Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: CHECK report for cn.mops on moscato2

This page was generated on 2014-10-08 08:54:23 -0700 (Wed, 08 Oct 2014).

Package 165/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cn.mops 1.10.1
Guenter Klambauer
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/cn.mops
Last Changed Rev: 93467 / Revision: 95116
Last Changed Date: 2014-08-19 05:44:55 -0700 (Tue, 19 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: cn.mops
Version: 1.10.1
Command: rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.mops.buildbin-libdir cn.mops_1.10.1.tar.gz >cn.mops-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cn.mops.buildbin-libdir --install="check:cn.mops-install.out" --force-multiarch --no-vignettes --timings cn.mops_1.10.1.tar.gz
StartedAt: 2014-10-07 23:58:16 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-08 00:03:26 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 310.5 seconds
RetCode: 0
Status:  OK  
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.mops.buildbin-libdir cn.mops_1.10.1.tar.gz >cn.mops-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cn.mops.buildbin-libdir --install="check:cn.mops-install.out" --force-multiarch --no-vignettes --timings cn.mops_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/cn.mops.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cn.mops/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.mops' version '1.10.1'
* 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 'cn.mops' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'IRanges'
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Biobase' 'BiocGenerics'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.cn.mopsC' '.convertToFastSegRes' '.makeLogRatios'
  '.referencecn.mops' 'segment'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 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 'E:/biocbld/bbs-2.14-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/i386/cn.mops.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.14-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64/cn.mops.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' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [70s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
calcFractionalCopyNumbers 18.77   0.02   18.78
referencecn.mops          15.62   0.01   15.63
cn.mops                   12.91   0.02   12.93
exomecn.mops               5.52   0.01    5.54
** running examples for arch 'x64' ... [66s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
calcFractionalCopyNumbers 15.09   0.00   15.10
cn.mops                   13.82   0.03   13.86
referencecn.mops          11.65   0.02   11.67
exomecn.mops               6.07   0.00    6.07
* 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
  'E:/biocbld/bbs-2.14-bioc/meat/cn.mops.Rcheck/00check.log'
for details.

cn.mops.Rcheck/00install.out:


install for i386

* installing *source* package 'cn.mops' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_cnmops.c -o R_init_cnmops.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cnmops.cpp -o cnmops.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
g++ -m32 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'cn.mops'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'cn.mops' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_cnmops.c -o R_init_cnmops.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cnmops.cpp -o cnmops.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
g++ -m64 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.mops' as cn.mops_1.10.1.zip
* DONE (cn.mops)

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

nameusersystemelapsed
CNVDetectionResult000
calcFractionalCopyNumbers18.77 0.0218.78
calcIntegerCopyNumbers0.660.010.67
cn.mops12.91 0.0212.93
cnvr0.360.000.36
cnvs0.50.00.5
exomecn.mops5.520.015.54
getReadCountsFromBAM0.250.000.25
getSegmentReadCountsFromBAM0.080.000.08
gr0.520.020.53
haplocn.mops1.710.001.71
individualCall0.390.000.39
iniCall0.390.000.39
integerCopyNumber0.390.000.39
localAssessments0.390.000.39
makeRobustCNVR0.600.000.59
normalizeChromosomes0.420.020.44
normalizeGenome0.540.000.55
normalizedData0.530.000.53
params0.560.000.56
posteriorProbs0.690.000.69
referencecn.mops15.62 0.0115.63
sampleNames0.320.000.33
segment0.040.000.03
segmentation0.350.000.36
segplot1.600.001.59
singlecn.mops1.260.001.27

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

nameusersystemelapsed
CNVDetectionResult000
calcFractionalCopyNumbers15.09 0.0015.10
calcIntegerCopyNumbers0.830.000.82
cn.mops13.82 0.0313.86
cnvr0.370.020.39
cnvs0.390.000.39
exomecn.mops6.070.006.07
getReadCountsFromBAM0.310.010.32
getSegmentReadCountsFromBAM0.080.000.08
gr0.450.000.45
haplocn.mops2.070.002.07
individualCall0.660.000.66
iniCall0.440.020.45
integerCopyNumber0.450.000.45
localAssessments0.450.000.46
makeRobustCNVR0.670.000.67
normalizeChromosomes0.490.020.50
normalizeGenome0.460.000.46
normalizedData0.630.000.63
params0.390.010.40
posteriorProbs0.390.000.39
referencecn.mops11.65 0.0211.67
sampleNames0.390.010.41
segment0.050.000.04
segmentation0.480.000.49
segplot1.800.001.79
singlecn.mops1.430.001.44