Back to Multiple platform build/check report for BioC 3.12 |
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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 24/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
affy 1.68.0 (landing page) Rafael A. Irizarry
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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.
affy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affy ### ############################################################################## ############################################################################## * 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)
affy.Rcheck/affy-Ex.timings
name | user | system | elapsed | |
AffyBatch-class | 4.175 | 0.173 | 4.390 | |
AffyRNAdeg | 2.123 | 0.067 | 2.195 | |
MAplot | 11.155 | 0.591 | 11.899 | |
ProbeSet-class | 0.421 | 0.017 | 0.440 | |
ProgressBarText-class | 0.848 | 0.044 | 18.667 | |
affy-options | 0.000 | 0.001 | 0.001 | |
barplot.ProbeSet | 0.814 | 0.032 | 0.848 | |
bgc | 3.297 | 0.283 | 3.656 | |
cleancdfname | 0.007 | 0.001 | 0.008 | |
expresso | 14.026 | 0.133 | 14.180 | |
expressoWidget | 0.001 | 0.000 | 0.000 | |
fit.li.wong | 3.722 | 0.079 | 3.807 | |
generateExprSet-methods | 0.432 | 0.006 | 0.437 | |
generateExprVal-methods | 0.418 | 0.015 | 0.438 | |
generateExprVal.method.avgdiff | 0.224 | 0.011 | 0.236 | |
list.celfiles | 0.000 | 0.001 | 0.000 | |
maffy.subset | 0.011 | 0.001 | 0.013 | |
mas5 | 32.241 | 0.159 | 32.462 | |
mas5calls | 1.653 | 0.041 | 1.697 | |
mva.pairs | 0.093 | 0.004 | 0.097 | |
normalize-methods | 0.348 | 0.007 | 0.357 | |
normalize.loess | 0.018 | 0.001 | 0.020 | |
plot.ProbeSet | 0.015 | 0.004 | 0.019 | |
plot.density | 0.834 | 0.035 | 0.872 | |
plotLocation | 1.381 | 0.141 | 1.528 | |
pmcorrect | 0.374 | 0.008 | 0.382 | |
ppsetApply | 0.002 | 0.001 | 0.002 | |
read.affybatch | 1.831 | 0.075 | 1.910 | |
rma | 1.697 | 0.029 | 1.728 | |
setAffyOptions | 0.000 | 0.000 | 0.001 | |
xy2indices | 1.814 | 0.169 | 1.990 | |