Repitools 1.8.6
Mark Robinson
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Repitools | | Last Changed Rev: 84306 / Revision: 88450 | | Last Changed Date: 2013-12-11 16:00:50 -0800 (Wed, 11 Dec 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/Repitools.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.8.6'
* 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 'Repitools' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... 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 'D:/biocbld/bbs-2.13-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/i386/Repitools.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64/Repitools.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. 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' ... NOTE
The following files are already in R: 'Sweave.sty'
Please remove them from your package.
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'Repitools_vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [363s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
methylEst 141.04 2.39 143.65
empBayes 69.11 0.53 70.13
BayMethList-class 23.24 0.64 24.22
determineOffset 17.02 0.34 17.80
cpgDensityCalc 16.03 0.63 17.54
sequenceCalc 15.62 0.73 16.35
maskOut 12.28 0.34 13.53
cpgDensityPlot 10.77 0.61 11.38
gcContentCalc 4.82 0.19 5.01
** running examples for arch 'x64' ... [341s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
methylEst 118.24 1.85 120.10
empBayes 63.68 0.44 64.12
BayMethList-class 23.84 0.58 24.41
cpgDensityCalc 16.27 0.70 16.98
maskOut 15.20 0.65 16.24
determineOffset 15.10 0.38 15.47
sequenceCalc 14.03 0.61 14.65
cpgDensityPlot 10.30 0.64 11.19
findClusters 6.46 0.02 6.47
gcContentCalc 5.70 0.27 5.96
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'tests.R' [160s]
[161s] OK
** running tests for arch 'x64'
Running 'tests.R' [152s]
[152s] OK
* 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
NOTE: There were 3 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/Repitools.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Repitools' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=core2 -c const.c -o const.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=core2 -c hyp2f1.c -o hyp2f1.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=core2 -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
./mconf.h:101:0: warning: "SING" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
./mconf.h:102:0: warning: "OVERFLOW" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
./mconf.h:103:0: warning: "UNDERFLOW" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
./mconf.h:104:0: warning: "TLOSS" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
./mconf.h:105:0: warning: "PLOSS" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
gcc -m32 -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'parallel::clusterApply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterApplyLB' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterCall' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterEvalQ' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterExport' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterMap' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterSplit' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parApply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parCapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parLapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parLapplyLB' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parRapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parSapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parSapplyLB' when loading 'Repitools'
Warning: replacing previous import by 'aroma.affymetrix::compare' when loading 'Repitools'
Warning: replacing previous import by 'parallel::detectCores' when loading 'Repitools'
Creating a new generic function for 'windows' in package 'Repitools'
in method for '.featureScores' with signature '"AffymetrixCelSet","GRanges"': no definition for class "AffymetrixCelSet"
in method for 'regionStats' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
Creating a new generic function for 'writeWig' in package 'Repitools'
in method for 'writeWig' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
in method for 'cpgBoxplots' with signature '"AffymetrixCelSet"': no definition for class "AffymetrixCelSet"
in method for '.blocksStats' with signature '"AffymetrixCelSet","GRanges"': no definition for class "AffymetrixCelSet"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'parallel::clusterApply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterApplyLB' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterCall' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterEvalQ' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterExport' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterMap' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterSplit' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parApply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parCapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parLapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parLapplyLB' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parRapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parSapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parSapplyLB' when loading 'Repitools'
Warning: replacing previous import by 'aroma.affymetrix::compare' when loading 'Repitools'
Warning: replacing previous import by 'parallel::detectCores' when loading 'Repitools'
install for x64
* installing *source* package 'Repitools' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=core2 -c const.c -o const.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=core2 -c hyp2f1.c -o hyp2f1.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=core2 -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:0:
./mconf.h:100:0: warning: "DOMAIN" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition
./mconf.h:101:0: warning: "SING" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition
./mconf.h:102:0: warning: "OVERFLOW" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition
./mconf.h:103:0: warning: "UNDERFLOW" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition
./mconf.h:104:0: warning: "TLOSS" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition
./mconf.h:105:0: warning: "PLOSS" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition
gcc -m64 -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import by 'parallel::clusterApply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterApplyLB' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterCall' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterEvalQ' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterExport' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterMap' when loading 'Repitools'
Warning: replacing previous import by 'parallel::clusterSplit' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parApply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parCapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parLapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parLapplyLB' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parRapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parSapply' when loading 'Repitools'
Warning: replacing previous import by 'parallel::parSapplyLB' when loading 'Repitools'
Warning: replacing previous import by 'aroma.affymetrix::compare' when loading 'Repitools'
Warning: replacing previous import by 'parallel::detectCores' when loading 'Repitools'
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.8.6.zip
* DONE (Repitools)