RWebServices 1.36.0
Martin Morgan
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/RWebServices | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RWebServices_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RWebServices.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RWebServices/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RWebServices’ version ‘1.36.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
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:
RWebServices/inst/unitTests/java/src/org/bioconductor/packages/rservices/Rinput/ClassUnionConverter.R
RWebServices/inst/unitTests/java/src/org/bioconductor/packages/rservices/testdata/MyUnionFactory.java
RWebServices/inst/unitTests/java/src/org/bioconductor/packages/rservices/testdata/MyUnionRCharFactory.java
RWebServices/inst/unitTests/java/src/org/bioconductor/packages/rservices/testdata/MyUnionRLogicalFactory.java
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 ‘RWebServices’ 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
* 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
Unexported object imported by a ':::' call: ‘tools:::.Rd_get_section’
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
.generateREnv : <anonymous>: no visible global function definition for
‘packageDescription’
checkJava2R: no visible global function definition for ‘capture.output’
checkPkgVersion: no visible global function definition for
‘packageDescription’
debugPrint: no visible global function definition for ‘str’
getRSessionInfo: no visible global function definition for
‘sessionInfo’
getRSessionInfo: no visible global function definition for
‘capture.output’
generateFuncTest,demo : <anonymous>: no visible binding for global
variable ‘JtypeSig’
generateJavaWrapper,jms: no visible global function definition for
‘packageDescription’
generateMainJavaAPI,demo: no visible binding for global variable
‘jTypeInfo’
typeInfo2Java,SimultaneousTypeSpecification: no visible global function
definition for ‘TypedSignature’
typeInfo2Java,function: no visible global function definition for
‘typeInfo’
typeInfo2Java,genericFunction: no visible global function definition
for ‘TypedSignature’
typeInfo2Java,genericFunction : updateASig: no visible binding for
global variable ‘InheritsTypeTest’
typeInfo2Java,genericFunction: no visible global function definition
for ‘InheritsTypeTest’
Undefined global functions or variables:
InheritsTypeTest JtypeSig TypedSignature capture.output jTypeInfo
packageDescription sessionInfo str typeInfo
Consider adding
importFrom("utils", "capture.output", "packageDescription",
"sessionInfo", "str")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/RWebServices.Rcheck/00check.log’
for details.
* installing *source* package ‘RWebServices’ ...
Guessing SJava home: /home/biocbuild/bbs-3.3-bioc/meat/RWebServices.Rcheck/SJava
checking Java support in R... configure: creating ./config.status
config.status: creating inst/scripts/RWebServicesEnv.properties
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include -fpic -g -O2 -Wall -c RWebServicesConverters.c -o RWebServicesConverters.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/../include -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o RWebServices.so RWebServicesConverters.o init.o -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/RWebServices.Rcheck/RWebServices/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RWebServices)