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BioC 3.0: CHECK report for affy on zin1

This page was generated on 2015-04-10 09:36:25 -0700 (Fri, 10 Apr 2015).

Package 14/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.44.0
Rafael A. Irizarry
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/affy
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  OK  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: affy
Version: 1.44.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.44.0.tar.gz
StartedAt: 2015-04-09 21:19:54 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:22:22 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 148.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affy.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/affy.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.44.0’
* 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 ‘affy’ can be installed ... [4s/4s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘tkWidgets’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘stats:::C_loess_raw’ ‘stats:::C_lowesp’ ‘stats:::C_lowesw’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘bg.correct’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls to a base package:
  .C(stats:::C_loess_raw, ...)
  .Fortran(stats:::C_lowesp, ...)
  .Fortran(stats:::C_lowesw, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... NOTE
AllButCelsForReadAffy: no visible global function definition for
  ‘fileBrowser’
AllButCelsForReadAffy: no visible global function definition for
  ‘hasSuffix’
expressoWidget: no visible global function definition for ‘tclVar’
expressoWidget : quit: no visible global function definition for
  ‘tkdestroy’
expressoWidget : end: no visible global function definition for
  ‘tclvalue’
expressoWidget: no visible global function definition for ‘tktoplevel’
expressoWidget: no visible global function definition for ‘tkdestroy’
expressoWidget: no visible global function definition for ‘tktitle<-’
expressoWidget: no visible global function definition for ‘tkpack’
expressoWidget: no visible global function definition for ‘tklabel’
expressoWidget: no visible global function definition for ‘tkframe’
expressoWidget: no visible global function definition for
  ‘dropdownList’
expressoWidget: no visible global function definition for ‘tclvalue’
expressoWidget: no visible global function definition for ‘tkgrid’
expressoWidget: no visible global function definition for
  ‘tkgrid.configure’
expressoWidget: no visible global function definition for ‘tkbutton’
expressoWidget: no visible global function definition for
  ‘tkwait.window’
* 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [84s/106s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  29.990  0.072  34.788
MAplot                16.353  0.136  16.585
expresso              12.021  0.036  13.046
AffyBatch-class        5.024  0.072   5.117
ProgressBarText-class  0.484  0.004  15.981
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/affy.Rcheck/00check.log’
for details.

affy.Rcheck/00install.out:

* installing *source* package ‘affy’ ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/affy.Rcheck/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘open’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘close’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘barplot’ from package ‘graphics’ in package ‘affy’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affy)

affy.Rcheck/affy-Ex.timings:

nameusersystemelapsed
AffyBatch-class5.0240.0725.117
AffyRNAdeg3.1240.0363.165
MAplot16.353 0.13616.585
ProbeSet-class0.3400.0080.349
ProgressBarText-class 0.484 0.00415.981
affy-options0.0040.0000.001
barplot.ProbeSet0.3600.0120.373
bgc2.0600.0322.096
cleancdfname0.0040.0040.007
expresso12.021 0.03613.046
expressoWidget0.0000.0000.001
fit.li.wong0.2440.0080.502
generateExprSet-methods0.3120.0080.417
generateExprVal-methods0.3760.0120.389
generateExprVal.method.avgdiff0.3600.0040.715
list.celfiles000
maffy.subset0.0480.0000.097
mas529.990 0.07234.788
mas5calls1.2960.0161.313
mva.pairs0.1160.0000.115
normalize-methods0.2560.0080.263
normalize.loess0.0200.0000.019
plot.ProbeSet0.0080.0040.014
plot.density0.7960.0040.798
plotLocation1.8160.0281.845
pmcorrect0.3080.0080.314
ppsetApply0.0000.0000.001
read.affybatch1.6880.0281.743
rma2.3970.0562.454
setAffyOptions0.0000.0000.001
xy2indices2.0160.0642.082