Package: affy

Version: 1.61.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affy_1.61.0.tar.gz

StartedAt: 2019-04-08 23:45:04 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:48:17 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 192.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affy.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affy_1.61.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/affy.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.61.0’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  $.AffyBatch barplot.ProbeSet merge.AffyBatch pairs.AffyBatch
  plot.ProbeSet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  41.328  0.346  41.681
expresso              18.020  0.253  18.286
MAplot                14.523  0.882  15.456
ProgressBarText-class  1.132  0.121  17.079
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/affy.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affy
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘affy’ ...
** using staged installation
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
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c chipbackground.c -o chipbackground.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c getall_locations.c -o getall_locations.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c rma2.c -o rma2.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/preprocessCore/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-affy/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (affy)

name	user	system	elapsed
AffyBatch-class	4.341	0.364	4.713
AffyRNAdeg	2.465	0.196	2.661
MAplot	14.523	0.882	15.456
ProbeSet-class	0.410	0.032	0.442
ProgressBarText-class	1.132	0.121	17.079
affy-options	0.001	0.001	0.001
barplot.ProbeSet	0.567	0.029	1.099
bgc	2.301	0.267	4.235
cleancdfname	0.010	0.002	0.012
expresso	18.020	0.253	18.286
expressoWidget	0.001	0.000	0.001
fit.li.wong	0.29	0.02	0.31
generateExprSet-methods	0.662	0.014	0.676
generateExprVal-methods	0.545	0.014	0.560
generateExprVal.method.avgdiff	0.409	0.028	0.437
list.celfiles	0.001	0.001	0.001
maffy.subset	0.023	0.001	0.024
mas5	41.328	0.346	41.681
mas5calls	2.054	0.189	2.243
mva.pairs	0.107	0.003	0.108
normalize-methods	0.325	0.027	0.351
normalize.loess	0.018	0.001	0.020
plot.ProbeSet	0.017	0.004	0.021
plot.density	0.647	0.134	0.782
plotLocation	1.688	0.160	1.853
pmcorrect	0.450	0.029	0.479
ppsetApply	0.002	0.000	0.003
read.affybatch	2.410	0.180	2.598
rma	1.844	0.048	1.893
setAffyOptions	0.001	0.000	0.001
xy2indices	2.051	0.255	2.311