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BioC 2.14: CHECK report for cn.mops on morelia

This page was generated on 2014-10-08 09:05:17 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.mops_1.10.1.tar.gz
StartedAt: 2014-10-07 22:03:53 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:07:05 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 191.4 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.mops_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/cn.mops.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cn.mops’ can be installed ... [14s/14s] 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/51s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
cn.mops                   10.437  0.081  10.538
calcFractionalCopyNumbers  9.389  0.049   9.451
referencecn.mops           6.301  0.029   6.337
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/cn.mops.Rcheck/00check.log’
for details.

cn.mops.Rcheck/00install.out:

* installing *source* package ‘cn.mops’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_cnmops.c -o R_init_cnmops.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c cnmops.cpp -o cnmops.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c segment.cpp -o segment.o
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
        double beta,nn;
               ^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:217:15: note: expanded from macro 'beta'
#define beta            Rf_beta
                        ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** 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
* DONE (cn.mops)

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

nameusersystemelapsed
CNVDetectionResult0.0030.0010.003
calcFractionalCopyNumbers9.3890.0499.451
calcIntegerCopyNumbers0.7990.0080.808
cn.mops10.437 0.08110.538
cnvr0.3800.0060.386
cnvs0.4160.0050.423
exomecn.mops4.7660.0444.816
getReadCountsFromBAM0.3050.0070.316
getSegmentReadCountsFromBAM0.0900.0020.097
gr0.4800.0100.524
haplocn.mops2.0350.0192.056
individualCall0.4340.0090.442
iniCall0.4090.0070.416
integerCopyNumber0.4350.0070.444
localAssessments0.4270.0080.435
makeRobustCNVR0.6120.0090.624
normalizeChromosomes0.4570.0220.494
normalizeGenome0.6920.0200.713
normalizedData0.4240.0080.433
params0.4090.0140.424
posteriorProbs0.4220.0080.432
referencecn.mops6.3010.0296.337
sampleNames0.3800.0070.388
segment0.0410.0000.042
segmentation0.4250.0070.432
segplot1.7780.0091.791
singlecn.mops1.6010.0251.629