affy 1.55.0
Rafael A. Irizarry
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf affy.buildbin-libdir affy.Rcheck && mkdir affy.buildbin-libdir affy.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affy.buildbin-libdir affy_1.55.0.tar.gz >affy.Rcheck\00install.out 2>&1 && cp affy.Rcheck\00install.out affy-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affy.buildbin-libdir --install="check:affy-install.out" --force-multiarch --no-vignettes --timings affy_1.55.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affy.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.55.0'
* 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 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
'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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affy.buildbin-libdir/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 the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mas5 24.84 0.09 24.93
MAplot 15.11 0.53 15.90
expresso 10.12 0.14 10.27
read.affybatch 2.81 0.09 7.61
ProgressBarText-class 0.50 0.00 16.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mas5 28.91 0.05 28.95
MAplot 17.58 0.71 18.29
expresso 15.02 0.08 15.09
ProgressBarText-class 0.80 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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/affy.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'affy' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c getall_locations.c -o getall_locations.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
C:/Rtools/mingw_32/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/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/affy.buildbin-libdir/affy/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'affy' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c getall_locations.c -o getall_locations.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -DHAVE_ZLIB -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
C:/Rtools/mingw_64/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/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/affy.buildbin-libdir/affy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affy' as affy_1.55.0.zip
* DONE (affy)