Package: affy

Version: 1.58.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings affy_1.58.0.tar.gz

StartedAt: 2018-10-15 22:19:22 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 22:21:42 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 139.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affy.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings affy_1.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/affy.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.58.0’
* 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 shell scripts ... 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  24.876  0.048  25.451
MAplot                11.876  0.152  12.040
expresso              10.784  0.008  10.816
ProgressBarText-class  0.636  0.012  16.143
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/affy.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL affy
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* 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-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/affy/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affy)

name	user	system	elapsed
AffyBatch-class	2.552	0.060	2.617
AffyRNAdeg	1.420	0.044	1.470
MAplot	11.876	0.152	12.040
ProbeSet-class	0.264	0.004	0.270
ProgressBarText-class	0.636	0.012	16.143
affy-options	0.000	0.000	0.001
barplot.ProbeSet	0.320	0.004	0.324
bgc	2.040	0.036	2.084
cleancdfname	0.004	0.000	0.004
expresso	10.784	0.008	10.816
expressoWidget	0.000	0.000	0.001
fit.li.wong	0.200	0.008	0.207
generateExprSet-methods	0.328	0.004	0.332
generateExprVal-methods	0.284	0.004	0.287
generateExprVal.method.avgdiff	0.152	0.000	0.152
list.celfiles	0.004	0.000	0.000
maffy.subset	0.008	0.000	0.010
mas5	24.876	0.048	25.451
mas5calls	1.056	0.000	1.058
mva.pairs	0.080	0.004	0.085
normalize-methods	0.260	0.004	0.266
normalize.loess	0.008	0.000	0.011
plot.ProbeSet	0.012	0.000	0.015
plot.density	0.848	0.016	0.866
plotLocation	1.736	0.024	1.764
pmcorrect	0.436	0.004	0.438
ppsetApply	0.000	0.000	0.001
read.affybatch	2.232	0.036	2.337
rma	2.144	0.008	2.169
setAffyOptions	0	0	0
xy2indices	1.760	0.036	1.796