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CHECK report for affy on merida1

This page was generated on 2020-04-15 12:33:45 -0400 (Wed, 15 Apr 2020).

Package 23/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.64.0
Rafael A. Irizarry
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/affy
Branch: RELEASE_3_10
Last Commit: 82d96e6
Last Changed Date: 2019-10-29 13:07:23 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: affy
Version: 1.64.0
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_1.64.0.tar.gz
StartedAt: 2020-04-15 00:16:16 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:18:54 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 157.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affy.Rcheck
Warnings: 1

Command output

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### Running 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_1.64.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/affy.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.64.0’
* 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 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                  32.971  0.212  33.413
expresso              14.521  0.154  14.933
MAplot                13.447  0.797  14.452
ProgressBarText-class  0.925  0.041  16.625
* 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-3.10-bioc/meat/affy.Rcheck/00check.log’
for details.



Installation output

affy.Rcheck/00install.out

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### Running command:
###
###   /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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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)

Tests output


Example timings

affy.Rcheck/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class4.0030.1794.241
AffyRNAdeg2.1020.0922.223
MAplot13.447 0.79714.452
ProbeSet-class0.4270.0160.450
ProgressBarText-class 0.925 0.04116.625
affy-options0.0010.0000.001
barplot.ProbeSet0.5970.0240.635
bgc1.8190.1351.986
cleancdfname0.0080.0010.010
expresso14.521 0.15414.933
expressoWidget0.0010.0000.001
fit.li.wong0.2710.0090.284
generateExprSet-methods0.5470.0070.559
generateExprVal-methods0.4580.0220.495
generateExprVal.method.avgdiff0.5270.0150.548
list.celfiles0.0010.0000.000
maffy.subset0.0150.0010.016
mas532.971 0.21233.413
mas5calls1.3460.0721.420
mva.pairs0.0910.0010.092
normalize-methods0.3480.0150.367
normalize.loess0.0160.0010.017
plot.ProbeSet0.0150.0020.017
plot.density1.0650.0601.134
plotLocation1.5950.1671.780
pmcorrect0.4070.0180.426
ppsetApply0.0020.0000.002
read.affybatch2.1960.0822.316
rma1.6500.0271.680
setAffyOptions0.0000.0000.001
xy2indices1.9000.1972.115