Package: ExpressionView

Version: 1.34.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExpressionView.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ExpressionView_1.34.0.tar.gz

StartedAt: 2019-04-13 02:10:10 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:14:00 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 229.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ExpressionView.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ExpressionView.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ExpressionView_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ExpressionView.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExportEV.Rd:25: file link 'ISAModules' in package 'eisa' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExportEV.Rd:28: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExportEV.Rd:67: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExportEV.Rd:73: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExpressionView-package.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExpressionView-package.Rd:20: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExpressionView-package.Rd:44: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/LaunchEV.Rd:19: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/OrderEV.Rd:20: file link 'ISAModules' in package 'eisa' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/OrderEV.Rd:61: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ExpressionView.Rcheck/00install.out' for details.
* 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
* 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 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-3.8-bioc/R/library/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
ExportEV 8.41   0.14    8.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
ExportEV 6.57   0.14    6.84
* 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, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/ExpressionView.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ExpressionView_1.34.0.tar.gz && rm -rf ExpressionView.buildbin-libdir && mkdir ExpressionView.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ExpressionView.buildbin-libdir ExpressionView_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ExpressionView_1.34.0.zip && rm ExpressionView_1.34.0.tar.gz ExpressionView_1.34.0.zip
###
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install for i386

* installing *source* package 'ExpressionView' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c order.cpp -o order.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ExpressionView.buildbin-libdir/ExpressionView/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'ExportEV' with signature 'biclusters="Biclust"': no definition for class "Biclust"
** help
*** installing help indices
  converting help for package 'ExpressionView'
    finding HTML links ... done
    ExportEV                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExportEV.Rd:25: file link 'ISAModules' in package 'eisa' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExportEV.Rd:28: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExportEV.Rd:67: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExportEV.Rd:73: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
    ExpressionView-package                  html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExpressionView-package.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExpressionView-package.Rd:20: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/ExpressionView-package.Rd:44: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
    LaunchEV                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/LaunchEV.Rd:19: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
    OrderEV                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/OrderEV.Rd:20: file link 'ISAModules' in package 'eisa' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp800d4M/R.INSTALLd4c7e756f48/ExpressionView/man/OrderEV.Rd:61: file link 'biclust' in package 'biclust' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ExpressionView' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c order.cpp -o order.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ExpressionView.buildbin-libdir/ExpressionView/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ExpressionView' as ExpressionView_1.34.0.zip
* DONE (ExpressionView)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ExpressionView' successfully unpacked and MD5 sums checked
In R CMD INSTALL