Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:20:58 -0400 (Wed, 17 Oct 2018).
Package 17/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
affy 1.58.0 Rafael A. Irizarry
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: affy |
Version: 1.58.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings affy_1.58.0.tar.gz |
StartedAt: 2018-10-15 22:19:22 -0400 (Mon, 15 Oct 2018) |
EndedAt: 2018-10-15 22:21:42 -0400 (Mon, 15 Oct 2018) |
EllapsedTime: 139.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: affy.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings affy_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/affy.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘1.58.0’ * 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 ... 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 ... 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 24.876 0.048 25.451 MAplot 11.876 0.152 12.040 expresso 10.784 0.008 10.816 ProgressBarText-class 0.636 0.012 16.143 * 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, 3 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/affy.Rcheck/00check.log’ for details.
affy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL affy ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘affy’ ... 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-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c mas5calls.c -o mas5calls.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include -fpic -g -O2 -Wall -c rma2.c -o rma2.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I"/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/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 * DONE (affy)
affy.Rcheck/affy-Ex.timings
name | user | system | elapsed | |
AffyBatch-class | 2.552 | 0.060 | 2.617 | |
AffyRNAdeg | 1.420 | 0.044 | 1.470 | |
MAplot | 11.876 | 0.152 | 12.040 | |
ProbeSet-class | 0.264 | 0.004 | 0.270 | |
ProgressBarText-class | 0.636 | 0.012 | 16.143 | |
affy-options | 0.000 | 0.000 | 0.001 | |
barplot.ProbeSet | 0.320 | 0.004 | 0.324 | |
bgc | 2.040 | 0.036 | 2.084 | |
cleancdfname | 0.004 | 0.000 | 0.004 | |
expresso | 10.784 | 0.008 | 10.816 | |
expressoWidget | 0.000 | 0.000 | 0.001 | |
fit.li.wong | 0.200 | 0.008 | 0.207 | |
generateExprSet-methods | 0.328 | 0.004 | 0.332 | |
generateExprVal-methods | 0.284 | 0.004 | 0.287 | |
generateExprVal.method.avgdiff | 0.152 | 0.000 | 0.152 | |
list.celfiles | 0.004 | 0.000 | 0.000 | |
maffy.subset | 0.008 | 0.000 | 0.010 | |
mas5 | 24.876 | 0.048 | 25.451 | |
mas5calls | 1.056 | 0.000 | 1.058 | |
mva.pairs | 0.080 | 0.004 | 0.085 | |
normalize-methods | 0.260 | 0.004 | 0.266 | |
normalize.loess | 0.008 | 0.000 | 0.011 | |
plot.ProbeSet | 0.012 | 0.000 | 0.015 | |
plot.density | 0.848 | 0.016 | 0.866 | |
plotLocation | 1.736 | 0.024 | 1.764 | |
pmcorrect | 0.436 | 0.004 | 0.438 | |
ppsetApply | 0.000 | 0.000 | 0.001 | |
read.affybatch | 2.232 | 0.036 | 2.337 | |
rma | 2.144 | 0.008 | 2.169 | |
setAffyOptions | 0 | 0 | 0 | |
xy2indices | 1.760 | 0.036 | 1.796 | |