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CHECK report for affy on merida1

This page was generated on 2021-05-06 12:34:16 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the affy package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 24/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.68.0  (landing page)
Rafael A. Irizarry
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/affy
Branch: RELEASE_3_12
Last Commit: 1664399
Last Changed Date: 2020-10-27 10:22:11 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: affy
Version: 1.68.0
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_1.68.0.tar.gz
StartedAt: 2021-05-05 23:04:44 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:07:31 -0400 (Wed, 05 May 2021)
EllapsedTime: 167.0 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_1.68.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/affy.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.68.0’
* 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
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.
* 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 ... OK
* 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 use of PKG_*FLAGS in Makefiles ... 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 (user + system) or elapsed time > 5s
                        user system elapsed
mas5                  32.241  0.159  32.462
expresso              14.026  0.133  14.180
MAplot                11.155  0.591  11.899
ProgressBarText-class  0.848  0.044  18.667
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-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/4.0/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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c chipbackground.c -o chipbackground.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getall_locations.c -o getall_locations.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma2.c -o rma2.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -mmacosx-version-min=10.13 -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/4.0/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-class4.1750.1734.390
AffyRNAdeg2.1230.0672.195
MAplot11.155 0.59111.899
ProbeSet-class0.4210.0170.440
ProgressBarText-class 0.848 0.04418.667
affy-options0.0000.0010.001
barplot.ProbeSet0.8140.0320.848
bgc3.2970.2833.656
cleancdfname0.0070.0010.008
expresso14.026 0.13314.180
expressoWidget0.0010.0000.000
fit.li.wong3.7220.0793.807
generateExprSet-methods0.4320.0060.437
generateExprVal-methods0.4180.0150.438
generateExprVal.method.avgdiff0.2240.0110.236
list.celfiles0.0000.0010.000
maffy.subset0.0110.0010.013
mas532.241 0.15932.462
mas5calls1.6530.0411.697
mva.pairs0.0930.0040.097
normalize-methods0.3480.0070.357
normalize.loess0.0180.0010.020
plot.ProbeSet0.0150.0040.019
plot.density0.8340.0350.872
plotLocation1.3810.1411.528
pmcorrect0.3740.0080.382
ppsetApply0.0020.0010.002
read.affybatch1.8310.0751.910
rma1.6970.0291.728
setAffyOptions0.0000.0000.001
xy2indices1.8140.1691.990