Package: affy

Version: 1.64.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings affy_1.64.0.tar.gz

StartedAt: 2020-04-15 00:09:12 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:11:26 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 134.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affy.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings affy_1.64.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/affy.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.64.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  25.216  0.060  25.353
MAplot                14.316  0.180  14.523
expresso              10.900  0.032  10.954
ProgressBarText-class  0.828  0.008  16.331
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/affy.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL affy
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.10-bioc/R/library/preprocessCore/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/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	3.624	0.140	4.115
AffyRNAdeg	2.012	0.044	2.060
MAplot	14.316	0.180	14.523
ProbeSet-class	0.296	0.012	0.308
ProgressBarText-class	0.828	0.008	16.331
affy-options	0.000	0.000	0.001
barplot.ProbeSet	0.560	0.004	0.566
bgc	2.388	0.032	2.429
cleancdfname	0.004	0.000	0.004
expresso	10.900	0.032	10.954
expressoWidget	0	0	0
fit.li.wong	0.284	0.008	0.293
generateExprSet-methods	0.600	0.000	0.602
generateExprVal-methods	0.584	0.004	0.590
generateExprVal.method.avgdiff	0.204	0.000	0.201
list.celfiles	0	0	0
maffy.subset	0.008	0.004	0.013
mas5	25.216	0.060	25.353
mas5calls	1.576	0.000	1.586
mva.pairs	0.096	0.000	0.099
normalize-methods	0.304	0.000	0.305
normalize.loess	0.004	0.004	0.010
plot.ProbeSet	0.012	0.000	0.013
plot.density	1.056	0.000	1.058
plotLocation	2.188	0.016	2.207
pmcorrect	0.268	0.000	0.269
ppsetApply	0	0	0
read.affybatch	1.988	0.020	2.448
rma	2.680	0.008	2.701
setAffyOptions	0	0	0
xy2indices	1.868	0.020	1.892