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BioC 2.12: CHECK report for cn.mops on george2

This page was generated on 2013-10-09 09:37:50 -0700 (Wed, 09 Oct 2013).

Package 134/671HostnameOS / ArchBUILDCHECKBUILD BIN
cn.mops 1.6.7
Guenter Klambauer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/cn.mops
Last Changed Rev: 81146 / Revision: 81334
Last Changed Date: 2013-10-03 23:56:20 -0700 (Thu, 03 Oct 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: cn.mops
Version: 1.6.7
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.6.7.tar.gz
StartedAt: 2013-10-09 01:03:14 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:08:14 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 300.4 seconds
RetCode: 0
Status:  OK 
CheckDir: cn.mops.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.6.7’
* 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 ... [24s/27s] OK
* checking installed package size ... OK
* checking package 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
* 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 for unstated 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
referencecn.mops: no visible binding for global variable ‘input’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [58s/63s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cn.mops      22.310  0.200  24.158
exomecn.mops  7.532  0.036   7.912
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/cn.mops.Rcheck/00check.log’
for details.

cn.mops.Rcheck/00install.out:

* installing *source* package ‘cn.mops’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c segment.cpp -o segment.o
segment.cpp: In function ‘SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
segment.cpp:60:20: warning: variable ‘globalSd’ set but not used [-Wunused-but-set-variable]
segment.cpp:61:9: warning: variable ‘oldStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:62:31: warning: variable ‘maxStatistic’ set but not used [-Wunused-but-set-variable]
segment.cpp:63:40: warning: variable ‘maxIdx’ set but not used [-Wunused-but-set-variable]
segment.cpp:65:9: warning: unused variable ‘Rf_beta’ [-Wunused-variable]
g++ -shared -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
CNVDetectionResult0.3560.0080.399
calcIntegerCopyNumbers1.3040.0201.505
cn.mops22.310 0.20024.158
cnvr0.4680.0040.493
cnvs0.4360.0000.437
exomecn.mops7.5320.0367.912
getReadCountsFromBAM0.3760.0000.423
getSegmentReadCountsFromBAM0.120.000.14
gr0.4800.0040.543
haplocn.mops2.3000.0042.748
individualCall0.5080.0040.618
iniCall0.4520.0040.459
integerCopyNumber0.4560.0000.498
localAssessments0.5440.0000.579
makeRobustCNVR0.8330.0040.842
normalizeChromosomes0.9040.0080.914
normalizeGenome1.3040.0001.304
normalizedData0.4920.0080.503
params0.4760.0080.485
posteriorProbs0.4760.0080.601
referencecn.mops2.3360.0122.450
sampleNames0.3960.0040.403
segment0.0600.0000.058
segmentation0.5120.0080.536
segplot2.2680.0042.283