gz

StartedAt: 2015-11-10 01:53:35 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:10:37 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 1021.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AnalysisPageServer.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnalysisPageServer_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/AnalysisPageServer.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnalysisPageServer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnalysisPageServer’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘fork’ ‘FastRWeb’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/htdocs/client/.bowerrc
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  AnalysisPageServer/inst/htdocs/client/js/src/models/parameters/combobox/createComboboxParameterModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/views/analysis/plot/sidebar/SidebarDownloadSectionView.js
  AnalysisPageServer/inst/htdocs/client/js/src/views/parameters/combobox/createComboboxParameterView.js

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnalysisPageServer’ can be installed ... [8s/313s] OK
* checking installed package size ... NOTE
  installed size is 31.9Mb
  sub-directories of 1Mb or more:
    doc     26.2Mb
    htdocs   4.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
* 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
'library' or 'require' calls in package code:
  ‘FastRWeb’ ‘fork’ ‘RUnit’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘log4r:::INFO’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
check.same.svgs: no visible global function definition for
  ‘checkEquals’
checkRookForkForVignettes: no visible binding for '<<-' assignment to
  ‘no.rook.fork.msg’
checkRookForkForVignettes : <anonymous>: no visible binding for global
  variable ‘no.rook.fork.msg’
checkRookForkForVignettes: no visible binding for global variable
  ‘no.rook.fork.msg’
client.ip: no visible binding for global variable ‘SERVER’
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to ‘GET’
new.FastRWeb.analysis.page.run : handler: no visible global function
  definition for ‘parse.multipart’
new.FastRWeb.analysis.page.run : handler: no visible binding for global
  variable ‘request’
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to ‘POST’
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to ‘SERVER’
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to ‘FILES’
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to ‘setContentType’
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to ‘setHeader’
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to ‘sendBin’
new.FastRWeb.analysis.page.run : handler: no visible binding for global
  variable ‘SERVER’
new.FastRWeb.analysis.page.run : handler: no visible global function
  definition for ‘WebResult’
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to ‘POST’
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to ‘GET’
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to ‘SERVER’
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to ‘FILES’
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to ‘setContentType’
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to ‘setHeader’
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to ‘sendBin’
new.rook.analysis.page.app: no visible binding for global variable
  ‘App’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘GET’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘POST’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘FILES’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘is.textarea.wrap.request’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘setContentType’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘setHeader’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘in.analysis’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘analysis.id’
rapache.app.from.registry : <anonymous>: no visible binding for '<<-'
  assignment to ‘analysis.id’
rapache.app.from.registry : <anonymous>: no visible binding for '<<-'
  assignment to ‘in.analysis’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘events’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘plot.file’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘sendBin’
rapache.app.from.registry : <anonymous> : <anonymous>: no visible
  global function definition for ‘process.response’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘params’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘clean.tmpdir’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘file.params’
rapache.app.from.registry : <anonymous>: no visible binding for '<<-'
  assignment to ‘plot.file’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘temp.plot.file’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘SERVER’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘analysis’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘brand’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘page.params’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘all.pages’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘status’
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable ‘retrieve’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘handlers’
rapache.app.from.registry : <anonymous>: no visible global function
  definition for ‘resources’
rapache.app.from.registry : <anonymous> : <anonymous>: no visible
  global function definition for ‘handler’
startRookAnalysisPageServer: no visible binding for '<<-' assignment to
  ‘server.pid’
startRookAnalysisPageServer: no visible binding for global variable
  ‘server.pid’
test.package: no visible global function definition for
  ‘defineTestSuite’
test.package: no visible global function definition for ‘runTestSuite’
test.package: no visible global function definition for
  ‘printTextProtocol’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'requestEnv.Rd':
  ‘appendCustomSection’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following directories should probably not be installed:
  ‘images’, ‘img’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [2s/30s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
execute.handler 0.097  0.026   9.958
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unit_tests.R’ [9s/93s]
 [10s/93s] 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: 1 WARNING, 9 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/AnalysisPageServer.Rcheck/00check.log’
for details.

* installing *source* package ‘AnalysisPageServer’ ...
** libs
** arch - 
R CMD SHLIB AnalysisPageSVG.cpp tinyxml2.cpp cor.cpp catch.c SearchReplace2.cpp R_init_AnalysisPageServer.cpp -o AnalysisPageServer.so
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o
AnalysisPageSVG.cpp: In function ‘int matchPlotPoints(XMLElementList, std::deque<double, std::allocator<double> >, std::deque<double, std::allocator<double> >, double, int, int)’:
AnalysisPageSVG.cpp:154: warning: comparison between signed and unsigned integer expressions
AnalysisPageSVG.cpp:157: warning: comparison between signed and unsigned integer expressions
AnalysisPageSVG.cpp:194: warning: comparison between signed and unsigned integer expressions
AnalysisPageSVG.cpp:210: warning: comparison between signed and unsigned integer expressions
AnalysisPageSVG.cpp:215: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c tinyxml2.cpp -o tinyxml2.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c cor.cpp -o cor.o
cor.cpp: In function ‘double basic_cor(const std::deque<double, std::allocator<double> >&, const std::deque<double, std::allocator<double> >&)’:
cor.cpp:24: warning: comparison between signed and unsigned integer expressions
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c catch.c -o catch.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c SearchReplace2.cpp -o SearchReplace2.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o AnalysisPageServer.so AnalysisPageSVG.o tinyxml2.o cor.o catch.o SearchReplace2.o R_init_AnalysisPageServer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/libs
** R
** inst
** preparing package for lazy loading
While loading AnalysisPageServer: urlEncode not found, providing a pure R implementation
While loading AnalysisPageServer: urlDecode not found, providing a pure R implementation
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnalysisPageServer)

name	user	system	elapsed
add.event	0.001	0.000	0.001
add.event.handler	0.002	0.000	0.003
analysis.page.link	0.001	0.001	0.002
aps.urlEncode	0.001	0.000	0.001
array.param	0.001	0.000	0.001
bool.param	0.001	0.000	0.001
build.service	0.002	0.000	0.002
checkPackageInstalled	0.002	0.000	0.003
clear.event.handlers	0.002	0.001	0.003
client.ip	0.001	0.000	0.001
combobox.param	0.001	0.000	0.001
compound.param	0.002	0.000	0.002
copy.front.end	0.001	0.000	0.001
data.frame.to.json	0.005	0.001	0.005
data.frame.to.list	0.002	0.001	0.002
default.param	0.001	0.000	0.002
default.param.set	0.002	0.000	0.002
dies.ok	0.015	0.001	0.015
embed.APS.dataset	0.001	0.000	0.001
event.names	0.001	0.000	0.001
execute.handler	0.097	0.026	9.958
file.param	0.001	0.000	0.001
get.APS.outdir	0.001	0.000	0.001
get.page	0.054	0.004	1.167
getTraceback	0.005	0.000	0.005
has.event	0.002	0.000	0.002
has.page	0.045	0.003	0.887
lives.ok	0.000	0.000	0.001
new.FastRWeb.analysis.page.run	0.001	0.000	0.001
new.analysis.page	0.036	0.002	0.927
new.datanode.array	0.016	0.002	0.303
new.datanode.html	0.001	0.000	0.001
new.datanode.simple	0.001	0.000	0.001
new.event.registry	0.001	0.000	0.000
new.registry	0.001	0.000	0.001
new.response	0.002	0.000	0.002
new.rook.analysis.page.app	0.001	0.000	0.001
pages	0.045	0.003	0.920
param.set	0.001	0.000	0.001
register.page	0.036	0.003	0.742
remove.event	0.001	0.000	0.001
requestEnv	0.001	0.000	0.001
reset.APS.outdir	0.000	0.000	0.001
rook.analysis.page.server.landing.page	0	0	0
select.param	0	0	0
set.APS.outdir	0.000	0.000	0.001
setup.APS.knitr	0.001	0.000	0.000
simple.param	0.001	0.000	0.001
slider.param	0.001	0.000	0.001
startRookAnalysisPageServer	0.002	0.001	0.001
static.analysis.page	0.01	0.00	0.01
trig.registry	0.084	0.004	1.787
trigger.event	0.002	0.000	0.001
tryKeepConditions	0.002	0.000	0.002
tryKeepTraceback	0.004	0.000	0.004
uniquify.ids.in.svg.files	0.038	0.019	1.955
validate.param.value	0.001	0.000	0.001
vwc.conditions	0.002	0.000	0.003
vwc.error	0.002	0.000	0.003
vwc.error.condition	0.001	0.000	0.001
vwc.error.traceback	0.006	0.000	0.005
vwc.is.error	0.002	0.000	0.002
vwc.messages	0.001	0.000	0.001
vwc.messages.conditions	0.002	0.001	0.001
vwc.messages.tracebacks	0.01	0.00	0.01
vwc.n	0.002	0.000	0.001
vwc.n.messages	0.001	0.000	0.002
vwc.n.warnings	0.001	0.000	0.001
vwc.tracebacks	0.010	0.001	0.011
vwc.value	0.001	0.000	0.001
vwc.warnings	0.001	0.000	0.002
vwc.warnings.conditions	0.001	0.000	0.002
vwc.warnings.tracebacks	0.011	0.001	0.010