Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for affy on zin1

This page was generated on 2016-09-21 03:35:38 -0700 (Wed, 21 Sep 2016).

Package 16/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.51.1
Rafael A. Irizarry
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy
Last Changed Rev: 120595 / Revision: 121152
Last Changed Date: 2016-08-30 14:18:04 -0700 (Tue, 30 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: affy
Version: 1.51.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.51.1.tar.gz
StartedAt: 2016-09-20 02:55:57 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 02:58:05 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 128.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affy.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.51.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/affy.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.51.1’
* 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 sizes of PDF files under ‘inst/doc’ ... 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                  22.092  0.016  28.553
MAplot                12.052  0.116  12.287
expresso               9.316  0.008   9.340
ProgressBarText-class  0.504  0.004  16.000
* 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-3.4-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-3.4-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c getall_locations.c -o getall_locations.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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-class2.9120.0523.167
AffyRNAdeg2.1280.0282.158
MAplot12.052 0.11612.287
ProbeSet-class0.2960.0040.300
ProgressBarText-class 0.504 0.00416.000
affy-options0.0000.0000.001
barplot.ProbeSet0.3320.0000.332
bgc2.2000.0282.259
cleancdfname0.0040.0000.003
expresso9.3160.0089.340
expressoWidget000
fit.li.wong0.2080.0080.217
generateExprSet-methods0.2840.0000.283
generateExprVal-methods0.3200.0040.323
generateExprVal.method.avgdiff0.2840.0000.283
list.celfiles000
maffy.subset0.0080.0000.011
mas522.092 0.01628.553
mas5calls1.2080.0041.210
mva.pairs0.0840.0040.085
normalize-methods0.2680.0000.269
normalize.loess0.0120.0000.009
plot.ProbeSet0.0080.0040.012
plot.density0.6520.0000.656
plotLocation1.4120.0161.430
pmcorrect0.2520.0160.266
ppsetApply0.0040.0000.001
read.affybatch1.6960.0081.719
rma2.3440.0002.353
setAffyOptions000
xy2indices1.7800.0321.822