Gabor Csardi
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ExpressionView |
| Branch: RELEASE_3_9 |
| Last Commit: dde1873 |
| Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:48:02 -0400 (Wed, 16 Oct 2019).
| Package 532/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ExpressionView 1.36.0 Gabor Csardi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ExpressionView |
| Version: 1.36.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExpressionView.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExpressionView_1.36.0.tar.gz |
| StartedAt: 2019-10-16 02:43:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:47:28 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 219.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ExpressionView.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ExpressionView.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ExpressionView_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ExpressionView.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExpressionView/DESCRIPTION’ ... OK
* this is package ‘ExpressionView’ version ‘1.36.0’
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ExpressionView/libs/ExpressionView.so’:
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ExportEV 11.349 1.937 13.339
OrderEV 4.720 1.128 5.849
* 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/ExpressionView.Rcheck/00check.log’
for details.
ExpressionView.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ExpressionView ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘ExpressionView’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c order.cpp -o order.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c orderclusters.cpp -o orderclusters.o clang++ -std=gnu++11 -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 -o ExpressionView.so order.o orderclusters.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-ExpressionView/00new/ExpressionView/libs ** 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 ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ExpressionView)
ExpressionView.Rcheck/ExpressionView-Ex.timings
| name | user | system | elapsed | |
| ExportEV | 11.349 | 1.937 | 13.339 | |
| LaunchEV | 0.000 | 0.001 | 0.000 | |
| OrderEV | 4.720 | 1.128 | 5.849 | |