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BioC 3.0: CHECK report for GlobalAncova on oaxaca

This page was generated on 2015-04-10 10:01:50 -0700 (Fri, 10 Apr 2015).

Package 384/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GlobalAncova 3.34.0
Manuela Hummel
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GlobalAncova
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: GlobalAncova
Version: 3.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GlobalAncova_3.34.0.tar.gz
StartedAt: 2015-04-10 00:05:44 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:08:24 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 159.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GlobalAncova.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GlobalAncova_3.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GlobalAncova.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GlobalAncova/DESCRIPTION’ ... OK
* this is package ‘GlobalAncova’ version ‘3.34.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GlobalAncova’ can be installed ... [13s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘annotate’
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 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:
  ‘corpcor’ ‘methods’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘GO.db’ ‘GSEABase’ ‘KEGG.db’ ‘annotate’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘corpcor’ ‘globaltest’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GlobalAncova/R/zzz.r’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.onAttach: no visible global function definition for ‘addVigs2WinMenu’
.pGAapprox : <anonymous>: no visible global function definition for
  ‘cov.shrink’
GABroad: no visible binding for global variable ‘collectionType’
GABroad: no visible binding for global variable ‘bcCategory’
GABroad: no visible global function definition for ‘mapIdentifiers’
GABroad: no visible global function definition for
  ‘AnnotationIdentifier’
GABroad: no visible binding for global variable ‘geneIds’
GAGO: no visible global function definition for ‘mappedkeys’
GAGO: no visible binding for global variable ‘Ontology’
GAGO : <anonymous>: no visible global function definition for ‘keys’
GAGO: no visible global function definition for ‘findFocus’
GAGO: no visible global function definition for ‘focusLevel’
GAKEGG: no visible global function definition for ‘mappedkeys’
expr.test : <anonymous>: no visible global function definition for
  ‘cov.shrink’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘GlobalAncova/libs/GlobalAncova.so’:
  Found ‘_putchar’, possibly from ‘putchar’ (C)
    Object: ‘matrix.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘matrix.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘matrix.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/12s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GlobalAncova.Rcheck/00check.log’
for details.

GlobalAncova.Rcheck/00install.out:

* installing *source* package ‘GlobalAncova’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GlobalAncova.c -o GlobalAncova.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c ludcmp.c -o ludcmp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matrix.c -o matrix.o
clang -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 GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/GlobalAncova.Rcheck/GlobalAncova/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GlobalAncova)

GlobalAncova.Rcheck/GlobalAncova-Ex.timings:

nameusersystemelapsed
GlobalAncova0.9180.0220.940
GlobalAncova.decomp0.3440.0140.360
Plot.all0.0670.0030.072
Plot.genes0.3500.0060.376
Plot.sequential0.0320.0020.034
Plot.subjects0.3460.0050.351
colon.normal0.0050.0010.005
colon.pheno0.0020.0000.002
colon.tumour0.0040.0010.005
genesettesting0.0000.0000.001
pair.compare3.0270.1213.174
pathways0.0020.0000.003
phenodata0.0020.0010.003
vantVeer0.0080.0010.009