AnalysisPageServer 1.4.1
Brad Friedman
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/AnalysisPageServer | | Last Changed Rev: 111591 / Revision: 116712 | | Last Changed Date: 2015-12-17 08:31:56 -0800 (Thu, 17 Dec 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings AnalysisPageServer_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/AnalysisPageServer.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.1’
* 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 ... [7s/7s] OK
* checking installed package size ... NOTE
installed size is 32.7Mb
sub-directories of 1Mb or more:
doc 26.3Mb
htdocs 4.7Mb
* 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’ ‘RUnit’ ‘fork’
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 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘unit_tests.R’ [7s/14s]
[7s/15s] 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
‘/home/biocbuild/bbs-3.2-bioc/meat/AnalysisPageServer.Rcheck/00check.log’
for details.
* installing *source* package ‘AnalysisPageServer’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o
AnalysisPageSVG.cpp: In function ‘int matchPlotPoints(XMLElementList, std::deque<double>, std::deque<double>, double, int, int)’:
AnalysisPageSVG.cpp:154:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(n != y.size()) throw "x and y have different lengths";
^
AnalysisPageSVG.cpp:157:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(els.size() < start + n) {
^
AnalysisPageSVG.cpp:194:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < x.size(); i++) {
^
AnalysisPageSVG.cpp:210:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < els_x.size(); i++) {
^
AnalysisPageSVG.cpp:215:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i = 0; i < els_y.size(); i++) {
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SearchReplace2.cpp -o SearchReplace2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c catch.c -o catch.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cor.cpp -o cor.o
cor.cpp: In function ‘double basic_cor(const std::deque<double>&, const std::deque<double>&)’:
cor.cpp:24:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(n != y.size()) throw "different sizes";
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tinyxml2.cpp -o tinyxml2.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o AnalysisPageServer.so AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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)