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BioC 3.1: CHECK report for cn.farms on moscato2

This page was generated on 2015-10-09 09:29:10 -0700 (Fri, 09 Oct 2015).

Package 182/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.farms 1.16.0
Andreas Mitterecker
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cn.farms
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cn.farms
Version: 1.16.0
Command: rm -rf cn.farms.buildbin-libdir cn.farms.Rcheck && mkdir cn.farms.buildbin-libdir cn.farms.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.16.0.tar.gz >cn.farms.Rcheck\00install.out 2>&1 && cp cn.farms.Rcheck\00install.out cn.farms-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cn.farms.buildbin-libdir --install="check:cn.farms-install.out" --force-multiarch --no-vignettes --timings cn.farms_1.16.0.tar.gz
StartedAt: 2015-10-09 00:30:24 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:34:21 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 236.6 seconds
RetCode: 0
Status:  OK  
CheckDir: cn.farms.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cn.farms.buildbin-libdir cn.farms.Rcheck && mkdir cn.farms.buildbin-libdir cn.farms.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.16.0.tar.gz >cn.farms.Rcheck\00install.out 2>&1 && cp cn.farms.Rcheck\00install.out cn.farms-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cn.farms.buildbin-libdir --install="check:cn.farms-install.out" --force-multiarch --no-vignettes --timings cn.farms_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/cn.farms.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cn.farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.farms' version '1.16.0'
* 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 'cn.farms' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
initializeBigMatrix: no visible global function definition for
  'isPackageLoaded'
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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 'E:/biocbld/bbs-3.1-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386/cn.farms.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x64/cn.farms.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' ... [20s] OK
** running examples for arch 'x64' ... [20s] 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
* DONE

Status: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/cn.farms.Rcheck/00check.log'
for details.


cn.farms.Rcheck/00install.out:


install for i386

* installing *source* package 'cn.farms' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:57: warning: 'I1right' may be used uninitialized in this function [-Wuninitialized]
laplace.cpp:393:127: warning: 'I1left' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sparse_farms.c -o sparse_farms.o
g++ -m32 -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'cn.farms' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
laplace.cpp:442:6: warning: unused variable 'method' [-Wunused-variable]
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:368:57: warning: 'I1right' may be used uninitialized in this function [-Wuninitialized]
laplace.cpp:393:127: warning: 'I1left' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sparse_farms.c -o sparse_farms.o
g++ -m64 -shared -s -static-libgcc -o cn.farms.dll tmp.def R_init_cnfarms.o laplace.o sparse_farms.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'cn.farms' as cn.farms_1.16.0.zip
* DONE (cn.farms)

cn.farms.Rcheck/examples_i386/cn.farms-Ex.timings:

nameusersystemelapsed
cn.farms0.010.000.02
combineData1.060.001.06
createAnnotation000
distributionDistance0.190.000.19
dnaCopySf0.110.000.11
fragLengCorr2.250.022.26
mlSummarization3.550.083.63
normalizeAverage000
normalizeCels000
normalizeNpData000
plotDendrogram0.150.000.16
plotDensity0.880.000.87
plotEvalIc0.590.000.59
plotRegions0.230.010.65
plotSmoothScatter0.610.000.61
plotViolines0.120.000.13
slSummarization2.90.03.1
sparseFarmsC000
summarizeFarmsExact0.020.000.02
summarizeFarmsExact2000
summarizeFarmsExact3000
summarizeFarmsGaussian000
summarizeFarmsMethods000
summarizeFarmsVariational000
summarizeWindowBps0.000.000.02
summarizeWindowMethods000
summarizeWindowStd000

cn.farms.Rcheck/examples_x64/cn.farms-Ex.timings:

nameusersystemelapsed
cn.farms000
combineData1.260.051.41
createAnnotation000
distributionDistance0.150.000.15
dnaCopySf0.130.000.13
fragLengCorr2.950.032.98
mlSummarization3.600.063.66
normalizeAverage000
normalizeCels000
normalizeNpData000
plotDendrogram0.380.000.37
plotDensity0.600.000.61
plotEvalIc0.380.000.38
plotRegions0.310.000.46
plotSmoothScatter0.670.000.68
plotViolines0.140.000.14
slSummarization3.520.053.76
sparseFarmsC000
summarizeFarmsExact000
summarizeFarmsExact20.020.000.02
summarizeFarmsExact3000
summarizeFarmsGaussian000
summarizeFarmsMethods0.010.000.01
summarizeFarmsVariational000
summarizeWindowBps000
summarizeWindowMethods0.020.000.02
summarizeWindowStd000