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BioC 3.5: CHECK report for affy on malbec2

This page was generated on 2017-08-16 13:12:09 -0400 (Wed, 16 Aug 2017).

Package 16/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.54.0
Rafael A. Irizarry
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/affy
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  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: affy
Version: 1.54.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.54.0.tar.gz
StartedAt: 2017-08-15 21:01:22 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:03:40 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 138.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affy.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/affy.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.54.0’
* 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 ... 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’
Undefined global functions or variables:
  dropdownList fileBrowser hasSuffix tclVar tclvalue tkbutton tkdestroy
  tkframe tkgrid tkgrid.configure tklabel tkpack tktitle<- tktoplevel
  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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  19.596  0.008  19.618
MAplot                12.348  0.100  12.454
expresso               9.696  0.012   9.714
ProgressBarText-class  0.604  0.004  16.104
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-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 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c getall_locations.c -o getall_locations.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.5-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/affy.Rcheck/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** 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-class3.1040.0483.397
AffyRNAdeg1.8480.0121.860
MAplot12.348 0.10012.454
ProbeSet-class0.3080.0040.314
ProgressBarText-class 0.604 0.00416.104
affy-options0.0000.0000.001
barplot.ProbeSet0.3400.0040.345
bgc2.0040.0322.042
cleancdfname0.0040.0000.005
expresso9.6960.0129.714
expressoWidget0.0000.0000.001
fit.li.wong0.2000.0080.206
generateExprSet-methods0.3960.0080.404
generateExprVal-methods0.4800.0120.492
generateExprVal.method.avgdiff0.3520.0000.352
list.celfiles000
maffy.subset0.0080.0040.011
mas519.596 0.00819.618
mas5calls1.4760.0041.481
mva.pairs0.1240.0000.125
normalize-methods0.2520.0000.254
normalize.loess0.0120.0000.009
plot.ProbeSet0.0120.0000.012
plot.density0.6920.0000.692
plotLocation1.4400.0121.449
pmcorrect0.2640.0000.263
ppsetApply000
read.affybatch2.0320.0362.109
rma2.6720.0082.688
setAffyOptions0.0120.0000.013
xy2indices2.1320.0402.173