| Back to "Blame Jeroen" build/check report for BioC 3.11 |
This page was generated on 2020-04-14 03:20:16 -0400 (Tue, 14 Apr 2020).
| These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html) |
| 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 2/89 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| affy 1.65.1 Rafael A. Irizarry
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK |
| Package: affy |
| Version: 1.65.1 |
| Command: C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings affy_1.65.1.tar.gz |
| StartedAt: 2020-04-13 22:33:33 -0400 (Mon, 13 Apr 2020) |
| EndedAt: 2020-04-13 22:38:03 -0400 (Mon, 13 Apr 2020) |
| EllapsedTime: 270.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: affy.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:affy.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings affy_1.65.1.tar.gz
###
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* using log directory 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/affy.Rcheck'
* using R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.65.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/affy/libs/i386/affy.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mas5 16.25 0.06 16.31
MAplot 11.89 0.33 12.30
expresso 7.62 0.03 7.66
read.affybatch 3.63 0.06 10.05
ProgressBarText-class 0.81 0.02 16.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mas5 22.10 0.07 22.22
MAplot 13.86 0.45 15.66
expresso 10.90 0.07 10.98
bgc 5.77 0.18 6.01
ProgressBarText-class 0.83 0.02 16.83
* 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
'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/affy.Rcheck/00check.log'
for details.
affy.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/affy_1.65.1.tar.gz && rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affy.buildbin-libdir affy_1.65.1.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL affy_1.65.1.zip && rm affy_1.65.1.tar.gz affy_1.65.1.zip
###
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install for i386
* installing *source* package 'affy' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
/mingw32/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o
/mingw32/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getall_locations.c -o getall_locations.o
/mingw32/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o
/mingw32/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o
/mingw32/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o
/mingw32/bin/gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -LC:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/affy.buildbin-libdir/00LOCK-affy/00new/affy/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'affy'
finding HTML links ... done
AffyBatch-class html
finding level-2 HTML links ... done
AffyRNAdeg html
MAplot html
ProbeSet-class html
ProgressBarText-class html
SpikeIn html
affy-deprecated html
affy-options html
affy.scalevalue.exprSet html
barplot.ProbeSet html
bg.adjust html
bgc html
cdfFromBioC html
cdfenv.example html
cleancdfname html
debug.affy123 html
expresso html
expressoWidget html
fit.li.wong html
generateExprSet-methods html
generateExprVal-methods html
generateExprVal.method.avgdiff html
generateExprVal.method.playerout html
hlog html
justrma html
list.celfiles html
maffy.subset html
mas5 html
mas5calls html
merge.AffyBatch html
mva.pairs html
normalize-methods html
normalize.constant html
normalize.contrast html
normalize.invariantset html
normalize.loess html
normalize.qspline html
normalize.quantiles html
normalize.quantiles.robust html
pairs.AffyBatch html
plot.ProbeSet html
plot.density html
plotLocation html
pmcorrect html
ppsetApply html
probeMatch-methods html
probeNames-methods html
read.affybatch html
read.probematrix html
rma html
setAffyOptions html
summary html
tukey.biweight html
whatcdf html
xy2indices html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'affy' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
/mingw64/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c chipbackground.c -o chipbackground.o
/mingw64/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getall_locations.c -o getall_locations.o
/mingw64/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mas5calls.c -o mas5calls.o
/mingw64/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma2.c -o rma2.o
/mingw64/bin/gcc -I"C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/include" -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -DHAVE_ZLIB -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rma_common.c -o rma_common.o
/mingw64/bin/gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -LC:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/affy.buildbin-libdir/affy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affy' as affy_1.65.1.zip
* DONE (affy)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'affy' successfully unpacked and MD5 sums checked
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affy.Rcheck/examples_i386/affy-Ex.timings
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affy.Rcheck/examples_x64/affy-Ex.timings
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