ExpressionView 1.28.0
Gabor Csardi
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ExpressionView | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf ExpressionView.buildbin-libdir ExpressionView.Rcheck && mkdir ExpressionView.buildbin-libdir ExpressionView.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ExpressionView.buildbin-libdir ExpressionView_1.28.0.tar.gz >ExpressionView.Rcheck\00install.out 2>&1 && cp ExpressionView.Rcheck\00install.out ExpressionView-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ExpressionView.buildbin-libdir --install="check:ExpressionView-install.out" --force-multiarch --no-vignettes --timings ExpressionView_1.28.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ExpressionView.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 'ExpressionView/DESCRIPTION' ... OK
* this is package 'ExpressionView' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'caTools' 'bitops' 'isa2' 'eisa' 'GO.db' 'KEGG.db' 'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'ExpressionView' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'methods' 'isa2' 'eisa' 'GO.db' 'KEGG.db' 'AnnotationDbi'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'AnnotationDbi' 'GO.db' 'KEGG.db'
Please remove these calls from your code.
'library' or 'require' call to 'affy' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'bitops' 'caTools'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Missing or unexported object: 'isa2::.onUnload'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .Last.lib will not be used unless it is exported
ExportEV.Biclust: no visible global function definition for
'annotation'
ExportEV.ISAModules: no visible global function definition for
'annotation'
ExportEV.ISAModules: no visible global function definition for
'featureNames'
ExportEV.ISAModules: no visible global function definition for
'sampleNames'
ExportEV.ISAModules: no visible global function definition for
'phenoData'
ExportEV.ISAModules: no visible global function definition for
'base64encode'
ExportEV.list: no visible global function definition for 'base64encode'
LaunchEV: no visible global function definition for 'URLencode'
LaunchEV: no visible global function definition for 'browseURL'
OrderEV.list: no visible global function definition for 'flush.console'
normalize: no visible global function definition for 'hist'
ExportEV,Biclust: no visible global function definition for
'annotation'
ExportEV,ISAModules: no visible global function definition for
'annotation'
ExportEV,ISAModules: no visible global function definition for
'featureNames'
ExportEV,ISAModules: no visible global function definition for
'sampleNames'
ExportEV,ISAModules: no visible global function definition for
'phenoData'
ExportEV,ISAModules: no visible global function definition for
'base64encode'
ExportEV,list: no visible global function definition for 'base64encode'
OrderEV,list: no visible global function definition for 'flush.console'
Undefined global functions or variables:
URLencode annotation base64encode browseURL featureNames
flush.console hist phenoData sampleNames
Consider adding
importFrom("graphics", "hist")
importFrom("utils", "URLencode", "browseURL", "flush.console")
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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ExpressionView.buildbin-libdir/ExpressionView/libs/i386/ExpressionView.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
ExportEV 9.69 0.11 9.9
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ExportEV 8.43 0.15 8.6
* 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: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/ExpressionView.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'ExpressionView' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c order.cpp -o order.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c orderclusters.cpp -o orderclusters.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ExpressionView.dll tmp.def order.o orderclusters.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/ExpressionView.buildbin-libdir/ExpressionView/libs/i386
** R
** inst
** preparing package for lazy loading
in method for 'ExportEV' with signature 'biclusters="Biclust"': no definition for class "Biclust"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'ExpressionView' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c order.cpp -o order.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -mtune=core2 -c orderclusters.cpp -o orderclusters.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ExpressionView.dll tmp.def order.o orderclusters.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/ExpressionView.buildbin-libdir/ExpressionView/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ExpressionView' as ExpressionView_1.28.0.zip
* DONE (ExpressionView)