Package: affy

Version: 1.60.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings affy_1.60.0.tar.gz

StartedAt: 2019-04-15 22:06:41 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:09:05 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 143.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affy.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings affy_1.60.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/affy.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.60.0’
* 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                  30.152  0.032  30.245
expresso              16.324  0.008  16.345
MAplot                15.280  0.168  15.480
ProgressBarText-class  1.028  0.008  16.537
* 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-3.8-bioc/meat/affy.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL affy
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* installing to library ‘/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.8-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.8-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.8-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-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	3.712	0.104	3.920
AffyRNAdeg	2.488	0.056	2.550
MAplot	15.280	0.168	15.480
ProbeSet-class	0.420	0.008	0.429
ProgressBarText-class	1.028	0.008	16.537
affy-options	0.004	0.000	0.000
barplot.ProbeSet	0.552	0.008	0.571
bgc	2.408	0.036	2.448
cleancdfname	0.004	0.004	0.007
expresso	16.324	0.008	16.345
expressoWidget	0	0	0
fit.li.wong	0.268	0.004	0.270
generateExprSet-methods	0.548	0.004	0.553
generateExprVal-methods	0.540	0.008	0.551
generateExprVal.method.avgdiff	0.284	0.000	0.288
list.celfiles	0.000	0.000	0.001
maffy.subset	0.012	0.000	0.014
mas5	30.152	0.032	30.245
mas5calls	1.044	0.008	1.056
mva.pairs	0.072	0.004	0.078
normalize-methods	0.256	0.004	0.259
normalize.loess	0.012	0.000	0.011
plot.ProbeSet	0.012	0.000	0.012
plot.density	0.904	0.004	0.909
plotLocation	2.064	0.040	2.110
pmcorrect	0.524	0.000	0.524
ppsetApply	0.000	0.004	0.000
read.affybatch	2.544	0.020	2.844
rma	2.768	0.000	2.778
setAffyOptions	0	0	0
xy2indices	2.220	0.040	2.265