Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:20 -0400 (Sat, 17 Oct 2020).
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 23/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
affy 1.66.0 Rafael A. Irizarry
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK |
Package: affy |
Version: 1.66.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings affy_1.66.0.tar.gz |
StartedAt: 2020-10-16 22:40:36 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 22:43:05 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 148.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: affy.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings affy_1.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/affy.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘1.66.0’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mas5 29.670 0.092 29.777 MAplot 12.485 0.188 12.673 expresso 11.438 0.024 11.463 ProgressBarText-class 0.984 0.012 16.489 * 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 ‘/home/biocbuild/bbs-3.11-bioc/meat/affy.Rcheck/00check.log’ for details.
affy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL affy ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c mas5calls.c -o mas5calls.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-bioc/R/library/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma2.c -o rma2.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-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-3.11-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-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-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)
affy.Rcheck/affy-Ex.timings
name | user | system | elapsed | |
AffyBatch-class | 4.217 | 0.132 | 4.349 | |
AffyRNAdeg | 1.515 | 0.028 | 1.543 | |
MAplot | 12.485 | 0.188 | 12.673 | |
ProbeSet-class | 0.525 | 0.008 | 0.533 | |
ProgressBarText-class | 0.984 | 0.012 | 16.489 | |
affy-options | 0.000 | 0.000 | 0.001 | |
barplot.ProbeSet | 0.910 | 0.008 | 0.917 | |
bgc | 4.746 | 0.068 | 4.815 | |
cleancdfname | 0.007 | 0.000 | 0.007 | |
expresso | 11.438 | 0.024 | 11.463 | |
expressoWidget | 0 | 0 | 0 | |
fit.li.wong | 4.018 | 0.044 | 4.062 | |
generateExprSet-methods | 0.604 | 0.000 | 0.604 | |
generateExprVal-methods | 0.347 | 0.000 | 0.348 | |
generateExprVal.method.avgdiff | 0.323 | 0.000 | 0.323 | |
list.celfiles | 0.001 | 0.000 | 0.000 | |
maffy.subset | 0.017 | 0.000 | 0.017 | |
mas5 | 29.670 | 0.092 | 29.777 | |
mas5calls | 1.574 | 0.000 | 1.574 | |
mva.pairs | 0.097 | 0.000 | 0.097 | |
normalize-methods | 0.431 | 0.004 | 0.439 | |
normalize.loess | 0.055 | 0.000 | 0.056 | |
plot.ProbeSet | 0.014 | 0.004 | 0.017 | |
plot.density | 0.945 | 0.016 | 0.969 | |
plotLocation | 1.750 | 0.032 | 1.785 | |
pmcorrect | 0.445 | 0.004 | 0.453 | |
ppsetApply | 0.000 | 0.000 | 0.001 | |
read.affybatch | 2.571 | 0.016 | 3.078 | |
rma | 2.518 | 0.012 | 2.530 | |
setAffyOptions | 0.001 | 0.000 | 0.001 | |
xy2indices | 2.721 | 0.048 | 2.773 | |